@article {pmid36989328, year = {2023}, author = {Villegas, LEM and Radl, J and Dimopoulos, G and Short, SM}, title = {Bacterial communities of Aedes aegypti mosquitoes differ between crop and midgut tissues.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {3}, pages = {e0011218}, doi = {10.1371/journal.pntd.0011218}, pmid = {36989328}, issn = {1935-2735}, abstract = {Microbiota studies of Aedes aegypti and other mosquitoes generally focus on the bacterial communities found in adult female midguts. However, other compartments of the digestive tract maintain communities of bacteria which remain almost entirely unstudied. For example, the Dipteran crop is a food storage organ, but few studies have looked at the microbiome of crops in mosquitoes, and only a single previous study has investigated the crop in Ae. aegypti. In this study, we used both culture-dependent and culture-independent methods to compare the bacterial communities in midguts and crops of laboratory reared Ae. aegypti. Both methods revealed a trend towards higher abundance, but also higher variability, of bacteria in the midgut than the crop. When present, bacteria from the genus Elizabethkingia (family Weeksellaceae) dominated midgut bacterial communities. In crops, we found a higher diversity of bacteria, and these communities were generally dominated by acetic acid bacteria (family Acetobacteriaceae) from the genera Tanticharoenia and Asaia. These three taxa drove significant community structure differences between the tissues. We used FAPROTAX to predict the metabolic functions of these communities and found that crop bacterial communities were significantly more likely to contain bacteria capable of methanol oxidation and methylotrophy. Both the presence of acetic acid bacteria (which commonly catabolize sugar to produce acetic acid) and the functional profile that includes methanol oxidation (which is correlated with bacteria found with natural sources like nectar) may relate to the presence of sugar, which is stored in the mosquito crop. A better understanding of what bacteria are present in the digestive tract of mosquitoes and how these communities assemble will inform how the microbiota impacts mosquito physiology and the full spectrum of functions provided by the microbiota. It may also facilitate better methods of engineering the mosquito microbiome for vector control or prevention of disease transmission.}, }
@article {pmid36989208, year = {2023}, author = {Rajamanikam, A and Isa, MNM and Samudi, C and Devaraj, S and Govind, SK}, title = {Gut bacteria influence Blastocystis sp. phenotypes and may trigger pathogenicity.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {3}, pages = {e0011170}, doi = {10.1371/journal.pntd.0011170}, pmid = {36989208}, issn = {1935-2735}, abstract = {Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.}, }
@article {pmid36988904, year = {2023}, author = {Awonuga, AO and Camp, OG and Abu-Soud, HM and Rappolee, DA and Puscheck, EE and Diamond, MP}, title = {Determinants of Embryo Implantation: Roles of the Endometrium and Embryo in Implantation Success.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {}, number = {}, pages = {}, pmid = {36988904}, issn = {1933-7205}, abstract = {Both uterine endometrium and embryo contribute to implantation success. However, their relative role in the implantation success is still a matter for debate, as are the roles of endometrial receptivity analysis (ERA), endometrial scratch (ES), endometrial microbiome, and intrauterine or intravenous measures that are currently advocated to improve the implantation success. There is insufficient evidence to suggest that the endometrium is more important than the embryo in determining the implantation success and the utility of these measures, especially when euploid embryos are transferred is limited. Although embryo implantation on epithelium other than the endometrium is a very rare event, evidence suggests that embryo implantation and growth is not limited to the endometrium alone. Embryos can implant and develop to result in livebirths on epithelium that lacks the typical endometrial development present at implantation. Currently, the role of embryo euploidy in implantation success is underappreciated. At a minimum, it is the author's opinion that until robust, definitive studies are conducted that demonstrate benefit, reproductive endocrinologists and infertility specialist should be prudent in the way they counsel patients about the utility of ERA, ES, and other measures in improving implantation success.}, }
@article {pmid36988458, year = {2023}, author = {Gierse, LC and Meene, A and Skorka, S and Cuypers, F and Surabhi, S and Ferrero-Bordera, B and Kreikemeyer, B and Becher, D and Hammerschmidt, S and Siemens, N and Urich, T and Riedel, K}, title = {Impact of Pneumococcal and Viral Pneumonia on the Respiratory and Intestinal Tract Microbiomes of Mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0344722}, doi = {10.1128/spectrum.03447-22}, pmid = {36988458}, issn = {2165-0497}, abstract = {With 2.56 million deaths worldwide annually, pneumonia is one of the leading causes of death. The most frequent causative pathogens are Streptococcus pneumoniae and influenza A virus. Lately, the interaction between the pathogens, the host, and its microbiome have gained more attention. The microbiome is known to promote the immune response toward pathogens; however, our knowledge on how infections affect the microbiome is still scarce. Here, the impact of colonization and infection with S. pneumoniae and influenza A virus on the structure and function of the respiratory and gastrointestinal microbiomes of mice was investigated. Using a meta-omics approach, we identified specific differences between the bacterial and viral infection. Pneumococcal colonization had minor effects on the taxonomic composition of the respiratory microbiome, while acute infections caused decreased microbial complexity. In contrast, richness was unaffected following H1N1 infection. Within the gastrointestinal microbiome, we found exclusive changes in structure and function, depending on the pathogen. While pneumococcal colonization had no effects on taxonomic composition of the gastrointestinal microbiome, increased abundance of Akkermansiaceae and Spirochaetaceae as well as decreased amounts of Clostridiaceae were exclusively found during invasive S. pneumoniae infection. The presence of Staphylococcaceae was specific for viral pneumonia. Investigation of the intestinal microbiomés functional composition revealed reduced expression of flagellin and rubrerythrin and increased levels of ATPase during pneumococcal infection, while increased amounts of acetyl coenzyme A (acetyl-CoA) acetyltransferase and enoyl-CoA transferase were unique after H1N1 infection. In conclusion, identification of specific taxonomic and functional profiles of the respiratory and gastrointestinal microbiome allowed the discrimination between bacterial and viral pneumonia. IMPORTANCE Pneumonia is one of the leading causes of death worldwide. Here, we compared the impact of bacterial- and viral-induced pneumonia on the respiratory and gastrointestinal microbiome. Using a meta-omics approach, we identified specific profiles that allow discrimination between bacterial and viral causative.}, }
@article {pmid36988354, year = {2023}, author = {Mitchell, SW and Moran, RA and Elbourne, LDH and Chapman, B and Bull, M and Muscatello, G and Coleman, NV}, title = {Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0159022}, doi = {10.1128/aem.01590-22}, pmid = {36988354}, issn = {1098-5336}, abstract = {Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A collection of 71 unique C1I[+] isolates (17 Actinobacteria and 54 Proteobacteria) was subjected to resistance profiling and genome sequencing. Farm horses yielded mostly C1I[+] Actinobacteria (Rhodococcus, Micrococcus, Microbacterium, Arthrobacter, Glutamicibacter, Kocuria), while vet horses primarily yielded C1I[+] Proteobacteria (Escherichia, Klebsiella, Enterobacter, Pantoea, Acinetobacter, Leclercia, Ochrobactrum); the vet isolates had more extensive resistance and stronger PC promoters in the C1Is. All integrons in Actinobacteria were flanked by copies of IS6100, except in Micrococcus, where a novel IS5 family element (ISMcte1) was implicated in mobilization. In the Proteobacteria, C1Is were predominantly associated with IS26 and also IS1, Tn21, Tn1721, Tn512, and a putative formaldehyde-resistance transposon (Tn7489). Several large C1I-containing plasmid contigs were retrieved; two of these (plasmid types Y and F) also had extensive sets of metal resistance genes, including a novel copper-resistance transposon (Tn7519). Both veterinary treatment and domestication increase the frequency of C1Is in equine gut microflora, and each of these anthropogenic factors selects for a distinct group of integron-containing bacteria. IMPORTANCE There is increasing acknowledgment that a "one health" approach is required to tackle the growing problem of antimicrobial resistance. This requires that the issue is examined from not only the perspective of human medicine but also includes consideration of the roles of antimicrobials in veterinary medicine and agriculture and recognizes the importance of other ecological compartments in the dissemination of ARGs and mobile genetic elements such as C1I. We have shown that domestication and veterinary treatment increase the frequency of occurrence of C1Is in the equine gut microflora and that, in healthy farm horses, the C1I are unexpectedly found in Actinobacteria, while in horses receiving antimicrobial veterinary treatments, a taxonomic shift occurs, and the more typical integron-containing Proteobacteria are found. We identified several new mobile genetic elements (plasmids, insertion sequences [IS], and transposons) on genomic contigs from the integron-containing equine bacteria.}, }
@article {pmid36987580, year = {2023}, author = {Chen, S and Tang, L and Nie, T and Fang, M and Cao, X}, title = {FOS ameliorates DNFB-induced atopic dermatitis-like skin lesions and the comorbid anxiety and depressive-like behaviors in mice by modulating the gut microbiota, neurotransmitter releases and immune responses.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.12582}, pmid = {36987580}, issn = {1097-0010}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by pruritus and eczema lesions and psychiatric comorbidities. The Gut-brain-skin axis plays a pivotal role during AD development, which could might be a novel therapeutic strategy for AD. Herein, the present study aims to uncover the protective effects and underlying mechanisms of fructo-oligofructose (FOS), a type of prebiotic, on AD-like skin manifestations and the comorbid anxiety and depression in AD mice.<br><br>RESULTS: Female Kunming mice were topically treated with 2, 4-dinitrofluorobenzene (DNFB) to induce AD-like symptoms and orally administrated with FOS daily for 14&#x2009;days. The results showed that FOS could markedly alleviate AD-like skin lesions as evidenced by a dramatic decrease in severity score, scratching bouts, IgE and Th1/Th2-related cytokine levels, and the infiltration of inflammatory cells and mast cells to the dermal tissues. The comorbid anxiety and depressive-like behaviors estimated by FST, TST, OFT and ZMT in AD mice were further significantly attenuated by FOS. Importantly, FOS significantly upregulated brain neurotransmitters levels of 5-hydroxytryptamine (5-HT) and dopamine (DA). Furthermore, FOS treatment increased the relative abundance of gut microbiota, such as Prevotella and Lactobacillus and the concentrations of SCFAs, especially acetate and iso-butyrate in feces of AD mice. The correlation analysis indicated that the reshaped gut microbiome composition and enhanced SCFAs formation are associated with skin inflammation and behavioral alteration.<br><br>CONCLUSION: Collectively, these data identify FOS as a promising microbiota-targeted treatment for AD-like skin inflammation and the comorbid anxiety and depressive-like behaviors. This article is protected by copyright. All rights reserved.}, }
@article {pmid36986899, year = {2023}, author = {Anderson, AJ and Hortin, JM and Jacobson, AR and Britt, DW and McLean, JE}, title = {Changes in Metal-Chelating Metabolites Induced by Drought and a Root Microbiome in Wheat.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/plants12061209}, pmid = {36986899}, issn = {2223-7747}, abstract = {The essential metals Cu, Zn, and Fe are involved in many activities required for normal and stress responses in plants and their microbiomes. This paper focuses on how drought and microbial root colonization influence shoot and rhizosphere metabolites with metal-chelation properties. Wheat seedlings, with and without a pseudomonad microbiome, were grown with normal watering or under water-deficit conditions. At harvest, metal-chelating metabolites (amino acids, low molecular weight organic acids (LMWOAs), phenolic acids, and the wheat siderophore) were assessed in shoots and rhizosphere solutions. Shoots accumulated amino acids with drought, but metabolites changed little due to microbial colonization, whereas the active microbiome generally reduced the metabolites in the rhizosphere solutions, a possible factor in the biocontrol of pathogen growth. Geochemical modeling with the rhizosphere metabolites predicted Fe formed Fe-Ca-gluconates, Zn was mainly present as ions, and Cu was chelated with the siderophore 2'-deoxymugineic acid, LMWOAs, and amino acids. Thus, changes in shoot and rhizosphere metabolites caused by drought and microbial root colonization have potential impacts on plant vigor and metal bioavailability.}, }
@article {pmid36986620, year = {2023}, author = {Froelich, A and Jakubowska, E and Jadach, B and Gadziński, P and Osmałek, T}, title = {Natural Gums in Drug-Loaded Micro- and Nanogels.}, journal = {Pharmaceutics}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/pharmaceutics15030759}, pmid = {36986620}, issn = {1999-4923}, abstract = {Gums are polysaccharide compounds obtained from natural sources, such as plants, algae and bacteria. Because of their excellent biocompatibility and biodegradability, as well as their ability to swell and their sensitivity to degradation by the colon microbiome, they are regarded as interesting potential drug carriers. In order to obtain properties differing from the original compounds, blends with other polymers and chemical modifications are usually applied. Gums and gum-derived compounds can be applied in the form of macroscopic hydrogels or can be formulated into particulate systems that can deliver the drugs via different administration routes. In this review, we present and summarize the most recent studies regarding micro- and nanoparticles obtained with the use of gums extensively investigated in pharmaceutical technology, their derivatives and blends with other polymers. This review focuses on the most important aspects of micro- and nanoparticulate systems formulation and their application as drug carriers, as well as the challenges related to these formulations.}, }
@article {pmid36986390, year = {2023}, author = {Viswanathan, S and Parida, S and Lingipilli, BT and Krishnan, R and Podipireddy, DR and Muniraj, N}, title = {Role of Gut Microbiota in Breast Cancer and Drug Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/pathogens12030468}, pmid = {36986390}, issn = {2076-0817}, abstract = {Breast cancer is the most common malignancy in women worldwide. The cause of cancer is multifactorial. An early diagnosis and the appropriate treatment of cancer can improve the chances of survival. Recent studies have shown that breast cancer is influenced by the microbiota. Different microbial signatures have been identified in the breast microbiota, which have different patterns depending on the stage and biological subgroups. The human digestive system contains approximately 100 trillion bacteria. The gut microbiota is an emerging field of research that is associated with specific biological processes in many diseases, including cardiovascular disease, obesity, diabetes, brain disease, rheumatoid arthritis, and cancer. In this review article, we discuss the impact of the microbiota on breast cancer, with a primary focus on the gut microbiota's regulation of the breast cancer microenvironment. Ultimately, updates on how immunotherapy can affect the breast cancer-based microbiome and further clinical trials on the breast and microbiome axis may be an important piece of the puzzle in better predicting breast cancer risk and prognosis.}, }
@article {pmid36986329, year = {2023}, author = {Yin, X and Wang, W and Seah, SYK and Mine, Y and Fan, MZ}, title = {Deglycosylation Differentially Regulates Weaned Porcine Gut Alkaline Phosphatase Isoform Functionality along the Longitudinal Axis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/pathogens12030407}, pmid = {36986329}, issn = {2076-0817}, abstract = {Gut alkaline phosphatases (AP) dephosphorylate the lipid moiety of endotoxin and other pathogen-associated-molecular patterns members, thus maintaining gut eubiosis and preventing metabolic endotoxemia. Early weaned pigs experience gut dysbiosis, enteric diseases and growth retardation in association with decreased intestinal AP functionality. However, the role of glycosylation in modulation of the weaned porcine gut AP functionality is unclear. Herein three different research approaches were taken to investigate how deglycosylation affected weaned porcine gut AP activity kinetics. In the first approach, weaned porcine jejunal AP isoform (IAP) was fractionated by the fast protein-liquid chromatography and purified IAP fractions were kinetically characterized to be the higher-affinity and lower-capacity glycosylated mature IAP (p < 0.05) in comparison with the lower-affinity and higher-capacity non-glycosylated pre-mature IAP. The second approach enzyme activity kinetic analyses showed that N-deglycosylation of AP by the peptide N-glycosidase-F enzyme reduced (p < 0.05) the IAP maximal activity in the jejunum and ileum and decreased AP affinity (p < 0.05) in the large intestine. In the third approach, the porcine IAP isoform-X1 (IAPX1) gene was overexpressed in the prokaryotic ClearColiBL21 (DE3) cell and the recombinant porcine IAPX1 was associated with reduced (p < 0.05) enzyme affinity and maximal enzyme activity. Therefore, levels of glycosylation can modulate plasticity of weaned porcine gut AP functionality towards maintaining gut microbiome and the whole-body physiological status.}, }
@article {pmid36986326, year = {2023}, author = {Cena, JA and Reis, LG and de Lima, AKA and Vieira Lima, CP and Stefani, CM and Dame-Teixeira, N}, title = {Enrichment of Acid-Associated Microbiota in the Saliva of Type 2 Diabetes Mellitus Adults: A Systematic Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/pathogens12030404}, pmid = {36986326}, issn = {2076-0817}, abstract = {It could conceivably be hypothesized that a link exists between an altered microbiota due to local hyperglycemia and the increased risk of caries in diabetes mellitus (DM). This systematic review aimed to perform a cross-study comparison into the salivary microbiota of adults with type 2 diabetes mellitus (T2D) compared to adults without T2D, particularly focusing on the abundance of acid-associated bacteria. This report follows PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). Studies using next-generation sequencing and other molecular techniques are included. The methodological quality of individual studies was assessed using appropriate Joanna Briggs Institute tools. The certainty of the evidence considering the effect direction was evaluated using the GRADE approach. From 2060 titles retrieved, 12 were included in the data synthesis, totalling 873 individuals with T2D and controls evaluated across the literature. Weighted averages of blood glucose levels (HbA1c-fasting blood glucose) were 8.21%-172.14 mg/dL and 5.12%-84.53 mg/dL for T2D and controls, respectively. In most studies, the relative abundance of acidogenic and aciduric bacteria was higher in diabetics when compared to their normoglycaemic controls. Whilst the evidence certainty was very low, there was a consistent Proteobacteria depletion and Firmicutes enrichment in T2D. As for the acid-associated genera, there was consistent enrichment of Lactobacillus and Veillonela for T2D. Tannerella/T. forsythia was enriched in T2D saliva, but the certainty is low. Further well-designed cohorts are needed to clarify the distribution of acid-associated microorganisms in the saliva of adults with T2D and how this can be clinically manifested (PROSPERO = CRD42021264350).}, }
@article {pmid36986299, year = {2023}, author = {Jastrząb, B and Paśnik-Chwalik, B and Dębska-Łasut, K and Konopka, T and Krajewski, PK and Szepietowski, JC and Matusiak, &#x141;}, title = {The Composition of Subgingival Microbiome in Hidradenitis Suppurativa and Periodontitis Patients.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/pathogens12030377}, pmid = {36986299}, issn = {2076-0817}, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder of the pilosebaceous unit of the intertriginous body areas. Recent findings have suggested the association between periodontitis and HS. This investigation aimed to characterize and compare the composition of subgingival microbiome between HS, periodontitis, and control patients. The nine crucial perio-pathogenic species and total bacteria were analyzed using RT-PCR based tests in samples collected from 30 patients with periodontitis, 30 patients with HS and 30 controls. Patients with HS were excluded if they had periodontitis and patients with periodontitis were excluded if they had HS. The mean total bacteria count was significantly higher in HS and periodontitis samples than in control samples (p < 0.05). The majority of perio-pathogens tested were more frequently detected in HS and periodontitis groups than among controls. Treponema denticola was the most common pathogen in individuals with HS (70%) and periodontitis (86.7%), while among controls Capnocytophyga gingivalis was the most frequently detected isolate (33.2%). The results of the present investigation demonstrated that HS and periodontitis patients share some similarities in their subgingival microbiome composition.}, }
@article {pmid36986288, year = {2023}, author = {Moore, C and Lashnits, E and Neupane, P and Herrin, BH and Lappin, M and André, MR and Breitschwerdt, EB}, title = {Feeding on a Bartonella henselae Infected Host Triggers Temporary Changes in the Ctenocephalides felis Microbiome.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/pathogens12030366}, pmid = {36986288}, issn = {2076-0817}, abstract = {The effect of Bartonella henselae on the microbiome of its vector, Ctenocephalides felis (the cat flea) is largely unknown, as the majority of C. felis microbiome studies have utilized wild-caught pooled fleas. We surveyed the microbiome of laboratory-origin C. felis fed on B. henselae-infected cats for 24 h or 9 days to identify changes to microbiome diversity and microbe prevalence compared to unfed fleas, and fleas fed on uninfected cats. Utilizing Next Generation Sequencing (NGS) on the Illumina platform, we documented an increase in microbial diversity in C. felis fed on Bartonella-infected cats for 24 h. These changes returned to baseline (unfed fleas or fleas fed on uninfected cats) after 9 days on the host. Increased diversity in the C. felis microbiome when fed on B. henselae-infected cats may be related to the mammalian, flea, or endosymbiont response. Poor B. henselae acquisition was documented with only one of four infected flea pools having B. henselae detected by NGS. We hypothesize this is due to the use of adult fleas, flea genetic variation, or lack of co-feeding with B. henselae-infected fleas. Future studies are necessary to fully characterize the effect of endosymbionts and C. felis diversity on B. henselae acquisition.}, }
@article {pmid36986264, year = {2023}, author = {Boytar, AN and Skinner, TL and Wallen, RE and Jenkins, DG and Dekker Nitert, M}, title = {The Effect of Exercise Prescription on the Human Gut Microbiota and Comparison between Clinical and Apparently Healthy Populations: A Systematic Review.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061534}, pmid = {36986264}, issn = {2072-6643}, abstract = {This study systematically reviewed all human longitudinal exercise interventions that reported changes in the gut microbiota; frequency, intensity, duration and type of exercise were assessed to determine the influence of these variables on changes to the gut microbiota in both healthy individuals and clinical populations (PROPERO registration: CRD42022309854). Using PRISMA guidelines, trials analysing gut microbiota change with exercise interventions were included independent of trial randomisation, population, trial duration or analysis technique. Studies were excluded when microbiota abundance was not reported or when exercise was combined with other interventions. Twenty-eight trials were included, of which twelve involved healthy populations only and sixteen involved mixed or clinical-only populations. The findings show that participation in exercise of moderate to high-intensity for 30-90 min ≥3 times per week (or between 150-270 min per week) for ≥8 weeks is likely to produce changes in the gut microbiota. Exercise appears to be effective in modifying the gut microbiota in both clinical and healthy populations. A more robust methodology is needed in future studies to improve the certainty of the evidence.}, }
@article {pmid36986240, year = {2023}, author = {Sidhu, SRK and Kok, CW and Kunasegaran, T and Ramadas, A}, title = {Effect of Plant-Based Diets on Gut Microbiota: A Systematic Review of Interventional Studies.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061510}, pmid = {36986240}, issn = {2072-6643}, abstract = {Plant-based diets have grown increasingly popular across the globe, mainly for their health and environmental benefits. Several studies have identified a link between plant-based diets and the decreased risk of developing cardiovascular diseases, obesity, and other health issues. We systematically reviewed human interventions to identify the relationship between various plant-based food items and the gut microbiome, alongside the biochemical and anthropometric measurements as secondary findings. The study selection process was completed using the COVIDENCE platform. Overall, 203 studies were identified, of which 101 were chosen for title and abstract screening by two independent authors. Following this process, 78 studies were excluded, and the full texts and the reference lists of the remaining 23 records were reviewed using the review eligibility criteria. A manual search yielded five additional articles. In the end, 12 studies were included in the systematic review. We found evidence for short- to moderate-term beneficial effects of plant-based diets versus conventional diets (duration ≤ 13 months) on gut microbiome composition and biochemical and anthropometric measurements in healthy participants as well as obese, cardiovascular, and rheumatoid arthritis patients. However, contradictory results were observed for Enterobacteriaceae, at the family level, and for Faecalibacterium and Coprococcus, at the genus level, of gut microbiome composition. The relationship between plant-based diets and the gut microbiome, alongside their underlying metabolic and inflammatory effects, remains largely unexplored. Hence more interventional studies are needed to address these questions.}, }
@article {pmid36986190, year = {2023}, author = {Ondee, T and Pongpirul, K and Udompornpitak, K and Sukkummee, W and Lertmongkolaksorn, T and Senaprom, S and Leelahavanichkul, A}, title = {High Fructose Causes More Prominent Liver Steatohepatitis with Leaky Gut Similar to High Glucose Administration in Mice and Attenuation by Lactiplantibacillus plantarum dfa1.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061462}, pmid = {36986190}, issn = {2072-6643}, abstract = {High-sugar diet-induced prediabetes and obesity are a global current problem that can be the result of glucose or fructose. However, a head-to-head comparison between both sugars on health impact is still lacking, and Lactiplantibacillus plantarum dfa1 has never been tested, and has recently been isolated from healthy volunteers. The mice were administered with the high glucose or fructose preparation in standard mouse chaw with or without L. plantarum dfa1 gavage, on alternate days, and in vitro experiments were performed using enterocyte cell lines (Caco2) and hepatocytes (HepG2). After 12 weeks of experiments, both glucose and fructose induced a similar severity of obesity (weight gain, lipid profiles, and fat deposition at several sites) and prediabetes condition (fasting glucose, insulin, oral glucose tolerance test, and Homeostatic Model Assessment for Insulin Resistance (HOMA score)). However, fructose administration induced more severe liver damage (serum alanine transaminase, liver weight, histology score, fat components, and oxidative stress) than the glucose group, while glucose caused more prominent intestinal permeability damage (FITC-dextran assay) and serum cytokines (TNF-α, IL-6, and IL-10) compared to the fructose group. Interestingly, all of these parameters were attenuated by L. plantarum dfa1 administration. Because there was a subtle change in the analysis of the fecal microbiome of mice with glucose or fructose administration compared to control mice, the probiotics altered only some microbiome parameters (Chao1 and Lactobacilli abundance). For in vitro experiments, glucose induced more damage to high-dose lipopolysaccharide (LPS) (1 µg/mL) to enterocytes (Caco2 cell) than fructose, as indicated by transepithelial electrical resistance (TEER), supernatant cytokines (TNF-α and IL-8), and glycolysis capacity (by extracellular flux analysis). Meanwhile, both glucose and fructose similarly facilitated LPS injury in hepatocytes (HepG2 cell) as evaluated by supernatant cytokines (TNF-α, IL-6, and IL-10) and extracellular flux analysis. In conclusion, glucose possibly induced a more severe intestinal injury (perhaps due to LPS-glucose synergy) and fructose caused a more prominent liver injury (possibly due to liver fructose metabolism), despite a similar effect on obesity and prediabetes. Prevention of obesity and prediabetes with probiotics was encouraged.}, }
@article {pmid36986165, year = {2023}, author = {Kurowska, A and Ziemichód, W and Herbet, M and Piątkowska-Chmiel, I}, title = {The Role of Diet as a Modulator of the Inflammatory Process in the Neurological Diseases.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061436}, pmid = {36986165}, issn = {2072-6643}, abstract = {Neurological diseases are recognized as major causes of disability and mortality worldwide. Due to the dynamic progress of diseases such as Alzheimer's disease (AD), Parkinson's Disease (PD), Schizophrenia, Depression, and Multiple Sclerosis (MD), scientists are mobilized to look for new and more effective methods of interventions. A growing body of evidence suggests that inflammatory processes and an imbalance in the composition and function of the gut microbiome, which play a critical role in the pathogenesis of various neurological diseases and dietary interventions, such as the Mediterranean diet the DASH diet, or the ketogenic diet can have beneficial effects on their course. The aim of this review was to take a closer look at the role of diet and its ingredients in modulating inflammation associated with the development and/or progression of central nervous system diseases. Presented data shows that consuming a diet abundant in fruits, vegetables, nuts, herbs, spices, and legumes that are sources of anti-inflammatory elements such as omega-3 fatty acids, polyphenols, vitamins, essential minerals, and probiotics while avoiding foods that promote inflammation, create a positive brain environment and is associated with a reduced risk of neurological diseases. Personalized nutritional interventions may constitute a non-invasive and effective strategy in combating neurological disorders.}, }
@article {pmid36986163, year = {2023}, author = {Mohammadi, F and Green, M and Tolsdorf, E and Greffard, K and Leclercq, M and Bilodeau, JF and Droit, A and Foster, J and Bertrand, N and Rudkowska, I}, title = {Industrial and Ruminant Trans-Fatty Acids-Enriched Diets Differentially Modulate the Microbiome and Fecal Metabolites in C57BL/6 Mice.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061433}, pmid = {36986163}, issn = {2072-6643}, abstract = {Industrially originated trans-fatty acids (I-tFAs), such as elaidic acid (EA), and ruminant trans-fatty acids (R-tFAs), such as trans-palmitoleic acid (TPA), may have opposite effects on metabolic health. The objective was to compare the effects of consuming 2-3% I-tFA or R-tFA on the gut microbiome and fecal metabolite profile in mice after 7 and 28 days. Forty C57BL/6 mice were assigned to one of the four prepared formulations: lecithin nanovesicles, lecithin nanovesicles with EA or TPA, or water. Fecal samples and animals' weights were collected on days 0, 7, and 28. Fecal samples were used to determine gut microbiome profiles by 16S rRNA sequencing and metabolite concentrations by GC/MS. At 28 days, TPA intake decreased the abundance of Staphylococcus sp55 but increased Staphylococcus sp119. EA intake also increased the abundance of Staphylococcus sp119 but decreased Ruminococcaceae UCG-014, Lachnospiraceae, and Clostridium sensu stricto 1 at 28 days. Fecal short-chain fatty acids were increased after TPA while decreased after EA after 7 and 28 days. This study shows that TPA and EA modify the abundance of specific microbial taxa and fecal metabolite profiles in distinct ways.}, }
@article {pmid36986148, year = {2023}, author = {Taylor, R and Keane, D and Borrego, P and Arcaro, K}, title = {Effect of Maternal Diet on Maternal Milk and Breastfed Infant Gut Microbiomes: A Scoping Review.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061420}, pmid = {36986148}, issn = {2072-6643}, support = {5R01CA230478-02/NH/NIH HHS/United States ; }, abstract = {While it is widely recognized that nutrition during pregnancy and lactation can affect the microbiome of breast milk as well as the formation of the infant gut microbiome, we are only just beginning to understand the extent to which maternal diet impacts these microbiomes. Given the importance of the microbiome for infant health, we conducted a comprehensive review of the published literature to explore the current scope of knowledge regarding associations between maternal diet and the breast milk and infant gut microbiomes. Papers included in this review assessed either diet during lactation or pregnancy, and the milk and/or infant gut microbiome. Sources included cohort studies, randomized clinical trials, one case-control study, and one crossover study. From an initial review of 808 abstracts, we identified 19 reports for a full analysis. Only two studies assessed the effects of maternal diet on both milk and infant microbiomes. Although the reviewed literature supports the importance of a varied, nutrient-dense maternal diet in the formation of the infant's gut microbiome, several studies found factors other than maternal diet to have a greater impact on the infant microbiome.}, }
@article {pmid36986142, year = {2023}, author = {Koemel, NA and Senior, AM and Benmarhnia, T and Holmes, A and Okada, M and Oulhote, Y and Parker, HM and Shah, S and Simpson, SJ and Raubenheimer, D and Gill, TP and Laouali, N and Skilton, MR}, title = {Diet Quality, Microbial Lignan Metabolites, and Cardiometabolic Health among US Adults.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061412}, pmid = {36986142}, issn = {2072-6643}, abstract = {The gut microbiome has been shown to play a role in the relationship between diet and cardiometabolic health. We sought to examine the degree to which key microbial lignan metabolites are involved in the relationship between diet quality and cardiometabolic health using a multidimensional framework. This analysis was undertaken using cross-sectional data from 4685 US adults (age 43.6 ± 16.5 years; 50.4% female) participating in the National Health and Nutrition Examination Survey for 1999-2010. Dietary data were collected from one to two separate 24-hour dietary recalls and diet quality was characterized using the 2015 Healthy Eating Index. Cardiometabolic health markers included blood lipid profile, glycemic control, adiposity, and blood pressure. Microbial lignan metabolites considered were urinary concentrations of enterolignans, including enterolactone and enterodiol, with higher levels indicating a healthier gut microbial environment. Models were visually examined using a multidimensional approach and statistically analyzed using three-dimensional generalized additive models. There was a significant interactive association between diet quality and microbial lignan metabolites for triglycerides, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, insulin, oral glucose tolerance, adiposity, systolic blood pressure, and diastolic blood pressure (all p < 0.05). Each of these cardiometabolic health markers displayed an association such that optimal cardiometabolic health was only observed in individuals with both high diet quality and elevated urinary enterolignans. When comparing effect sizes on the multidimensional response surfaces and model selection criteria, the strongest support for a potential moderating relationship of the gut microbiome was observed for fasting triglycerides and oral glucose tolerance. In this study, we revealed interactive associations of diet quality and microbial lignan metabolites with cardiometabolic health markers. These findings suggest that the overall association of diet quality on cardiometabolic health may be affected by the gut microbiome.}, }
@article {pmid36986123, year = {2023}, author = {Chen, A and Gibney, PA}, title = {Dietary Trehalose as a Bioactive Nutrient.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061393}, pmid = {36986123}, issn = {2072-6643}, abstract = {Trehalose is a naturally occurring, non-reducing disaccharide comprising two covalently-linked glucose molecules. It possesses unique physiochemical properties, which account for multiple biological roles in a variety of prokaryotic and eukaryotic organisms. In the past few decades, intensive research on trehalose has uncovered its functions, and extended its uses as a sweetener and stabilizer in the food, medical, pharmaceutical, and cosmetic industries. Further, increased dietary trehalose consumption has sparked research on how trehalose affects the gut microbiome. In addition to its role as a dietary sugar, trehalose has gained attention for its ability to modulate glucose homeostasis, and potentially as a therapeutic agent for diabetes. This review discusses the bioactive effects of dietary trehalose, highlighting its promise in future industrial and scientific contributions.}, }
@article {pmid36986068, year = {2023}, author = {Rodriguez, DM and Hintze, KJ and Rompato, G and Stewart, EC and Barton, AH and Mortensen-Curtis, E and Green, PA and Van Wettere, AJ and Thomas, AJ and Benninghoff, AD}, title = {Basal Diet Fed to Recipient Mice Was the Driving Factor for Colitis and Colon Tumorigenesis, despite Fecal Microbiota Transfer from Mice with Severe or Mild Disease.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061338}, pmid = {36986068}, issn = {2072-6643}, abstract = {Consumption of the total Western diet (TWD) in mice has been shown to increase gut inflammation, promote colon tumorigenesis, and alter fecal microbiome composition when compared to mice fed a healthy diet, i.e., AIN93G (AIN). However, it is unclear whether the gut microbiome contributes directly to colitis-associated CRC in this model. The objective of this study was to determine whether dynamic fecal microbiota transfer (FMT) from donor mice fed either the AIN basal diet or the TWD would alter colitis symptoms or colitis-associated CRC in recipient mice, which were fed either the AIN diet or the TWD, using a 2 × 2 factorial experiment design. Time-matched FMT from the donor mice fed the TWD did not significantly enhance symptoms of colitis, colon epithelial inflammation, mucosal injury, or colon tumor burden in the recipient mice fed the AIN diet. Conversely, FMT from the AIN-fed donors did not impart a protective effect on the recipient mice fed the TWD. Likewise, the composition of fecal microbiomes of the recipient mice was also affected to a much greater extent by the diet they consumed than by the source of FMT. In summary, FMT from the donor mice fed either basal diet with differing colitis or tumor outcomes did not shift colitis symptoms or colon tumorigenesis in the recipient mice, regardless of the basal diet they consumed. These observations suggest that the gut microbiome may not contribute directly to the development of disease in this animal model.}, }
@article {pmid36986043, year = {2023}, author = {Dogra, SK and Dardinier, A and Mainardi, F and Siegwald, L and Bartova, S and Le Roy, C and Chou, CJ}, title = {Application of Computational Data Modeling to a Large-Scale Population Cohort Assists the Discovery of Inositol as a Strain-Specific Substrate for Faecalibacterium prausnitzii.}, journal = {Nutrients}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/nu15061311}, pmid = {36986043}, issn = {2072-6643}, abstract = {Faecalibacterium prausnitzii (F. prausnitzii) is a bacterial taxon in the human gut with anti-inflammatory properties, and this may contribute to the beneficial effects of healthy eating habits. However, little is known about the nutrients that enhance the growth of F. prausnitzii other than simple sugars and fibers. Here, we combined dietary and microbiome data from the American Gut Project (AGP) to identify nutrients that may be linked to the relative abundance of F. prausnitzii. Using a machine learning approach in combination with univariate analyses, we identified that sugar alcohols, carbocyclic sugar, and vitamins may contribute to F. prausnitzii growth. We next explored the effects of these nutrients on the growth of two F. prausnitzii strains in vitro and observed robust and strain-dependent growth patterns on sorbitol and inositol, respectively. In the context of a complex community using in vitro fermentation, neither inositol alone nor in combinations with vitamin B exerted a significant growth-promoting effect on F. prausnitzii, partly due to high variability among the fecal microbiota community from four healthy donors. However, the fecal communities that showed an increase in F. prausnitzii on inulin also responded with at least 60% more F. prausnitzii on any of inositol containing media than control. Future nutritional studies aiming to increase the relative abundance of F. prausnitzii should explore a personalized approach accounting for strain-level genetic variations and community-level microbiome composition.}, }
@article {pmid36985379, year = {2023}, author = {Dossaji, Z and Khattak, A and Tun, KM and Hsu, M and Batra, K and Hong, AS}, title = {Efficacy of Fecal Microbiota Transplant on Behavioral and Gastrointestinal Symptoms in Pediatric Autism: A Systematic Review.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030806}, pmid = {36985379}, issn = {2076-2607}, abstract = {Background and Aims: There is a high prevalence of gastrointestinal-related (GI) symptoms among children with autism spectrum disorder (ASD), which is associated with the severity of behavioral symptoms. Fecal microbiota transplantation (FMT) is a proposed therapeutic strategy that aims to address the dysregulation of the gut microbiome among children with ASD. Our study performed the first systematic review aimed to evaluate the benefits of FMT on the behavioral and gastrointestinal symptoms of pediatric patients with autism. Methods: A literature search was performed using variations of the keywords "pediatrics" and "fecal microbiota transplantation" in PubMed, EMBASE, CINAHL, Cochrane, and Web of Science from inception to 30 June 2022. Four studies that met the eligibility criteria were included in the systematic review. The efficacy of FMT on behavioral symptoms was measured by the difference in Aberrant Behavior Checklist (ABC) and Child Autism Rating Scale (CARS) scores before and after FMT. Results: We found a statistically significant improvement (p < 0.05) in ABC and CARS scores following FMT, with a statistically significant decrease in scores observed across all studies. In addition, substantial improvements in gastrointestinal symptoms were observed across all studies. Conclusion: Our findings suggest that FMT may offer a promising intervention for treating both behavioral and gastrointestinal symptoms in pediatric patients with autism.}, }
@article {pmid36985376, year = {2023}, author = {Baev, V and Apostolova, E and Gotcheva, V and Koprinarova, M and Papageorgiou, M and Rocha, JM and Yahubyan, G and Angelov, A}, title = {16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030803}, pmid = {36985376}, issn = {2076-2607}, abstract = {Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.}, }
@article {pmid36985370, year = {2023}, author = {Remmal, I and Bel Mokhtar, N and Maurady, A and Reda Britel, M and El Fakhouri, K and Asimakis, E and Tsiamis, G and Stathopoulou, P}, title = {Characterization of the Bacterial Microbiome in Natural Populations of Barley Stem Gall Midge, Mayetiola hordei, in Morocco.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030797}, pmid = {36985370}, issn = {2076-2607}, abstract = {Mayetiola hordei (Kieffer), known as barley stem gall midge, is one of the most destructive barley pests in many areas around the world, inflicting significant qualitative and quantitative damage to crop production. In this study, we investigate the presence of reproductive symbionts, the effect of geographical origin on the bacterial microbiome's structure, and the diversity associated with natural populations of M. hordei located in four barley-producing areas in Morocco. Wolbachia infection was discovered in 9% of the natural populations using a precise 16S rDNA PCR assay. High-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene indicated that the native environments of samples had a substantial environmental impact on the microbiota taxonomic assortment. Briefly, 5 phyla, 7 classes, and 42 genera were identified across all the samples. To our knowledge, this is the first report on the bacterial composition of M. hordei natural populations. The presence of Wolbachia infection may assist in the diagnosis of ideal natural populations, providing a new insight into the employment of Wolbachia in the control of barley midge populations, in the context of the sterile insect technique or other biological control methods.}, }
@article {pmid36985351, year = {2023}, author = {Retter, A and Haas, JC and Birk, S and Stumpp, C and Hausmann, B and Griebler, C and Karwautz, C}, title = {From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030779}, pmid = {36985351}, issn = {2076-2607}, abstract = {Rivers are the "tip of the iceberg", with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.}, }
@article {pmid36985350, year = {2023}, author = {Ullah Goraya, M and Li, R and Gu, L and Deng, H and Wang, G}, title = {Blood Stream Microbiota Dysbiosis Establishing New Research Standards in Cardio-Metabolic Diseases, A Meta-Analysis Study.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030777}, pmid = {36985350}, issn = {2076-2607}, abstract = {AIMS: Scientists have recently discovered a link between the circulating microbiome and homeostasis, as well as the pathogenesis of a number of metabolic diseases. It has been demonstrated that low-grade chronic inflammation is one of the primary mechanisms that has long been implicated in the risk of cardio-metabolic disease (CMDs) and its progression. Currently, the dysbiosis of circulating bacteria is considered as a key regulator for chronic inflammation in CMDs, which is why we have conducted this systemic review focused on circulating bacterial dysbiosis.<br><br>METHODS: A systemic review of clinical and research-based studies was conducted via PubMed, Scopus, Medline, and Web of Science. Literature was considered for risk of bias and patterns of intervention effects. A randomized effect model was used to evaluate the dysbiosis of circulating microbiota and clinical outcomes. We conducted a meta-analysis considering the circulating bacteria in both healthy people and people with cardio-metabolic disorders, in reports published mainly from 2008 to 2022, according to the PRISMA guidelines.<br><br>RESULTS: We searched 627 studies and, after completing the risk of bias and selection, 31 studies comprising of 11,132 human samples were considered. This meta-analysis found that dysbiosis of phyla Proteobacteria, Firmicutes, and Bacteroidetes was associated with metabolic diseases.<br><br>CONCLUSIONS: In most instances, metabolic diseases are linked to higher diversity and elevated bacterial DNA levels. Bacteroides abundance was higher in healthy people than with metabolic disorders. However, more rigorous studies are required to determine the role of bacterial dysbiosis in cardio-metabolic diseases. Understanding the relationship between dysbiosis and cardio-metabolic diseases, we can use the bacteria as therapeutics for the reversal of dysbiosis and targets for therapeutics use in cardio-metabolic diseases. In the future, circulating bacterial signatures can be used as biomarkers for the early detection of metabolic diseases.}, }
@article {pmid36985349, year = {2023}, author = {Zhao, W and Ban, Y and Su, Z and Li, S and Liu, X and Guo, Q and Ma, P}, title = {Colonization Ability of Bacillus subtilis NCD-2 in Different Crops and Its Effect on Rhizosphere Microorganisms.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030776}, pmid = {36985349}, issn = {2076-2607}, abstract = {Bacillus subtilis strain NCD-2 is a promising biocontrol agent for soil-borne plant diseases and shows potential for promoting the growth of some crops. The purposes of this study were to analyze the colonization ability of strain NCD-2 in different crops and reveal the plant growth promotion mechanism of strain NCD-2 by rhizosphere microbiome analysis. qRT-PCR was used to determine the populations of strain NCD-2, and microbial communities' structures were analyzed through amplicon sequencing after application of strain NCD-2. Results demonstrated that strain NCD-2 had a good growth promotion effect on tomato, eggplant and pepper, and it was the most abundant in eggplant rhizosphere soil. There were significantly differences in the types of beneficial microorganisms recruited for different crops after application of strain NCD-2. PICRUSt analysis showed that the relative abundances of functional genes for amino acid transport and metabolism, coenzyme transport and metabolism, lipid transport and metabolism, inorganic ion transport and metabolism, and defense mechanisms were enriched in the rhizospheres of pepper and eggplant more than in the rhizospheres of cotton, tomato and maize after application of strain NCD-2. In summary, the colonization ability of strain NCD-2 for five plants was different. There were differences in microbial communities' structure in rhizosphere of different plants after application of strain NCD-2. Based on the results obtained in this study, it was concluded that the growth promoting ability of strain NCD-2 were correlated with its colonization quantity and the microbial species it recruited.}, }
@article {pmid36985339, year = {2023}, author = {Lin, BM and Cho, H and Liu, C and Roach, J and Ribeiro, AA and Divaris, K and Wu, D}, title = {BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030766}, pmid = {36985339}, issn = {2076-2607}, abstract = {Integration of multi-omics data is a challenging but necessary step to advance our understanding of the biology underlying human health and disease processes. To date, investigations seeking to integrate multi-omics (e.g., microbiome and metabolome) employ simple correlation-based network analyses; however, these methods are not always well-suited for microbiome analyses because they do not accommodate the excess zeros typically present in these data. In this paper, we introduce a bivariate zero-inflated negative binomial (BZINB) model-based network and module analysis method that addresses this limitation and improves microbiome-metabolome correlation-based model fitting by accommodating excess zeros. We use real and simulated data based on a multi-omics study of childhood oral health (ZOE 2.0; investigating early childhood dental caries, ECC) and find that the accuracy of the BZINB model-based correlation method is superior compared to Spearman's rank and Pearson correlations in terms of approximating the underlying relationships between microbial taxa and metabolites. The new method, BZINB-iMMPath, facilitates the construction of metabolite-species and species-species correlation networks using BZINB and identifies modules of (i.e., correlated) species by combining BZINB and similarity-based clustering. Perturbations in correlation networks and modules can be efficiently tested between groups (i.e., healthy and diseased study participants). Upon application of the new method in the ZOE 2.0 study microbiome-metabolome data, we identify that several biologically-relevant correlations of ECC-associated microbial taxa with carbohydrate metabolites differ between healthy and dental caries-affected participants. In sum, we find that the BZINB model is a useful alternative to Spearman or Pearson correlations for estimating the underlying correlation of zero-inflated bivariate count data and thus is suitable for integrative analyses of multi-omics data such as those encountered in microbiome and metabolome studies.}, }
@article {pmid36985338, year = {2023}, author = {Xiao, Y and Zhang, P and Zhang, H and Wang, H and Min, G and Wang, H and Wang, Y and Xu, J}, title = {Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030765}, pmid = {36985338}, issn = {2076-2607}, abstract = {Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.}, }
@article {pmid36985333, year = {2023}, author = {Deng, Q and Sun, X and Gao, D and Wang, Y and Liu, Y and Li, N and Wang, Z and Liu, M and Wang, J and Wang, Q}, title = {Characterization of Two Novel Rumen-Derived Exo-Polygalacturonases: Catalysis and Molecular Simulations.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030760}, pmid = {36985333}, issn = {2076-2607}, abstract = {Pectinases are a series of enzymes that degrade pectin and have been used extensively in the food, feed, and textile industries. The ruminant animal microbiome is an excellent source for mining novel pectinases. Two polygalacturonase genes, IDSPga28-4 and IDSPga28-16, from rumen fluid cDNA, were cloned and heterologously expressed. Recombinant IDSPGA28-4 and IDSPGA28-16 were stable from pH 4.0 to 6.0, with activities of 31.2 ± 1.5 and 330.4 ± 12.4 U/mg, respectively, against polygalacturonic acid. Hydrolysis product analysis and molecular dynamics simulation revealed that IDSPGA28-4 was a typical processive exo-polygalacturonase and cleaved galacturonic acid monomers from polygalacturonic acid. IDSPGA28-16 cleaved galacturonic acid only from substrates with a degree of polymerization greater than two, suggesting a unique mode of action. IDSPGA28-4 increased the light transmittance of grape juice from 1.6 to 36.3%, and IDSPGA28-16 increased the light transmittance of apple juice from 1.9 to 60.6%, indicating potential application in the beverage industry, particularly for fruit juice clarification.}, }
@article {pmid36985320, year = {2023}, author = {Soltis, MP and Moorey, SE and Egert-McLean, AM and Voy, BH and Shepherd, EA and Myer, PR}, title = {Rumen Biogeographical Regions and Microbiome Variation.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030747}, pmid = {36985320}, issn = {2076-2607}, abstract = {The rumen is a complex organ that is critical for its host to convert low-quality feedstuffs into energy. The conversion of lignocellulosic biomass to volatile fatty acids and other end products is primarily driven by the rumen microbiome and its interaction with the host. Importantly, the rumen is demarcated into five distinct rumen sacs as a result of anatomical structure, resulting in variable physiology among the sacs. However, rumen nutritional and microbiome studies have historically focused on the bulk content or fluids sampled from single regions within the rumen. Examining the rumen microbiome from only one or two biogeographical regions is likely not sufficient to provide a comprehensive analysis of the rumen microbiome and its fermentative capacity. Rumen biogeography, digesta fraction, and microbial rumen-tissue association all impact the diversity and function of the entirety of the rumen microbiome. Therefore, this review discusses the importance of the rumen biographical regions and their contribution to microbiome variation.}, }
@article {pmid36985314, year = {2023}, author = {Lozano, FM and Lledó, B and Morales, R and Cascales, A and Hortal, M and Bernabeu, A and Bernabeu, R}, title = {Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030741}, pmid = {36985314}, issn = {2076-2607}, abstract = {An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.}, }
@article {pmid36985296, year = {2023}, author = {Gkolfakis, P and Tziatzios, G and Leite, G and Papanikolaou, IS and Xirouchakis, E and Panayiotides, IG and Karageorgos, A and Millan, MJ and Mathur, R and Weitsman, S and Dimitriadis, GD and Giamarellos-Bourboulis, EJ and Pimentel, M and Triantafyllou, K}, title = {Prevalence of Small Intestinal Bacterial Overgrowth Syndrome in Patients with Non-Alcoholic Fatty Liver Disease/Non-Alcoholic Steatohepatitis: A Cross-Sectional Study.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030723}, pmid = {36985296}, issn = {2076-2607}, abstract = {INTRODUCTION: Non-alcoholic fatty liver disease (NAFLD) is a multifactorial, wide-spectrum liver disorder. Small intestinal bacterial overgrowth (SIBO) is characterized by an increase in the number and/or type of colonic bacteria in the upper gastrointestinal tract. SIBO, through energy salvage and induction of inflammation, may be a pathophysiological factor for NAFLD development and progression.<br><br>AIM/METHODS: Consecutive patients with histological, biochemical, or radiological diagnosis of any stage of NAFLD (non-alcoholic fatty liver [NAFL], non-alcoholic steatohepatitis [NASH], cirrhosis) underwent upper gastrointestinal endoscopy. Duodenal fluid (2cc) was aspirated from the 3rd-4th part of duodenum into sterile containers. SIBO was defined as &#x2265;10[3] aerobic colony-forming units (CFU)/mL of duodenal aspirate and/or the presence of colonic-type bacteria. Patients without any liver disease undergoing gastroscopy due to gastroesophageal reflux disease (GERD) comprised the healthy control (HC) group. Concentrations (pg/mL) of tumor necrosis factor alpha (TNF&#x3b1;), interleukin (IL)-1&#x3b2;, and IL-6 were also measured in the duodenal fluid. The primary endpoint was to evaluate the prevalence of SIBO in NAFLD patients, while the comparison of SIBO prevalence among NAFLD patients and healthy controls was a secondary endpoint.<br><br>RESULTS: We enrolled 125 patients (51 NAFL, 27 NASH, 17 cirrhosis, and 30 HC) aged 54 &#xb1; 11.9 years and with a weight of 88.3 &#xb1; 19.6 kg (NAFLD vs. HC 90.7 &#xb1; 19.1 vs. 80.8 &#xb1; 19.6 kg, p = 0.02). Overall, SIBO was diagnosed in 23/125 (18.4%) patients, with Gram-negative bacteria being the predominant species (19/23; 82.6%). SIBO prevalence was higher in the NAFLD cohort compared to HC (22/95; 23.2% vs. 1/30; 3.3%, p = 0.014). Patients with NASH had higher SIBO prevalence (6/27; 22.2%) compared to NAFL individuals (8/51; 15.7%), but this difference did not reach statistical significance (p = 0.11). Patients with NASH-associated cirrhosis had a higher SIBO prevalence compared to patients with NAFL (8/17; 47.1% vs. 8/51; 15.7%, p = 0.02), while SIBO prevalence between patients with NASH-associated cirrhosis and NASH was not statistically different (8/17; 47.1% vs. 6/27; 22.2%, p = 0.11). Mean concentration of TNF-&#x3b1;, IL-1&#x3b2;, and IL-6 did not differ among the different groups.<br><br>CONCLUSION: The prevalence of SIBO is significantly higher in a cohort of patients with NAFLD compared to healthy controls. Moreover, SIBO is more prevalent in patients with NASH-associated cirrhosis compared to patients with NAFL.}, }
@article {pmid36985292, year = {2023}, author = {Liu, QY and Liao, Y and Wu, YX and Diao, H and Du, Y and Chen, YW and Xie, JR and Xue, WQ and He, YQ and Wang, TM and Zheng, XH and Jia, WH}, title = {The Oral Microbiome as Mediator between Oral Hygiene and Its Impact on Nasopharyngeal Carcinoma.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030719}, pmid = {36985292}, issn = {2076-2607}, abstract = {Oral hygiene and the alteration of the oral microbiome have been linked to nasopharyngeal carcinoma (NPC). This study aimed to investigate whether the oral microbiome plays a mediating role in the relationship between oral hygiene and NPC, and identify differential microbial taxonomies that potentially mediated this association. We conducted a case-control study that involved 218 NPC patients and 192 healthy controls. The 16S rRNA gene sequencing of the V4 region was performed to evaluate the composition of the oral microbiome. Mediation analysis was applied to explore the relationship among oral hygiene, the oral microbiome and NPC. We found that dental fillings and poor oral hygiene score were associated with increased risks of NPC (OR = 2.51 (1.52-4.25) and OR = 1.54 (1.02-2.33)). Mediation analysis indicated that dental fillings increased the risk of NPC by altering the abundance of Erysipelotrichales, Erysipelotrichaceae, Solobacterium and Leptotrichia wadei. In addition, Leptotrichia wadei also mediated the association between oral hygiene score and the risk of NPC. Our study confirmed that poor oral hygiene increased the risk of NPC, which was partly mediated by the oral microbiome. These findings might help us to understand the potential mechanism of oral hygiene influencing the risk of NPC via the microbiome.}, }
@article {pmid36985280, year = {2023}, author = {Jamwal, VL and Rather, IA and Ahmed, S and Kumar, A and Gandhi, SG}, title = {Changing Rhizosphere Microbial Community and Metabolites with Developmental Stages of Coleus barbatus.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030705}, pmid = {36985280}, issn = {2076-2607}, abstract = {Coleus barbatus is a medicinal herb belonging to Lamiaceae. It is the only living organism known to produce forskolin, which is a labdane diterpene and is reported to activate adenylate cyclase. Microbes associated with plants play an important role in maintaining plant health. Recently, the targeted application of beneficial plant-associated microbes and their combinations in abiotic and biotic stress tolerance has gained momentum. In this work, we carried out the rhizosphere metagenome sequencing of C. barbatus at different developmental stages to understand how rhizosphere microflora are affected by and affect the metabolite content in plants. We found that the Kaistobacter genus was abundantly present in the rhizosphere of C. barbatus and its accumulation pattern appears to correlate with the quantities of forskolin in the roots at different developmental stages. Members of the Phoma genus, known for several pathogenic species, were in lower numbers in the C. barbatus rhizosphere in comparison with C. blumei. To our knowledge, this is the first metagenomic study of the rhizospheric microbiome of C. barbatus, which may help to explore and exploit the culturable and non-culturable microbial diversity present in the rhizosphere.}, }
@article {pmid36985258, year = {2023}, author = {Pérez-Losada, M and Castro-Nallar, E and Laerte Boechat, J and Delgado, L and Azenha Rama, T and Berrios-Farías, V and Oliveira, M}, title = {Nasal Bacteriomes of Patients with Asthma and Allergic Rhinitis Show Unique Composition, Structure, Function and Interactions.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030683}, pmid = {36985258}, issn = {2076-2607}, abstract = {Allergic rhinitis and asthma are major public health concerns and economic burdens worldwide. However, little is known about nasal bacteriome dysbiosis during allergic rhinitis, alone or associated with asthma comorbidity. To address this knowledge gap we applied 16S rRNA high-throughput sequencing to 347 nasal samples from participants with asthma (AS = 12), allergic rhinitis (AR = 53), allergic rhinitis with asthma (ARAS = 183) and healthy controls (CT = 99). One to three of the most abundant phyla, and five to seven of the dominant genera differed significantly (p < 0.021) between AS, AR or ARAS and CT groups. All alpha-diversity indices of microbial richness and evenness changed significantly (p < 0.01) between AR or ARAS and CT, while all beta-diversity indices of microbial structure differed significantly (p < 0.011) between each of the respiratory disease groups and controls. Bacteriomes of rhinitic and healthy participants showed 72 differentially expressed (p < 0.05) metabolic pathways each related mainly to degradation and biosynthesis processes. A network analysis of the AR and ARAS bacteriomes depicted more complex webs of interactions among their members than among those of healthy controls. This study demonstrates that the nose harbors distinct bacteriotas during health and respiratory disease and identifies potential taxonomic and functional biomarkers for diagnostics and therapeutics in asthma and rhinitis.}, }
@article {pmid36985253, year = {2023}, author = {Zamorano, D and Ivulic, D and Viver, T and Morales, F and López-Kostner, F and Vidal, RM}, title = {Microbiota Phenotype Promotes Anastomotic Leakage in a Model of Rats with Ischemic Colon Resection.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030680}, pmid = {36985253}, issn = {2076-2607}, abstract = {Anastomotic leakage (AL) is a major cause of morbidity and mortality after colorectal surgery, but the mechanism behind this complication is still not fully understood. Despite the advances in surgical techniques and perioperative care, the complication rates have remained steady. Recently, it has been suggested that colon microbiota may be involved in the development of complications after colorectal surgery. The aim of this study was to evaluate the association of gut microbiota in the development of colorectal AL and their possible virulence strategies to better understand the phenomenon. Using 16S rRNA sequencing of samples collected on the day of surgery and the sixth day following surgery, we analyzed the changes in tissue-associated microbiota at anastomotic sites created in a model of rats with ischemic colon resection. We discovered a trend for lower microbial diversity in the AL group compared to non-leak anastomosis (NLA). There were no differences in relative abundance in the different types of microbial respiration between these groups and the high abundance of the facultative anaerobic Gemella palaticanis is a marker species that stands out as a distinctive feature.}, }
@article {pmid36985245, year = {2023}, author = {Cruz-Silva, A and Laureano, G and Pereira, M and Dias, R and Silva, JMD and Oliveira, N and Gouveia, C and Cruz, C and Gama-Carvalho, M and Alagna, F and Duarte, B and Figueiredo, A}, title = {A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030672}, pmid = {36985245}, issn = {2076-2607}, abstract = {Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.}, }
@article {pmid36985236, year = {2023}, author = {Gargiulo Isacco, C and Balzanelli, MG and Garzone, S and Lorusso, M and Inchingolo, F and Nguyen, KCD and Santacroce, L and Mosca, A and Del Prete, R}, title = {Alterations of Vaginal Microbiota and Chlamydia trachomatis as Crucial Co-Causative Factors in Cervical Cancer Genesis Procured by HPV.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030662}, pmid = {36985236}, issn = {2076-2607}, abstract = {Chlamydia trachomatis and human papillomavirus (HPV) are the most common pathogens found in sexually transmitted infections (STIs), and both are known to increase the risk of cervical cancer (CC) and infertility. HPV is extremely common worldwide, and scientists use it to distinguish between low-risk and high-risk genotypes. In addition, HPV transmission can occur via simple contact in the genital area. From 50 to 80% of sexually active individuals become infected with both C. trachomatis and HPV viruses during their lifetime, and up to 50% become infected with an HPV oncogenic genotype. The natural history of this coinfection is strongly conditioned by the balance between the host microbiome and immune condition and the infecting agent. Though the infection often regresses, it tends to persist throughout adult life asymptomatically and silently. The partnership between HPV and C. trachomatis is basically due to their similarities: common transmission routes, reciprocal advantages, and the same risk factors. C. trachomatis is a Gram-negative bacteria, similar to HPV, and an intracellular bacterium, which shows a unique biphasic development that helps the latter continue its steady progression into the host throughout the entire life. Indeed, depending on the individual's immune condition, the C. trachomatis infection tends to migrate toward the upper genital tract and spread to the uterus, and the fallopian tubes open up a pathway to HPV invasion. In addition, most HPV and C. trachomatis infections related to the female genital tract are facilitated by the decay of the first line of defense in the vaginal environment, which is constituted by a healthy vaginal microbiome that is characterized by a net equilibrium of all its components. Thus, the aim of this paper was to highlight the complexity and fragility of the vaginal microenvironment and accentuate the fundamental role of all elements and systems involved, including the Lactobacillus strains (Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus crispatus) and the immune-endocrine system, in preserving it from oncogenic mutation. Therefore, age, diet, and genetic predisposition together with an unspecific, persistent low-grade inflammatory state were found to be implicated in a high frequency and severity grade of disease, potentially resulting in pre-cancerous and cancerous cervical lesions.}, }
@article {pmid36985231, year = {2023}, author = {Bandarupalli, VVK and St-Pierre, B}, title = {Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030658}, pmid = {36985231}, issn = {2076-2607}, abstract = {In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.}, }
@article {pmid36985217, year = {2023}, author = {Djondji Kamga, FM and Mugenzi, LMJ and Tchouakui, M and Sandeu, MM and Maffo, CGT and Nyegue, MA and Wondji, CS}, title = {Contrasting Patterns of Asaia Association with Pyrethroid Resistance Escalation between the Malaria Vectors Anopheles funestus and Anopheles gambiae.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030644}, pmid = {36985217}, issn = {2076-2607}, abstract = {Microbiome composition has been associated with insecticide resistance in malaria vectors. However, the contribution of major symbionts to the increasingly reported resistance escalation remains unclear. This study explores the possible association of a specific endosymbiont, Asaia spp., with elevated levels of pyrethroid resistance driven by cytochrome P450s enzymes and voltage-gated sodium channel mutations in Anopheles funestus and Anopheles gambiae. Molecular assays were used to detect the symbiont and resistance markers (CYP6P9a/b, 6.5 kb, L1014F, and N1575Y). Overall, genotyping of key mutations revealed an association with the resistance phenotype. The prevalence of Asaia spp. in the FUMOZ_X_FANG strain was associated with the resistance phenotype at a 5X dose of deltamethrin (OR = 25.7; p = 0.002). Mosquitoes with the resistant allele for the markers tested were significantly more infected with Asaia compared to those possessing the susceptible allele. Furthermore, the abundance correlated with the resistance phenotype at 1X concentration of deltamethrin (p = 0.02, Mann-Whitney test). However, for the MANGOUM_X_KISUMU strain, findings rather revealed an association between Asaia load and the susceptible phenotype (p = 0.04, Mann-Whitney test), demonstrating a negative link between the symbiont and permethrin resistance. These bacteria should be further investigated to establish its interactions with other resistance mechanisms and cross-resistance with other insecticide classes.}, }
@article {pmid36985201, year = {2023}, author = {Hartwig, C and Drechsler, S and Vainshtein, Y and Maneth, M and Schmitt, T and Ehling-Schulz, M and Osuchowski, M and Sohn, K}, title = {From Gut to Blood: Spatial and Temporal Pathobiome Dynamics during Acute Abdominal Murine Sepsis.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030627}, pmid = {36985201}, issn = {2076-2607}, abstract = {Abdominal sepsis triggers the transition of microorganisms from the gut to the peritoneum and bloodstream. Unfortunately, there is a limitation of methods and biomarkers to reliably study the emergence of pathobiomes and to monitor their respective dynamics. Three-month-old CD-1 female mice underwent cecal ligation and puncture (CLP) to induce abdominal sepsis. Serial and terminal endpoint specimens were collected for fecal, peritoneal lavage, and blood samples within 72 h. Microbial species compositions were determined by NGS of (cell-free) DNA and confirmed by microbiological cultivation. As a result, CLP induced rapid and early changes of gut microbial communities, with a transition of pathogenic species into the peritoneum and blood detected at 24 h post-CLP. NGS was able to identify pathogenic species in a time course-dependent manner in individual mice using cfDNA from as few as 30 microliters of blood. Absolute levels of cfDNA from pathogens changed rapidly during acute sepsis, demonstrating its short half-life. Pathogenic species and genera in CLP mice significantly overlapped with pathobiomes from septic patients. The study demonstrated that pathobiomes serve as reservoirs following CLP for the transition of pathogens into the bloodstream. Due to its short half-life, cfDNA can serve as a precise biomarker for pathogen identification in blood.}, }
@article {pmid36985199, year = {2023}, author = {Kann, S and Eberhardt, K and Hinz, R and Schwarz, NG and Dib, JC and Aristizabal, A and Mendoza, GAC and Hagen, RM and Frickmann, H and Barrantes, I and Kreikemeyer, B}, title = {The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030625}, pmid = {36985199}, issn = {2076-2607}, abstract = {An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population.}, }
@article {pmid36985184, year = {2023}, author = {Tlak Gajger, I and Nejedli, S and Cvetnić, L}, title = {Influence of Probiotic Feed Supplement on Nosema spp. Infection Level and the Gut Microbiota of Adult Honeybees (Apis mellifera L.).}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030610}, pmid = {36985184}, issn = {2076-2607}, abstract = {Honeybees' gut microbiota can provide new valuable access into the pathogenesis-related factors included in infections. Hence, we researched the presence and comparison of gut microbiota groups in control and Nosema spp.-infected honeybee colonies through high-throughput sequencing of the 16S rRNA. As the newest approach in apiary management, we hypothesize that the EM[®] probiotic for bees could have an important role in therapeutic and immunomodulatory effects on honeybee colonies. The aim of this study was to estimate its impact on the gut microbiota composition of adult honeybees. The major genera were detected, where Lactobacillus was the most abundant genus, followed by Gilliamela, Snodgrassella, and Bifidobacterium. Inoculation with Nosema spp. spores made the relative proportions of Bifidobacterium lower, which was ameliorated by EM[®] for bees' application. In addition, EM[®] for bee applied treatments suppressed the increase in the number of Nosema spp. spores. This result points out that continuous EM[®] for bees treatment shall change bees' gut microbiome composition and mitigate the influence of Nosema spp. infection. Snodgrassella alvi was a major member of the honeybee gut microbiota and may be significantly increased by long-term treatment with EM[®] for bees. Toward these results, it is possible that EM[®] for bees treatment will protect honeybees from herbicide glyphosate negative effects in agricultural fields by improving microbiome and immune functions.}, }
@article {pmid36985147, year = {2023}, author = {Banaszak, M and Górna, I and Woźniak, D and Przysławski, J and Drzymała-Czyż, S}, title = {Association between Gut Dysbiosis and the Occurrence of SIBO, LIBO, SIFO and IMO.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030573}, pmid = {36985147}, issn = {2076-2607}, abstract = {Gut microbiota is the aggregate of all microorganisms in the human digestive system. There are 10[14] CFU/mL of such microorganisms in the human body, including bacteria, viruses, fungi, archaea and protozoa. The Firmicutes and Bacteroidetes bacteria phyla comprise 90% of the human gut microbiota. The microbiota support the healthy functioning of the human body by helping with digestion (mainly via short-chain fatty acids and amino acids) and producing short-chain fatty acids. In addition, it exhibits many physiological functions, such as forming the intestinal epithelium, intestinal integrity maintenance, the production of vitamins, and protection against pathogens. An altered composition or the number of microorganisms, known as dysbiosis, disrupts the body's homeostasis and can lead to the development of inflammatory bowel disease, irritable bowel syndrome, and metabolic diseases such as diabetes, obesity and allergies. Several types of disruptions to the gut microbiota have been identified: SIBO (Small Intestinal Bacterial Overgrowth), LIBO (Large Intestinal Bacterial Overgrowth), SIFO (Small Intestinal Fungal Overgrowth), and IMO (Intestinal Methanogen Overgrowth). General gastrointestinal problems such as abdominal pain, bloating, gas, diarrhoea and constipation are the main symptoms of dysbiosis. They lead to malabsorption, nutrient deficiencies, anaemia and hypoproteinaemia. Increased lipopolysaccharide (LPS) permeability, stimulating the inflammatory response and resulting in chronic inflammation, has been identified as the leading cause of microbial overgrowth in the gut. The subject literature is extensive but of limited quality. Despite the recent interest in the gut microbiome and its disorders, more clinical research is needed to determine the pathophysiology, effective treatments, and prevention of small and large intestinal microbiota overgrowth. This review was designed to provide an overview of the available literature on intestinal microbial dysbiosis (SIBO, LIBO, SIFO and IMO) and to determine whether it represents a real threat to human health.}, }
@article {pmid36985137, year = {2023}, author = {Aželytė, J and Wu-Chuang, A and Maitre, A and Žiegytė, R and Mateos-Hernández, L and Obregón, D and Palinauskas, V and Cabezas-Cruz, A}, title = {Avian Malaria Parasites Modulate Gut Microbiome Assembly in Canaries.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030563}, pmid = {36985137}, issn = {2076-2607}, abstract = {Rodent and human malaria parasites cause dysbiosis in the host gut microbiome, but whether Plasmodium species affecting birds cause dysbiosis in their hosts is currently unknown. Here we used a model of avian malaria infection to test whether parasite infection modulates the bird microbiome. To this aim, bird fecal microbiomes were characterized at different time points after infection of canaries with the avian malaria parasite Plasmodium homocircumflexum. Avian malaria caused no significant changes in the alpha and beta diversity of the microbiome in infected birds. In contrast, we discovered changes in the composition and abundance of several taxa. Co-occurrence networks were used to characterize the assembly of the microbiome and trajectories of microbiome structural states progression were found to be different between infected and uninfected birds. Prediction of functional profiles in bacterial communities using PICRUSt2 showed infection by P. homocircumflexum to be associated with the presence of specific degradation and biosynthesis metabolic pathways, which were not found in healthy birds. Some of the metabolic pathways with decreased abundance in the infected group had significant increase in the later stage of infection. The results showed that avian malaria parasites affect bacterial community assembly in the host gut microbiome. Microbiome modulation by malaria parasites could have deleterious consequences for the host bird. Knowing the intricacies of bird-malaria-microbiota interactions may prove helpful in determining key microbial players and informing interventions to improve animal health.}, }
@article {pmid36985135, year = {2023}, author = {Ren, X and Whitton, MM and Yu, SJ and Trotter, T and Bajagai, YS and Stanley, D}, title = {Application of Phytogenic Liquid Supplementation in Soil Microbiome Restoration in Queensland Pasture Dieback.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030561}, pmid = {36985135}, issn = {2076-2607}, abstract = {Pasture production is vital in cattle farming as it provides animals with food and nutrients. Australia, as a significant global beef producer, has been experiencing pasture dieback, a syndrome of deteriorating grassland that results in the loss of grass and the expansion of weeds. Despite two decades of research and many remediation attempts, there has yet to be a breakthrough in understanding the causes or mechanisms involved. Suggested causes of this phenomenon include soil and plant microbial pathogens, insect infestation, extreme heat stress, radiation, and others. Plants produce a range of phytomolecules with antifungal, antibacterial, antiviral, growth-promoting, and immunostimulant effects to protect themselves from a range of environmental stresses. These products are currently used more in human and veterinary health than in agronomy. In this study, we applied a phytogenic product containing citric acid, carvacrol, and cinnamaldehyde, to investigate its ability to alleviate pasture dieback. The phytogenic liquid-based solution was sprayed twice, one week apart, at 5.4 L per hectare. The soil microbial community was investigated longitudinally to determine long-term effects, and pasture productivity and plant morphometric improvements were explored. The phytogenic liquid significantly improved post-drought recovery of alpha diversity and altered temporal and spatial change in the community. The phytogenic liquid reduced biomarker genera associated with poor and polluted soils and significantly promoted plant and soil beneficial bacteria associated with plant rhizosphere and a range of soil benefits. Phytogenic liquid application produced plant morphology improvements and a consistent enhancement of pasture productivity extending beyond 18 months post-application. Our data show that phytogenic products used in the livestock market as an alternative to antibiotics may also have a beneficial role in agriculture, especially in the light of climate change-related soil maintenance and remediation.}, }
@article {pmid36985125, year = {2023}, author = {Cezar-de-Mello, PFT and Ryan, S and Fichorova, RN}, title = {The microRNA Cargo of Human Vaginal Extracellular Vesicles Differentiates Parasitic and Pathobiont Infections from Colonization by Homeostatic Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030551}, pmid = {36985125}, issn = {2076-2607}, abstract = {The disturbed vaginal microbiome defined as bacterial vaginosis (BV) and the parasitic infection by Trichomonas vaginalis (TV), the most common non-viral sexually transmitted pathogen, have well-established adverse effects on reproductive outcomes and susceptibility to infection and cancer. Molecular mechanisms underlying these associations and the failure of antibiotic therapy to mitigate adverse consequences are not fully elucidated. In an in vitro human vaginal colonization model, we tested the hypothesis that responses to TV and/or BV-bacteria will disrupt the micro(mi)RNA cargo of extracellular vesicles (EV) with the potential to modify pathways associated with reproductive function, cancer, and infection. miRNAs were quantified by HTG EdgeSeq. MiRNA differential expression (DE) was established in response to TV, the BV signature pathobiont Prevotella bivia and a homeostatic Lactobacillus crispatus with adjusted p < 0.05 using R. Validated gene targets, pathways, protein-protein interaction networks, and hub genes were identified by miRWalk, STRING, Cytoscape, and CytoHubba. In contrast to L. crispatus, TV and the BV pathobiont dysregulated a massive number of EV-miRNAs, over 50% shared by both pathogens. Corresponding target pathways, protein interaction clusters and top hub genes were related to cancer, infectious disease, circadian rhythm, steroid hormone signaling, pregnancy, and reproductive tissue terms. These data support the emerging concept that bacteria and parasitic eukaryotes disturbing the human vaginal microbiome may impact reproductive health through EV-miRNA dysregulation.}, }
@article {pmid36985120, year = {2023}, author = {Guo, Y and Yuan, W and Lyu, N and Pan, Y and Cao, X and Wang, Y and Han, Y and Zhu, B}, title = {Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030546}, pmid = {36985120}, issn = {2076-2607}, abstract = {Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.}, }
@article {pmid36984895, year = {2023}, author = {Radford-Smith, DE and Anthony, DC}, title = {Mechanisms of Maternal Diet-Induced Obesity Affecting the Offspring Brain and Development of Affective Disorders.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030455}, pmid = {36984895}, issn = {2218-1989}, abstract = {Depression and metabolic disease are common disorders that share a bidirectional relationship and continue to increase in prevalence. Maternal diet and maternal behaviour both profoundly influence the developmental trajectory of offspring during the perinatal period. At an epidemiological level, both maternal depression and obesity during pregnancy have been shown to increase the risk of neuropsychiatric disease in the subsequent generation. Considerable progress has been made to understand the mechanisms by which maternal obesity disrupts the developing offspring gut-brain axis, priming offspring for the development of affective disorders. This review outlines such mechanisms in detail, including altered maternal care, the maternal microbiome, inflammation, breast milk composition, and maternal and placental metabolites. Subsequently, offspring may be prone to developing gut-brain interaction disorders with concomitant changes to brain energy metabolism, neurotransmission, and behaviour, alongside gut dysbiosis. The gut microbiome may act as a key modifiable, and therefore treatable, feature of the relationship between maternal obesity and the offspring brain function. Further studies examining the relationship between maternal nutrition, the maternal microbiome and metabolites, and offspring neurodevelopment are warranted to identify novel therapeutic targets.}, }
@article {pmid36984891, year = {2023}, author = {Qin, F and Li, J and Mao, T and Feng, S and Li, J and Lai, M}, title = {2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030451}, pmid = {36984891}, issn = {2218-1989}, abstract = {2-hydroxybutyric acid (2HB) serves as an important regulatory factor in a variety of diseases. The circulating level of 2HB in serum is significantly higher in multiple diseases, such as cancer and type 2 diabetes (T2D). However, there is currently no systematic study on 2HB-producing bacteria that demonstrates whether gut bacteria contribute to the circulating 2HB pool. To address this question, we used BLASTP to reveal the taxonomic profiling of 2HB-producing bacteria in the human microbiome, which are mainly distributed in the phylum Proteobacteria and Firmicutes. In vitro experiments showed that most gut bacteria (21/32) have at least one path to produce 2HB, which includes Aspartic acid, methionine, threonine, and 2-aminobutyric acid. Particularly, Fusobacterium nucleatum has the strongest ability to synthesize 2HB, which is sufficient to alter colon 2HB concentration in mice. Nevertheless, neither antibiotic (ABX) nor Fusobacterium nucleatum gavage significantly affected mouse serum 2HB levels during the time course of this study. Taken together, our study presents the profiles of 2HB-producing bacteria and demonstrates that gut microbiota was a major contributor to 2HB concentration in the intestinal lumen but a relatively minor contributor to serum 2HB concentration.}, }
@article {pmid36984872, year = {2023}, author = {Costello, SM and Cheney, AM and Waldum, A and Tripet, B and Cotrina-Vidal, M and Kaufmann, H and Norcliffe-Kaufmann, L and Lefcort, F and Copié, V}, title = {A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030433}, pmid = {36984872}, issn = {2218-1989}, support = {R01-DK117473; P20GM-103474/NH/NIH HHS/United States ; }, abstract = {Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer's (AD) and Parkinson's (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the ELP1 gene. FD patients represent a well-defined population who can help us better understand the cellular networks underlying neurodegeneration, and how disease traits are affected by metabolic dysfunction, which in turn may contribute to dysregulation of the gut-brain axis of FD. Here, [1]H NMR spectroscopy was employed to characterize the serum and fecal metabolomes of FD patients, and to assess similarities and differences in the polar metabolite profiles between FD patients and healthy relative controls. Findings from this work revealed noteworthy metabolic alterations reflected in energy (ATP) production, mitochondrial function, amino acid and nucleotide catabolism, neurosignaling molecules, and gut-microbial metabolism. These results provide further evidence for a close interconnection between metabolism, neurodegeneration, and gut microbiome dysbiosis in FD, and create an opportunity to explore whether metabolic interventions targeting the gut-brain-metabolism axis of FD could be used to redress or slow down the progressive neurodegeneration observed in FD patients.}, }
@article {pmid36984862, year = {2023}, author = {Stinson, LF and George, AD}, title = {Human Milk Lipids and Small Metabolites: Maternal and Microbial Origins.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030422}, pmid = {36984862}, issn = {2218-1989}, abstract = {Although there has been limited application in the field to date, human milk omics research continues to gain traction. Human milk lipidomics and metabolomics research is particularly important, given the significance of milk lipids and metabolites for infant health. For researchers conducting compositional milk analyses, it is important to consider the origins of these compounds. The current review aims to provide a summary of the existing evidence on the sources of human milk lipids and small metabolites. Here, we describe five major sources of milk lipids and metabolites: de novo synthesis from mammary cells, production by the milk microbiota, dietary consumption, release from non-mammary tissue, and production by the gut microbiota. We synthesize the literature to provide evidence and understanding of these pathways in the context of mammary gland biology. We recommend future research focus areas to elucidate milk lipid and small metabolite synthesis and transport pathways. Better understanding of the origins of human milk lipids and metabolites is important to improve translation of milk omics research, particularly regarding the modulation of these important milk components to improve infant health outcomes.}, }
@article {pmid36984847, year = {2023}, author = {Kim, JK and Hong, S and Park, J and Kim, S}, title = {Metabolic and Transcriptomic Changes in the Mouse Brain in Response to Short-Term High-Fat Metabolic Stress.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030407}, pmid = {36984847}, issn = {2218-1989}, abstract = {The chronic consumption of diets rich in saturated fats leads to obesity and associated metabolic disorders including diabetes and atherosclerosis. Intake of a high-fat diet (HFD) is also recognized to dysregulate neural functions such as cognition, mood, and behavior. However, the effects of short-term high-fat diets on the brain are elusive. Here, we investigated molecular changes in the mouse brain following an acute HFD for 10 days by employing RNA sequencing and metabolomics profiling. Aberrant expressions of 92 genes were detected in the brain tissues of acute HFD-exposed mice. The differentially expressed genes were enriched for various pathways and processes such as superoxide metabolism. In our global metabolomic profiling, a total of 59 metabolites were significantly altered by the acute HFD. Metabolic pathways upregulated from HFD-exposed brain tissues relative to control samples included oxidative stress, oxidized polyunsaturated fatty acids, amino acid metabolism (e.g., branched-chain amino acid catabolism, and lysine metabolism), and the gut microbiome. Acute HFD also elevated levels of N-acetylated amino acids, urea cycle metabolites, and uracil metabolites, further suggesting complex changes in nitrogen metabolism. The observed molecular events in the present study provide a valuable resource that can help us better understand how acute HFD stress impacts brain homeostasis.}, }
@article {pmid36984841, year = {2023}, author = {Cohen, CC and Huneault, H and Accardi, CJ and Jones, DP and Liu, K and Maner-Smith, KM and Song, M and Welsh, JA and Ugalde-Nicalo, PA and Schwimmer, JB and Vos, MB}, title = {Metabolome × Microbiome Changes Associated with a Diet-Induced Reduction in Hepatic Fat among Adolescent Boys.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030401}, pmid = {36984841}, issn = {2218-1989}, support = {UL1TR001442/TR/NCATS NIH HHS/United States ; UL1TR001442/TR/NCATS NIH HHS/United States ; P30ES019776/ES/NIEHS NIH HHS/United States ; P20GM103436/GM/NIGMS NIH HHS/United States ; P20GM113226/GM/NIGMS NIH HHS/United States ; P20GM106396/GM/NIGMS NIH HHS/United States ; T32DK07658/DK/NIDDK NIH HHS/United States ; F32DK131757/DK/NIDDK NIH HHS/United States ; R01DK125701/DK/NIDDK NIH HHS/United States ; R01NR019083/NR/NINR NIH HHS/United States ; }, abstract = {Dietary sugar reduction is one therapeutic strategy for improving nonalcoholic fatty liver disease (NAFLD), and the underlying mechanisms for this effect warrant further investigation. Here, we employed metabolomics and metagenomics to examine systemic biological adaptations associated with dietary sugar restriction and (subsequent) hepatic fat reductions in youth with NAFLD. Data/samples were from a randomized controlled trial in adolescent boys (11-16 years, mean ± SD: 13.0 ± 1.9 years) with biopsy-proven NAFLD who were either provided a low free-sugar diet (LFSD) (n = 20) or consumed their usual diet (n = 20) for 8 weeks. Plasma metabolomics was performed on samples from all 40 participants by coupling hydrophilic interaction liquid chromatography (HILIC) and C18 chromatography with mass spectrometry. In a sub-sample (n = 8 LFSD group and n = 10 usual diet group), 16S ribosomal RNA (rRNA) sequencing was performed on stool to examine changes in microbial composition/diversity. The diet treatment was associated with differential expression of 419 HILIC and 205 C18 metabolite features (p < 0.05), which were enriched in amino acid pathways, including methionine/cysteine and serine/glycine/alanine metabolism (p < 0.05), and lipid pathways, including omega-3 and linoleate metabolism (p < 0.05). Quantified metabolites that were differentially changed in the LFSD group, compared to usual diet group, and representative of these enriched metabolic pathways included increased serine (p = 0.001), glycine (p = 0.004), 2-aminobutyric acid (p = 0.012), and 3-hydroxybutyric acid (p = 0.005), and decreased linolenic acid (p = 0.006). Microbiome changes included an increase in richness at the phylum level and changes in a few genera within Firmicutes. In conclusion, the LFSD treatment, compared to usual diet, was associated with metabolome and microbiome changes that may reflect biological mechanisms linking dietary sugar restriction to a therapeutic decrease in hepatic fat. Studies are needed to validate our findings and test the utility of these "omics" changes as response biomarkers.}, }
@article {pmid36984818, year = {2023}, author = {Jarmakiewicz-Czaja, S and Gruszecka, J and Filip, R}, title = {What Do NAFLD, Liver Fibrosis, and Inflammatory Bowel Disease Have in Common? Review of the Current Literature.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030378}, pmid = {36984818}, issn = {2218-1989}, abstract = {Liver disease is one of the most common extraintestinal manifestations of inflammatory bowel disease (IBD). Often the course of liver disease is associated with an exacerbation of the underlying disease (Crohn's Disease/Ulcerative Colitis). Nonalcoholic steatohepatitis encompasses a wide spectrum of liver damage. The most common form is nonalcoholic fatty liver disease (NAFLD) (75-80%), and the less common but more dangerous form is nonalcoholic steatohepatitis (NASH). NAFLD is now the most common cause of chronic liver disease in developed countries and the leading indication for liver transplantation in the United States. Genetic, demographic, clinical, and environmental factors can play a role in the pathogenesis of NAFLD. The increasing prevalence of NAFLD is associated with a widespread obesity epidemic, metabolic complications, including hypertension, type 2 diabetes, and dyslipidaemia. Some of the most common manifestations of IBD are liver, biliary tract, and gallbladder diseases. The liver fibrosis process has a complex pathophysiology and is often dependent on exogenous factors such as the treatment used and endogenous factors such as the gut microbiome. However, the factors that link IBD and liver fibrosis are not yet clear. The main purpose of the review is to try to find links between IBD and selected liver diseases and to identify knowledge gaps that will inform further research.}, }
@article {pmid36984815, year = {2023}, author = {Reva, K and Laranjinha, J and Rocha, BS}, title = {Epigenetic Modifications Induced by the Gut Microbiota May Result from What We Eat: Should We Talk about Precision Diet in Health and Disease?.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030375}, pmid = {36984815}, issn = {2218-1989}, abstract = {Diet is currently considered one of the most important adjustable determinants of human health. The gut microbiota, the collection of microorganisms that inhabit (mainly) the distal bowel, has recently been shown to ensure critical physiological functions, such as immune, metabolic and neuropsychiatric. Many of these biological effects result from the production of bacterial metabolites that may target host cells, tissues and organs. In line with this rationale, epigenetics has brought new insights to our understanding of how environmental factors influence gene expression and, interestingly, gut microbiota metabolites have recently been proposed as novel and significant inducers of epigenetic modifications. Efforts have been dedicated to unveil how the production of specific metabolites influences the activity of epigenetic writers and erasers in order to establish a mechanistic link between gut microbiota, epigenetic modifications and health. Recent data is now evidencing how specific microbial metabolites shape the epigenetic landscape of eukaryotic cells, paving new avenues for innovative therapeutic strategies relying on diet-driven microbiota: epigenetic interactions. Herein is discussed the impact of diet on gut microbiota and the molecular mechanisms underlying microbiota-host interactions, highlighting the influence of diet on microbiota metabolome and how this may induce epigenetic modifications in host cells. Furthermore, it is hypothesized that epigenetics may be a key process transducing the effects of diet on gut microbiota with consequences for health and disease. Accordingly, innovating strategies of disease prevention based on a "precision diet", a personalized dietary planning according to specific epigenetic targets, are discussed.}, }
@article {pmid36984798, year = {2023}, author = {Dailey, A and Solano-Aguilar, G and Urban, JF and Couch, RD}, title = {LC-QToF-Based Metabolomics Identifies Aberrant Tissue Metabolites Associated with a Higher-Fat Diet and Their 'Reversion to Healthy' with Dietary Probiotic Supplementation.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030358}, pmid = {36984798}, issn = {2218-1989}, abstract = {Over 33% of Americans are labeled as obese, leading the World Health Organization to designate obesity as a major public health problem. One consequence of obesity is the development of metabolic syndrome, a condition which has been correlated to an increased risk for developing cardiovascular disease and Type 2 diabetes. Prolonged ingestion of a higher-fat diet, one cause of obesity, results in alterations to the gut microbiome. These alterations are implicated to have a profound role in the evolution and progression of obesity-linked diseases. Probiotics are associated with positive health effects such as limiting pathogen colonization, aiding in digestion, and vitamin synthesis. Using Ossabaw pigs as a model for obesity, and in conjunction with our previous research, we performed an in-depth, nontargeted, metabolomic analysis on select organs to elucidate the effects of dietary supplementation with the probiotic Lacticaseibacillus paracasei. We focused our analysis on the effects of probiotic supplementation on a higher-fat (obesogenic) diet and a nutritionally balanced diet. Notably, our findings reveal that the brain cortex is highly sensitive to dietary influencers, and with probiotic supplementation, several aberrant metabolites associated with a higher-fat diet revert to healthy levels, thus demonstrating the potential for a probiotic intervention for obesity-linked disease.}, }
@article {pmid36984795, year = {2023}, author = {Kråkström, M and Dickens, AM and Alves, MA and Forssten, SD and Ouwehand, AC and Hyötyläinen, T and Orešič, M and Lamichhane, S}, title = {Dynamics of the Lipidome in a Colon Simulator.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030355}, pmid = {36984795}, issn = {2218-1989}, abstract = {Current evidence suggests that gut microbiome-derived lipids play a crucial role in the regulation of host lipid metabolism. However, not much is known about the dynamics of gut microbial lipids within the distinct gut biogeographic. Here we applied targeted and untargeted lipidomics to in vitro-derived feces. Simulated intestinal chyme was collected from in vitro gut vessels (V1-V4), representing proximal to distal parts of the colon after 24 and 48 h with/without polydextrose treatment. In total, 44 simulated chyme samples were collected from the in vitro colon simulator. Factor analysis showed that vessel and time had the strongest impact on the simulated intestinal chyme lipid profiles. We found that levels of phosphatidylcholines, sphingomyelins, triacylglycerols, and endocannabinoids were altered in at least one vessel (V1-V4) during simulation. We also found that concentrations of triacylglycerols, diacylglycerols, and endocannabinoids changed with time (24 vs. 48 h of simulation). Together, we found that the simulated intestinal chyme revealed a wide range of lipids that remained altered in different compartments of the human colon model over time.}, }
@article {pmid36984505, year = {2023}, author = {Kountouras, J and Doulberis, M and Papaefthymiou, A and Polyzos, SA and Zavos, C and Kazakos, E and Arapoglou, S and Kyrailidi, F and Mouratidou, MC and Boziki, M and Vardaka, E}, title = {Controlling the Impact of Helicobacter pylori-Related Hyperhomocysteinemia on Neurodegeneration.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {59}, number = {3}, pages = {}, doi = {10.3390/medicina59030504}, pmid = {36984505}, issn = {1648-9144}, abstract = {Helicobacter pylori infection consists a high global burden affecting more than 50% of the world's population. It is implicated, beyond substantiated local gastric pathologies, i.e., peptic ulcers and gastric cancer, in the pathophysiology of several neurodegenerative disorders, mainly by inducing hyperhomocysteinemia-related brain cortical thinning (BCT). BCT has been advocated as a possible biomarker associated with neurodegenerative central nervous system disorders such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and/or glaucoma, termed as "ocular Alzheimer's disease". According to the infection hypothesis in relation to neurodegeneration, Helicobacter pylori as non-commensal gut microbiome has been advocated as trigger and/or mediator of neurodegenerative diseases, such as the development of Alzheimer's disease. Among others, Helicobacter pylori-related inflammatory mediators, defensins, autophagy, vitamin D, dietary factors, role of probiotics, and some pathogenetic considerations including relevant involved genes are discussed within this opinion article. In conclusion, by controlling the impact of Helicobacter pylori-related hyperhomocysteinemia on neurodegenerative disorders might offer benefits, and additional research is warranted to clarify this crucial topic currently representing a major worldwide burden.}, }
@article {pmid36984484, year = {2023}, author = {Pan, SY and Chen, WC and Huang, CP and Hsu, CY and Chang, YH}, title = {The Association of Prostate Cancer and Urinary Tract Infections: A New Perspective of Prostate Cancer Pathogenesis.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {59}, number = {3}, pages = {}, doi = {10.3390/medicina59030483}, pmid = {36984484}, issn = {1648-9144}, abstract = {Background and objectives: Microbiota of the urinary tract may be associated with urinary tract malignancy, including prostate cancer. Materials and Methods: We retrospectively collected patients with newly diagnosed prostate cancer and subjects without prostate cancer from the National Health Insurance Research Database (NHIRD) in Taiwan between 1 January 2000 and 31 December 2016. A total of 5510 subjects were recruited and followed until the diagnosis of a primary outcome (urinary tract infection, pyelonephritis, cystitis, and prostatitis). Results: We found that the patients with prostate cancer had a significantly higher risk of urinary tract infections than those without prostate cancer. The adjusted hazard ratios for pyelonephritis, prostatitis, and cystitis were 2.30 (95% CI = 1.36-3.88), 2.04 (95% CI = 1.03-4.05), and 4.02 (95 % CI = 2.11-7.66), respectively. We clearly identified the sites of infection and associated comorbidities in the prostate cancer patients with urinary tract infections. In addition, we found that the patients receiving radiotherapy and androgen deprivation therapy had a lower risk of urinary tract infections than the patients in corresponding control groups. Conclusions: Our study suggests that an abnormal urine microbiome could potentially contribute to the development of prostate cancer through inflammation and immune dysregulation. Furthermore, an imbalanced microbiome may facilitate bacterial overgrowth in urine, leading to urinary tract infections. These findings have important implications for the diagnosis and treatment of prostate cancer. Further research is needed to better understand the role of the urine microbiome in prostate cancer pathogenesis and to identify potential microbiome-targeted therapies for the prevention and treatment of prostate cancer.}, }
@article {pmid36983967, year = {2023}, author = {Heidar, NA and Bhat, TA and Shabir, U and Hussein, AA}, title = {The Urinary Microbiome and Bladder Cancer.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/life13030812}, pmid = {36983967}, issn = {2075-1729}, abstract = {Bladder cancer is the 10th most common cancer worldwide. Approximately 75% of patients with bladder cancer will present with non-muscle invasive disease. Patients are usually treated with transurethral resection of bladder tumor (TURBT), in addition to adjuvant intravesical therapy (chemotherapy or anti-cancer immunotherapy with Bacillus Calmette Guerin- BCG) for those at intermediate-risk and high-risk of recurrence and progression. For many years, urine has been thought to be "sterile"; however, advanced microbiological and molecular techniques, including 16S ribosomal RNA (16S rRNA) sequencing, have negated that previous paradigm and confirmed the presence of a urinary microbiome. The urinary microbiome has been associated with several urological diseases, including interstitial cystitis, urgency urinary incontinence, neurogenic bladder dysfunction, and others. More recently, many reports are emerging about the role of the urinary microbiome in urothelial carcinogenesis, including gender disparity in bladder cancer and responses to treatments. The urinary microbiome may serve as a biomarker that can help with risk stratification as well as prediction of the response to intravesical therapies. However, the microbiome literature has been hampered by the lack of a unified standardized methodology for sample collection, type, preservation, processing, as well as bioinformatics analysis. Herein we describe and critique the literature on the association between urinary microbiome and bladder cancer and highlight some of the future directions.}, }
@article {pmid36983939, year = {2023}, author = {Stope, MB}, title = {The Connection between Immunocompetence and Reproduction in Wildlife.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/life13030785}, pmid = {36983939}, issn = {2075-1729}, abstract = {Reproduction rate is important for the survival of animal populations. During gravidity, a trade-off occurs between the individual well-being of gravid females and investment in offspring. Due to the high synthesis and energy requirements for the growing fetus, other physiological activities are downregulated in pregnant females. This causes changes in the composition of the reproductive microbiome and a decreased immune response to presented antigens and pathogens. As a result, the immunocompetence of gravid wild animals declines. In general, therefore, increased infection rates during pregnancy can be observed in all wildlife species studied. In the course of evolution, however, this has apparently evolved as a suitable strategy to ensure the survival of the population as a whole.}, }
@article {pmid36983902, year = {2023}, author = {Tamás, B and Gabriella, K and Kristóf, &#xc1; and Anett, I and János Pál, K and Bálint, T and Péter, L and Márton, P and Katalin, N}, title = {The Effects of Lakitelek Thermal Water and Tap Water on Skin Microbiome, a Randomized Control Pilot Study.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/life13030746}, pmid = {36983902}, issn = {2075-1729}, abstract = {The beneficial effects of balneotherapy have been proven by numerous clinical studies on locomotor disorders. To date, there is only scant data on changes in the microbiome system of the skin during balneotherapy. The aim of this study was to compare the effects of thermal water and tap water on the skin's microbiome in healthy volunteers. 30 healthy female volunteers participated in the study. The experimental group (of 15 women) spent 30-min 10 times, in Gabriella Spring's thermal baths (i.e., mineral water containing sodium hydrogen carbonate).The controlled group (15 women) had the same, but in tap water. The results of this study have proven that there is a difference in the influencing effects of tap water and medicinal water on the microbiome of the skin. After bathing in the thermal water of Lakitelek, Deinococcus increased significantly at the genus level, and the tendency for Rothia mucilaginosa bacteria also increased. At the species level, Rothia mucilaginosa increased significantly, while Paracoccus aminovorans and the tendency for Paracoccus marcusii decreased. When the values of the two trial groups after bathing at the genus level were compared, Rothia bacteria increased significantly, while Haemophilus tended to increase, Pseudomonas tended to decrease, Neisseria tended to increase significantly, and Flavobacterium tended to decrease. At the species level, Geobacillus vulcani decreased significantly, and the tendency for Burkholderia gladioli decreased. The growth of Rothia mucilaginosa and the decrease in the tendency of Paracoccus, Pseudomonas, Flavobacteroium, and Burkholderia gladioli confirm the beneficial effect of balneotherapy. In this study, trends are represented by the uncorrected p value. The main result was that the thermal water changed certain bacteria of the skin, both on the genus and species levels, but there were no significant changes in the tap water used, either at the genus or species level. We first compared the worlds of thermal water and tap water's microbiome systems. The thermal water decreased the number of certain inflammatory infectious agents and could enhance some of their positive effects, which have been proven at the molecular level. Our results can provide an important clue in the treatment of certain skin diseases. The research of the skin microbiome during balneotherapy can be one of the most intriguing and exciting topics of the future and can bring us closer to understanding the mechanism of action of balneotherapy.}, }
@article {pmid36983881, year = {2023}, author = {Bharindwal, S and Goswami, N and Jha, P and Pandey, S and Jobby, R}, title = {Prospective Use of Probiotics to Maintain Astronaut Health during Spaceflight.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/life13030727}, pmid = {36983881}, issn = {2075-1729}, abstract = {Maintaining an astronaut's health during space travel is crucial. Multiple studies have observed various changes in the gut microbiome and physiological health. Astronauts on board the International Space Station (ISS) had changes in the microbial communities in their gut, nose, and skin. Additionally, immune system cell alterations have been observed in astronauts with changes in neutrophils, monocytes, and T-cells. Probiotics help tackle these health issues caused during spaceflight by inhibiting pathogen adherence, enhancing epithelial barrier function by reducing permeability, and producing an anti-inflammatory effect. When exposed to microgravity, probiotics demonstrated a shorter lag phase, faster growth, improved acid tolerance, and bile resistance. A freeze-dried Lactobacillus casei strain Shirota capsule was tested for its stability on ISS for a month and has been shown to enhance innate immunity and balance intestinal microbiota. The usage of freeze-dried spores of B. subtilis proves to be advantageous to long-term spaceflight because it qualifies for all the aspects tested for commercial probiotics under simulated conditions. These results demonstrate a need to further study the effect of probiotics in simulated microgravity and spaceflight conditions and to apply them to overcome the effects caused by gut microbiome dysbiosis and issues that might occur during spaceflight.}, }
@article {pmid36983812, year = {2023}, author = {Wazir, HU and Narang, P and Silvani, G and Mehner, C and Poole, K and Burke, C and Chou, J}, title = {Bacterial Virulence and Prevention for Human Spaceflight.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/life13030656}, pmid = {36983812}, issn = {2075-1729}, abstract = {With the advancement in reusable rocket propulsion technology, space tourist trips into outer space are now becoming a possibility at a cost-effective rate. As such, astronauts will face a host of health-related challenges, particularly on long-duration space missions where maintaining a balanced healthy microbiome is going to be vital for human survival in space exploration as well as mission success. The human microbiome involves a whole list of micro-organisms that reside in and on the human host, and plays an integral role in keeping the human host healthy. However, imbalances in the microbiome have been directly linked to many human diseases. Research findings have clearly shown that the outer space environment can directly affect the normal microbiome of astronauts when the astronaut is exposed to the microgravity environment. In this study, we show that the simulation of microgravity on earth can mimic the outer space microgravity environment. Staphylococus aureus (S. aureus) was chosen for this study as it is an opportunistic pathogen, which is part of the normal human skin microflora and the nasal passages. This study's results show that S. aureus proliferation was significantly increased under a microgravity environment compared to Earth's gravity conditions, which complements previous work performed on bacteria in the outer space environment in the International Space Station (ISS). This demonstrates that this technology can be utilised here on Earth to mimic the outer space environment and to study challenging health-related questions. This in return saves us the cost on conducting experiments in the ISS and can help advance knowledge at a faster rate and produce countermeasures to mitigate the negative side effects of the hostile outer space environment on humans.}, }
@article {pmid36983718, year = {2023}, author = {Zhang, Z and Chen, H and Huang, J and Zhang, S and Li, Z and Kong, C and Mao, Y and Han, B}, title = {Early Administration of Vancomycin Inhibits Pulmonary Embolism by Remodeling Gut Microbiota.}, journal = {Journal of personalized medicine}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/jpm13030537}, pmid = {36983718}, issn = {2075-4426}, abstract = {Pulmonary embolism (PE) is a common and potentially fatal condition in the emergency department, and early identification of modifiable risk factors for prevention and management is highly desirable. Although gut dysbiosis is associated with a high incidence of venous thromboembolism, the role and mechanisms of the gut microbiome in the pathogenesis of venous thromboembolism, especially PE, remain unexplored. Here, we attempted to elucidate the benefits of the gut microbiome in the pathogenesis of PE using multiple antibiotics and fecal microbiota transplantation (FMT) for early intervention in a classical mouse model of PE. The results showed that early administration of various antibiotics (except ampicillin) could inhibit pulmonary thrombosis to a certain extent and reduced mortality in young and old mice with PE. Among them, vancomycin has the best inhibitory effect on PE. With the help of gut microbiota sequencing analysis, we found that antibiotic treatment can reshape the gut microbiota; especially vancomycin can significantly improve the gut microbiota structure in PE mice. Furthermore, FMT could transfer vancomycin-modified gut microbes into mice and inhibit the pathogenesis of PE, possibly due to increased intestinal colonization by Parasutterella. These data elucidate the underlying molecular mechanism by which early administration of vancomycin can remodel the gut microbiota to suppress PE, providing new clues for clinical optimization and development of PE prevention strategies.}, }
@article {pmid36983633, year = {2023}, author = {Kartti, S and Bendani, H and Boumajdi, N and Bouricha, EM and Zarrik, O and El Agouri, H and Fokar, M and Aghlallou, Y and El Jaoudi, R and Belyamani, L and Elkhannoussi, B and Ibrahimi, A}, title = {Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues.}, journal = {Journal of personalized medicine}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/jpm13030450}, pmid = {36983633}, issn = {2075-4426}, abstract = {Breast cancer is one of the main global priorities in terms of public health. It remains the most frequent cancer in women and is the leading cause of their death. The human microbiome plays various roles in maintaining health by ensuring a dynamic balance with the host or in the appearance of various pathologies including breast cancer. In this study, we performed an analysis of bacterial signature differences between tumor and adjacent tissues of breast cancer patients in Morocco. Using 16S rRNA gene sequencing, we observed that adjacent tissue contained a much higher percentage of the Gammaproteobacteria class (35.7%) while tumor tissue was characterized by a higher percentage of Bacilli and Actinobacteria classes, with about 18.8% and 17.2% average abundance, respectively. Analysis of tumor subtype revealed enrichment of genus Sphingomonodas in TNBC while Sphingomonodas was predominant in HER2. The LEfSe and the genus level heatmap analysis revealed a higher abundance of the Rothia genus in tumor tissues. The identified microbial communities can therefore serve as potential biomarkers for prognosis and diagnosis, while also helping to develop new strategies for the treatment of breast cancer patients.}, }
@article {pmid36983516, year = {2023}, author = {Esposito, MM and Patsakos, S and Borruso, L}, title = {The Role of the Mycobiome in Women's Health.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, doi = {10.3390/jof9030348}, pmid = {36983516}, issn = {2309-608X}, abstract = {Although the human bacteriome and virome have gained a great deal of attention over the years, the human mycobiome has been far more neglected despite having significant value and implications in human health. In women, mycobiome profiles in breastmilk, vaginal regions, the gut, skin, and the oral cavity can provide insight into women's health, diseases, and microbiome dysbiosis. Analyses of mycobiome composition under factors, such as health, age, diet, weight, and drug exposure (including antibiotic therapies), help to elucidate the various roles of women's mycobiome in homeostasis, microbiome interactions (synergistic and antagonistic), and health. This review summarizes the most recent updates to mycobiome knowledge in these critical areas.}, }
@article {pmid36983496, year = {2023}, author = {Bačić, A and Milivojević, V and Petković, I and Kekić, D and Gajić, I and Medić Brkić, B and Popadić, D and Milosavljević, T and Rajilić-Stojanović, M}, title = {In Search for Reasons behind Helicobacter pylori Eradication Failure-Assessment of the Antibiotics Resistance Rate and Co-Existence of Helicobacter pylori with Candida Species.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, doi = {10.3390/jof9030328}, pmid = {36983496}, issn = {2309-608X}, abstract = {Helicobacter pylori eradication is characterized by decreasing successful eradication rates. Although treatment failure is primarily associated with resistance to antibiotics, other unknown factors may influence the eradication outcome. This study aimed to assess the presence of the antibiotics resistance genes in H. pylori and the presence of Candida spp., which are proposed to be endosymbiotic hosts of H. pylori, in gastric biopsies of H. pylori-positive patients while simultaneously assessing their relationship. The detection and identification of Candida yeasts and the detection of mutations specific for clarithromycin and fluoroquinolones were performed by using the real-time PCR (RT-PCR) method on DNA extracted from 110 gastric biopsy samples of H. pylori-positive participants. Resistance rate to clarithromycin and fluoroquinolone was 52% and 47%, respectively. Antibiotic resistance was associated with more eradication attempts (p < 0.05). Candida species were detected in nine (8.18%) patients. Candida presence was associated with older age (p < 0.05). A high rate of antibiotic resistance was observed, while Candida presence was scarce, suggesting that endosymbiosis between H. pylori and Candida may not be a major contributing factor to the eradication failure. However, the older age favored Candida gastric mucosa colonization, which could contribute to gastric pathologies and microbiome dysbiosis.}, }
@article {pmid36983217, year = {2023}, author = {An, J and Kwon, H and Kim, YJ}, title = {The Firmicutes/Bacteroidetes Ratio as a Risk Factor of Breast Cancer.}, journal = {Journal of clinical medicine}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/jcm12062216}, pmid = {36983217}, issn = {2077-0383}, abstract = {The gut microbiome can reflect the health condition of the entire body. Firmicutes and Bacteroidetes, the major phyla of the colon, can influence diseases related to obesity which are also risk factors for breast cancer. Therefore, the Firmicutes/Bacteroidetes (F/B) ratio was analyzed in patients with breast cancer. Bacterial extracellular vesicles were extracted from the serum of patients with breast cancer and healthy controls. Phyla Firmicutes and Bacteroidetes were analyzed using microbiome sequencing. Prognostic factors for breast cancer and serological test results were analyzed for correlations with the F/B ratio. The F/B ratio was three times lower in patients with breast cancer than in healthy controls. In addition, the risk factor for breast cancer, such as fasting serum glucose, was found to be related to the F/B ratio. The F/B ratio can be used as a risk factor of breast cancer and as a clue to explain underlying mechanisms affecting the development of breast cancer.}, }
@article {pmid36983199, year = {2023}, author = {Palumbo, VD and Tutino, R and Messina, M and Santarelli, M and Nigro, C and Lo Secco, G and Piceni, C and Montanari, E and Barletta, G and Venturelli, P and Geraci, G and Bonventre, S and Lo Monte, AI}, title = {Altered Gut Microbic Flora and Haemorrhoids: Could They Have a Possible Relationship?.}, journal = {Journal of clinical medicine}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/jcm12062198}, pmid = {36983199}, issn = {2077-0383}, abstract = {To date, the exact pathophysiology of haemorrhoids is poorly understood. The different philosophies on haemorrhoids aetiology may lead to different approaches of treatment. A pathogenic theory involving a correlation between altered anal canal microflora, local inflammation, and muscular dyssynergia is proposed through an extensive review of the literature. Since the middle of the twentieth century, three main theories exist: (1) the varicose vein theory, (2) the vascular hyperplasia theory, and (3) the concept of a sliding anal lining. These phenomena determine changes in the connective tissue (linked to inflammation), including loss of organization, muscular hypertrophy, fragmentation of the anal subepithelial muscle and the elastin component, and vascular changes, including abnormal venous dilatation and vascular thrombosis. Recent studies have reported a possible involvement of gut microbiota in gut motility alteration. Furthermore, dysbiosis seems to represent the leading cause of bowel mucosa inflammation in any intestinal district. The alteration of the gut microbioma in the anorectal district could be responsible for haemorrhoids and other anorectal disorders. A deeper knowledge of the gut microbiota in anorectal disorders lays the basis for unveiling the roles of these various gut microbiota components in anorectal disorder pathogenesis and being conductive to instructing future therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics, and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in anorectal disorders.}, }
@article {pmid36983163, year = {2023}, author = {Silverio, A and Cancro, FP and Esposito, L and Bellino, M and D'Elia, D and Verdoia, M and Vassallo, MG and Ciccarelli, M and Vecchione, C and Galasso, G and De Luca, G}, title = {Secondary Cardiovascular Prevention after Acute Coronary Syndrome: Emerging Risk Factors and Novel Therapeutic Targets.}, journal = {Journal of clinical medicine}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/jcm12062161}, pmid = {36983163}, issn = {2077-0383}, abstract = {The control of cardiovascular risk factors, the promotion of a healthy lifestyle, and antithrombotic therapy are the cornerstones of secondary prevention after acute coronary syndrome (ACS). However, many patients have recurrent ischemic events despite the optimal control of traditional modifiable risk factors and the use of tailored pharmacological therapy, including new-generation antiplatelet and lipid-lowering agents. This evidence emphasizes the importance of identifying novel risk factors and targets to optimize secondary preventive strategies. Lipoprotein(a) (Lp(a)) has emerged as an independent predictor of adverse events after ACS. New molecules such as anti-PCSK9 monoclonal antibodies, small interfering RNAs, and antisense oligonucleotides can reduce plasma Lp(a) levels and are associated with a long-term outcome benefit after the index event. The inflammatory stimulus and the inflammasome, pivotal elements in the development and progression of atherosclerosis, have been widely investigated in patients with coronary artery disease. More recently, randomized clinical trials including post-ACS patients treated with colchicine and monoclonal antibodies targeting cytokines yielded promising results in the reduction in major cardiovascular events after an ACS. Gut dysbiosis has also raised great interest for its potential pathophysiological role in cardiovascular disease. This evidence, albeit preliminary and needing confirmation by larger population-based studies, suggests the possibility of targeting the gut microbiome in particularly high-risk populations. The risk of recurrent ischemic events after ACS is related to the complex interaction between intrinsic predisposing factors and environmental triggers. The identification of novel risk factors and targets is fundamental to customizing patient clinical management with a precision medicine perspective.}, }
@article {pmid36983122, year = {2023}, author = {Alsayed, AR and Abed, A and Jarrar, YB and Alshammari, F and Alshammari, B and Basheti, IA and Zihlif, M}, title = {Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma-COPD Overlap during and after an Exacerbation.}, journal = {Journal of clinical medicine}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/jcm12062118}, pmid = {36983122}, issn = {2077-0383}, abstract = {The immediate aim of this study was to comparatively examine the bacterial respiratory microbiome of patients in a stable state and during an exacerbation of asthma-COPD (chronic obstructive pulmonary disease) overlap (ACO). This prospective observational study took place in Jordan between 1 September 2021 and 30 April 2022. Sputum samples from patients with recognized ACO were acquired within 48 h of the exacerbation onset and again at 3 weeks following the exacerbation. The next-generation sequencing Illumina MiSeq was employed and uncovered significantly high bacterial diversity in the sputa. The results showed a significant decrease in the taxonomic richness in the sputum samples collected during the exacerbation episodes compared with those collected from patients in a stable state (p = 0.008), with an increase in the taxonomic evenness (p < 0.005). This change in the composition of the airway bacterial community suggests that the replacement of a significant portion of the airway microbiome with certain microorganisms may play a role in the decrease in microbial diversity observed during an ACO exacerbation. Greater knowledge of this link could allow for a more focused administration of antibiotics, especially during exacerbations, improving clinical efficacy and patient outcomes.}, }
@article {pmid36983053, year = {2023}, author = {Lozenov, S and Krastev, B and Nikolaev, G and Peshevska-Sekulovska, M and Peruhova, M and Velikova, T}, title = {Gut Microbiome Composition and Its Metabolites Are a Key Regulating Factor for Malignant Transformation, Metastasis and Antitumor Immunity.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065978}, pmid = {36983053}, issn = {1422-0067}, abstract = {The genetic and metabolomic abundance of the microbiome exemplifies that the microbiome comprises a more extensive set of genes than the entire human genome, which justifies the numerous metabolic and immunological interactions between the gut microbiota, macroorganisms and immune processes. These interactions have local and systemic impacts that can influence the pathological process of carcinogenesis. The latter can be promoted, enhanced or inhibited by the interactions between the microbiota and the host. This review aimed to present evidence that interactions between the host and the gut microbiota might be a significant exogenic factor for cancer predisposition. It is beyond doubt that the cross-talk between microbiota and the host cells in terms of epigenetic modifications can regulate gene expression patterns and influence cell fate in both beneficial and adverse directions for the host's health. Furthermore, bacterial metabolites could shift pro- and anti-tumor processes in one direction or another. However, the exact mechanisms behind these interactions are elusive and require large-scale omics studies to better understand and possibly discover new therapeutic approaches for cancer.}, }
@article {pmid36983020, year = {2023}, author = {Vanstokstraeten, R and Callewaert, E and Blotwijk, S and Rombauts, E and Crombé, F and Emmerechts, K and Soetens, O and Vandoorslaer, K and De Geyter, D and Allonsius, C and Vander Donck, L and Blockeel, C and Wybo, I and Piérard, D and Demuyser, T and Mackens, S}, title = {Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065947}, pmid = {36983020}, issn = {1422-0067}, abstract = {It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal-cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.}, }
@article {pmid36982954, year = {2023}, author = {Wei, JJ and Li, XJ and Liu, W and Chai, XJ and Zhu, XY and Sun, PH and Liu, F and Zhao, YK and Huang, JL and Liu, YF and Zhao, ST}, title = {Eucommia Polysaccharides Ameliorate Aging-Associated Gut Dysbiosis: A Potential Mechanism for Life Extension in Drosophila.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065881}, pmid = {36982954}, issn = {1422-0067}, abstract = {The gut microbiota is increasingly considered to play a key role in human immunity and health. The aging process alters the microbiota composition, which is associated with inflammation, reactive oxygen species (ROS), decreased tissue function, and increased susceptibility to age-related diseases. It has been demonstrated that plant polysaccharides have beneficial effects on the gut microbiota, particularly in reducing pathogenic bacteria abundance and increasing beneficial bacteria populations. However, there is limited evidence of the effect of plant polysaccharides on age-related gut microbiota dysbiosis and ROS accumulation during the aging process. To explore the effect of Eucommiae polysaccharides (EPs) on age-related gut microbiota dysbiosis and ROS accumulation during the aging process of Drosophila, a series of behavioral and life span assays of Drosophila with the same genetic background in standard medium and a medium supplemented with EPs were performed. Next, the gut microbiota composition and protein composition of Drosophila in standard medium and the medium supplemented with EPs were detected using 16S rRNA gene sequencing analysis and quantitative proteomic analysis. Here, we show that supplementation of Eucommiae polysaccharides (EPs) during development leads to the life span extension of Drosophila. Furthermore, EPs decreased age-related ROS accumulation and suppressed Gluconobacter, Providencia, and Enterobacteriaceae in aged Drosophila. Increased Gluconobacter, Providencia, and Enterobacteriaceae in the indigenous microbiota might induce age-related gut dysfunction in Drosophila and shortens their life span. Our study demonstrates that EPs can be used as prebiotic agents to prevent aging-associated gut dysbiosis and reactive oxidative stress.}, }
@article {pmid36982871, year = {2023}, author = {Kar, B and Castillo, SR and Sabharwal, A and Clark, KJ and Ekker, SC}, title = {Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065798}, pmid = {36982871}, issn = {1422-0067}, support = {AI 142773/NH/NIH HHS/United States ; }, abstract = {Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.}, }
@article {pmid36982838, year = {2023}, author = {Sillo, TO and Beggs, AD and Middleton, G and Akingboye, A}, title = {The Gut Microbiome, Microsatellite Status and the Response to Immunotherapy in Colorectal Cancer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065767}, pmid = {36982838}, issn = {1422-0067}, support = {/MRC_/Medical Research Council/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; }, abstract = {There is increasing evidence in a range of cancer types that the microbiome plays a direct role in modulating the anti-cancer immune response both at the gut level and systemically. Differences in the gut microbiota have been shown to correlate with differences in immunotherapy responses in a range of non-gastrointestinal tract cancers. DNA mismatch repair-deficient (dMMR) colorectal cancer (CRC) is radically different to DNA mismatch repair-proficient (pMMR) CRC in clinical phenotype and in its very good responses to immunotherapy. While this has usually been thought to be due to the high mutational burden in dMMR CRC, the gut microbiome is radically different in dMMR and pMMR CRC in terms of both composition and diversity. It is probable that differences in the gut microbiota contribute to the varied responses to immunotherapy in dMMR versus pMMR CRC. Targeting the microbiome offers a way to boost the response and increase the selection of patients who might benefit from this therapy. This paper reviews the available literature on the role of the microbiome in the response to immunotherapy in dMMR and pMMR CRC, explores the potential causal relationship and discusses future directions for study in this exciting and rapidly changing field.}, }
@article {pmid36982799, year = {2023}, author = {Jovandaric, MZ and Dugalic, S and Babic, S and Babovic, IR and Milicevic, S and Mihajlovic, D and Culjic, M and Zivanovic, T and Trklja, A and Markovic, B and Plesinac, V and Jestrovic, Z and Medjo, B and Raus, M and Dugalic, MG}, title = {Programming Factors of Neonatal Intestinal Dysbiosis as a Cause of Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065723}, pmid = {36982799}, issn = {1422-0067}, abstract = {The intestinal microbiota consists of trillions of bacteria, viruses, and fungi that achieve a perfect symbiosis with the host. They perform immunological, metabolic, and endocrine functions in the body. The microbiota is formed intrauterine. Dysbiosis is a microbiome disorder characterized by an imbalance in the composition of the microbiota, as well as changes in their functional and metabolic activities. The causes of dysbiosis include improper nutrition in pregnant women, hormone therapy, the use of drugs, especially antibiotics, and a lack of exposure to the mother's vaginal microbiota during natural birth. Changes in the intestinal microbiota are increasingly being identified in various diseases, starting in the early neonatal period into the adult period. Conclusions: In recent years, it has become more and more obvious that the components of the intestinal microbiota are crucial for the proper development of the immune system, and its disruption leads to disease.}, }
@article {pmid36982746, year = {2023}, author = {Liu, YH and Peng, P and Hung, WC and Wu, PH and Kao, CY and Wu, PY and Huang, JC and Hung, CH and Su, HM and Chen, SC and Kuo, CH}, title = {Comparative Gut Microbiome Differences between High and Low Aortic Arch Calcification Score in Patients with Chronic Diseases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065673}, pmid = {36982746}, issn = {1422-0067}, abstract = {Gut dysbiosis can induce chronic inflammation and contribute to atherosclerosis and vascular calcification. The aortic arch calcification (AoAC) score is a simple, noninvasive, and semiquantitative assessment tool to evaluate vascular calcification on chest radiographs. Few studies have discussed the relationship between gut microbiota and AoAC. Therefore, this study aimed to compare the microbiota composition between patients with chronic diseases and high or low AoAC scores. A total of 186 patients (118 males and 68 females) with chronic diseases, including diabetes mellitus (80.6%), hypertension (75.3%), and chronic kidney disease (48.9%), were enrolled. Gut microbiota in fecal samples were analyzed by sequencing of the 16S rRNA gene, and differences in microbial function were examined. The patients were divided into three groups according to AoAC score, including 103 patients in the low AoAC group (AoAC ≤ 3), 40 patients in the medium AoAC group (3 < AoAC ≤ 6), and 43 patients in the high AoAC group (AoAC > 6). Compared to the low AoAC group, the high AoAC group had a significantly lower microbial species diversity (Chao1 index and Shannon index) and increased microbial dysbiosis index. Beta diversity showed that the microbial community composition was significantly different among the three groups (p = 0.041, weighted UniFrac PCoA). A distinct microbial community structure was found in the patients with a low AoAC, with an increased abundance at the genus level of Agathobacter, Eubacterium coprostanoligenes group, Ruminococcaceae UCG-002, Barnesiella, Butyricimonas, Oscillibacter, Ruminococcaceae DTU089, and Oxalobacter. In addition, there was an increased relative abundance of class Bacilli in the high AoAC group. Our findings support the association between gut dysbiosis and the severity of AoAC in patients with chronic diseases.}, }
@article {pmid36982702, year = {2023}, author = {Cheng, HS and Tan, SP and Wong, DMK and Koo, WLY and Wong, SH and Tan, NS}, title = {The Blood Microbiome and Health: Current Evidence, Controversies, and Challenges.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065633}, pmid = {36982702}, issn = {1422-0067}, abstract = {Blood is conventionally thought to be sterile. However, emerging evidence on the blood microbiome has started to challenge this notion. Recent reports have revealed the presence of genetic materials of microbes or pathogens in the blood circulation, leading to the conceptualization of a blood microbiome that is vital for physical wellbeing. Dysbiosis of the blood microbial profile has been implicated in a wide range of health conditions. Our review aims to consolidate recent findings about the blood microbiome in human health and to highlight the existing controversies, prospects, and challenges around this topic. Current evidence does not seem to support the presence of a core healthy blood microbiome. Common microbial taxa have been identified in some diseases, for instance, Legionella and Devosia in kidney impairment, Bacteroides in cirrhosis, Escherichia/Shigella and Staphylococcus in inflammatory diseases, and Janthinobacterium in mood disorders. While the presence of culturable blood microbes remains debatable, their genetic materials in the blood could potentially be exploited to improve precision medicine for cancers, pregnancy-related complications, and asthma by augmenting patient stratification. Key controversies in blood microbiome research are the susceptibility of low-biomass samples to exogenous contamination and undetermined microbial viability from NGS-based microbial profiling, however, ongoing initiatives are attempting to mitigate these issues. We also envisage future blood microbiome research to adopt more robust and standardized approaches, to delve into the origins of these multibiome genetic materials and to focus on host-microbe interactions through the elaboration of causative and mechanistic relationships with the aid of more accurate and powerful analytical tools.}, }
@article {pmid36982670, year = {2023}, author = {Zmysłowska-Polakowska, E and Płoszaj, T and Skoczylas, S and Mojsak, P and Ciborowski, M and Kretowski, A and Lukomska-Szymanska, M and Szadkowska, A and Mlynarski, W and Zmysłowska, A}, title = {Evaluation of the Oral Bacterial Genome and Metabolites in Patients with Wolfram Syndrome.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065596}, pmid = {36982670}, issn = {1422-0067}, abstract = {In Wolfram syndrome (WFS), due to the loss of wolframin function, there is increased ER stress and, as a result, progressive neurodegenerative disorders, accompanied by insulin-dependent diabetes. The aim of the study was to evaluate the oral microbiome and metabolome in WFS patients compared with patients with type 1 diabetes mellitus (T1DM) and controls. The buccal and gingival samples were collected from 12 WFS patients, 29 HbA1c-matched T1DM patients (p = 0.23), and 17 healthy individuals matched by age (p = 0.09) and gender (p = 0.91). The abundance of oral microbiota components was obtained by Illumina sequencing the 16S rRNA gene, and metabolite levels were measured by gas chromatography-mass spectrometry. Streptococcus (22.2%), Veillonella (12.1%), and Haemophilus (10.8%) were the most common bacteria in the WFS patients, while comparisons between groups showed significantly higher abundance of Olsenella, Dialister, Staphylococcus, Campylobacter, and Actinomyces in the WFS group (p < 0.001). An ROC curve (AUC = 0.861) was constructed for the three metabolites that best discriminated WFS from T1DM and controls (acetic acid, benzoic acid, and lactic acid). Selected oral microorganisms and metabolites that distinguish WFS patients from T1DM patients and healthy individuals may suggest their possible role in modulating neurodegeneration and serve as potential biomarkers and indicators of future therapeutic strategies.}, }
@article {pmid36982624, year = {2023}, author = {Perdew, GH and Esser, C and Snyder, M and Sherr, DH and van den Bogaard, EH and McGovern, K and Fernández-Salguero, PM and Coumoul, X and Patterson, AD}, title = {The Ah Receptor from Toxicity to Therapeutics: Report from the 5th AHR Meeting at Penn State University, USA, June 2022.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065550}, pmid = {36982624}, issn = {1422-0067}, support = {ES028244/ES/NIEHS NIH HHS/United States ; ES028288/ES/NIEHS NIH HHS/United States ; }, abstract = {The aryl hydrocarbon receptor (AHR) is a sensor of low-molecular-weight molecule signals that originate from environmental exposures, the microbiome, and host metabolism. Building upon initial studies examining anthropogenic chemical exposures, the list of AHR ligands of microbial, diet, and host metabolism origin continues to grow and has provided important clues as to the function of this enigmatic receptor. The AHR has now been shown to be directly involved in numerous biochemical pathways that influence host homeostasis, chronic disease development, and responses to toxic insults. As this field of study has continued to grow, it has become apparent that the AHR is an important novel target for cancer, metabolic diseases, skin conditions, and autoimmune disease. This meeting attempted to cover the scope of basic and applied research being performed to address possible applications of our basic knowledge of this receptor on therapeutic outcomes.}, }
@article {pmid36982560, year = {2023}, author = {Stewart, KL and Lephart, ED}, title = {Overview of BPH: Symptom Relief with Dietary Polyphenols, Vitamins and Phytochemicals by Nutraceutical Supplements with Implications to the Prostate Microbiome.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065486}, pmid = {36982560}, issn = {1422-0067}, abstract = {Benign prostatic hyperplasia (BPH) is an age-related disorder, which is one of the most prevalent and costly benign neoplasms in men with over 94 million cases worldwide. Starting before or around 50 years of age, there is a linear increase in prostate volume and BPH symptoms, which are influenced by changes in hormonal, inflammatory, growth factors, cell receptor signaling, diet, physical activity, and the microbiome of the prostate that leads to cellular proliferation. While current pharmaceutical or surgical treatments are currently available, each treatment has serious side effects. This dilemma has motived men to seek treatment without negative side effects from medicinal plants such as botanicals, phytochemicals, and vitamins that have established safety records. This narrative overview focuses on several botanicals, phytochemicals and vitamins that are widely used in the treatment of BPH and emphasizes how, in some cases, combinations of these natural ingredients may provide better BPH symptom relief compared to utilization of a single medicinal plant product (monotherapy). Finally, this overview highlights in vitro, in vivo animal studies and mainly clinical data of journal reports published in the past 5 years from January 2018 to January 2023 on BPH and nutraceuticals. Notably, there is an evolving perspective or rethinking of the role that medicinal phytochemicals and natural vitamins usage play; that is, they may hold promise or are likely to alleviate BPH symptoms.}, }
@article {pmid36982492, year = {2023}, author = {Al Samarraie, A and Pichette, M and Rousseau, G}, title = {Role of the Gut Microbiome in the Development of Atherosclerotic Cardiovascular Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065420}, pmid = {36982492}, issn = {1422-0067}, abstract = {Atherosclerotic cardiovascular disease (ASCVD) is the primary cause of death globally, with nine million deaths directly attributable to ischemic heart diseases in 2020. Since the last few decades, great effort has been put toward primary and secondary prevention strategies through identification and treatment of major cardiovascular risk factors, including hypertension, diabetes, dyslipidemia, smoking, and a sedentary lifestyle. Once labelled "the forgotten organ", the gut microbiota has recently been rediscovered and has been found to play key functions in the incidence of ASCVD both directly by contributing to the development of atherosclerosis and indirectly by playing a part in the occurrence of fundamental cardiovascular risk factors. Essential gut metabolites, such as trimethylamine N-oxide (TMAO), secondary bile acids, lipopolysaccharides (LPS), and short-chain fatty acids (SCFAs), have been associated with the extent of ischemic heart diseases. This paper reviews the latest data on the impact of the gut microbiome in the incidence of ASCVD.}, }
@article {pmid36982444, year = {2023}, author = {Redondo-Castillejo, R and Garcimartín, A and Hernández-Martín, M and López-Oliva, ME and Bocanegra, A and Macho-González, A and Bastida, S and Benedí, J and Sánchez-Muniz, FJ}, title = {Proanthocyanidins: Impact on Gut Microbiota and Intestinal Action Mechanisms in the Prevention and Treatment of Metabolic Syndrome.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065369}, pmid = {36982444}, issn = {1422-0067}, abstract = {The metabolic syndrome (MS) is a cluster of risk factors, such as central obesity, hyperglycemia, dyslipidemia, and arterial hypertension, which increase the probability of causing premature mortality. The consumption of high-fat diets (HFD), normally referred to high-saturated fat diets, is a major driver of the rising incidence of MS. In fact, the altered interplay between HFD, microbiome, and the intestinal barrier is being considered as a possible origin of MS. Consumption of proanthocyanidins (PAs) has a beneficial effect against the metabolic disturbances in MS. However, there are no conclusive results in the literature about the efficacy of PAs in improving MS. This review allows a comprehensive validation of the diverse effects of the PAs on the intestinal dysfunction in HFD-induced MS, differentiating between preventive and therapeutic actions. Special emphasis is placed on the impact of PAs on the gut microbiota, providing a system to facilitate comparison between the studies. PAs can modulate the microbiome toward a healthy profile and strength barrier integrity. Nevertheless, to date, published clinical trials to verify preclinical findings are scarce. Finally, the preventive consumption of PAs in MS-associated dysbiosis and intestinal dysfunction induced by HFD seems more successful than the treatment strategy.}, }
@article {pmid36982305, year = {2023}, author = {Kozak, M and Pawlik, A}, title = {The Role of the Oral Microbiome in the Development of Diseases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065231}, pmid = {36982305}, issn = {1422-0067}, abstract = {Periodontal disease (PD) is a complex and infectious illness that begins with a disruption of bacterial homeostasis. This disease induces a host inflammatory response, leading to damage of the soft and connective tooth-supporting tissues. Moreover, in advanced cases, it can contribute to tooth loss. The aetiological factors of PDs have been widely researched, but the pathogenesis of PD has still not been totally clarified. There are a number of factors that have an effect on the aetiology and pathogenesis of PD. It is purported that microbiological, genetic susceptibility and lifestyle can determine the development and severity of the disease. The human body's defence response to the accumulation of plaque and its enzymes is known to be a major factor for PD. The oral cavity is colonised by a characteristic and complex microbiota that grows as diverse biofilms on all mucosal and dental surfaces. The aim of this review was to provide the latest updates in the literature regarding still-existing problems with PD and to highlight the role of the oral microbiome in periodontal health and disease. Better awareness and knowledge of the causes of dysbiosis, environmental risk factors and periodontal therapy can reduce the growing worldwide prevalence of PDs. The promotion of good oral hygiene, limiting smoking, alcohol consumption and exposure to stress and comprehensive treatment to decrease the pathogenicity of oral biofilm can help reduce PD as well as other diseases. Evidence linking disorders of the oral microbiome to various systemic diseases has increased the understanding of the importance of the oral microbiome in regulating many processes in the human body and, thus, its impact on the development of many diseases.}, }
@article {pmid36982303, year = {2023}, author = {Giuffrè, M and Moretti, R and Tiribelli, C}, title = {Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065229}, pmid = {36982303}, issn = {1422-0067}, abstract = {The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe-disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.}, }
@article {pmid36981226, year = {2023}, author = {Sivamaruthi, BS and Alagarsamy, K and Thangaleela, S and Bharathi, M and Kesika, P and Chaiyasut, C}, title = {Composition, Microbiota, Mechanisms, and Anti-Obesity Properties of Rice Bran.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/foods12061300}, pmid = {36981226}, issn = {2304-8158}, abstract = {Rice is a major cereal crop and a staple food for nearly 50% of people worldwide. Rice bran (RB) is a nutrient-rich by-product of rice processing. RB is rich in carbohydrates, fibers, proteins, lipids, minerals, and several trace elements (phosphorus, calcium, magnesium, potassium, and manganese). The extraction process and storage have influenced RB extracts and RB oil's quality. The RB composition has also varied on the rice cultivars. The color of RB indicates the richness of the bioactive compounds, especially anthocyanins. γ-oryzanol, tocopherols, tocotrienols, and unsaturated fatty acids are major components of RB oil. It has been established that RB supplementation could improve the host's health status. Several preclinical and clinical studies have reported that RB has antioxidant, anticancer, anti-inflammatory, anticolitis, and antidiabetic properties. The beneficial biological properties of RB are partially attributed to its ability to alter the host microbiome and help to maintain and restore eubiosis. Non-communicable diseases (NCDs), including heart disease, diabetes, cancer, and lung disease, account for 74% of deaths worldwide. Obesity is a global health problem and is a major reason for the development of NCDs. The medical procedures for managing obesity are expensive and long-term health supplements are required to maintain a healthy weight. Thus, cost-effective natural adjuvant therapeutic strategy is crucial to treat and manage obesity. Several studies have revealed that RB could be a complementary pharmacological candidate to treat obesity. A comprehensive document with basic information and recent scientific results on the anti-obesity activity of RB and RB compounds is obligatory. Thus, the current manuscript was prepared to summarize the composition of RB and the influence of RB on the host microbiome, possible mechanisms, and preclinical and clinical studies on the anti-obesity properties of RB. This study suggested that the consumption of RB oil and dietary RB extracts might assist in managing obesity-associated health consequences. Further, extended clinical studies in several ethnic groups are required to develop dietary RB-based functional and nutritional supplements, which could serve as an adjuvant therapeutic strategy to treat obesity.}, }
@article {pmid36981048, year = {2023}, author = {Sushytskyi, L and Synytsya, A and Čopíková, J and Lukáč, P and Rajsiglová, L and Tenti, P and Vannucci, LE}, title = {Perspectives in the Application of High, Medium, and Low Molecular Weight Oat β-d-Glucans in Dietary Nutrition and Food Technology-A Short Overview.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/foods12061121}, pmid = {36981048}, issn = {2304-8158}, abstract = {For centuries human civilization has cultivated oats, and now they are consumed in various forms of food, from instant breakfasts to beverages. They are a nutrient-rich food containing linear mixed-linkage (1 → 3) (1 → 4)-β-d-glucans, which are relatively well soluble in water and responsible for various biological effects: the regulation of the blood cholesterol level, as well as being anti-inflammatory, prebiotic, antioxidant, and tumor-preventing. Numerous studies, especially in the last two decades, highlight the differences in the biological properties of the oat β-d-glucan fractions of low, medium, and high molecular weight. These fractions differ in their features due to variations in bioavailability related to the rheological properties of these polysaccharides, and their association with food matrices, purity, and mode of preparation or modification. There is strong evidence that, under different conditions, the molecular weight may determine the potency of oat-extracted β-d-glucans. In this review, we intend to give a concise overview of the properties and studies of the biological activities of oat β-d-glucan preparations depending on their molecular weight and how they represent a prospective ingredient of functional food with the potential to prevent or modulate various pathological conditions.}, }
@article {pmid36980913, year = {2023}, author = {Manning, S and Xiao, J and Li, Y and Saraithong, P and Paster, BJ and Chen, G and Wu, Y and Wu, TT}, title = {Novel Clustering Methods Identified Three Caries Status-Related Clusters Based on Oral Microbiome in Thai Mother-Child Dyads.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030641}, pmid = {36980913}, issn = {2073-4425}, support = {R01 DE019455, R01 DE013937, R01 DE031025/DE/NIDCR NIH HHS/United States ; }, abstract = {Early childhood caries (ECC) is a disease that globally affects pre-school children. It is important to identify both protective and risk factors associated with this disease. This paper examined a set of saliva samples of Thai mother-child dyads and aimed to analyze how the maternal factors and oral microbiome of the dyads influence the development of ECC. However, heterogeneous latent subpopulations may exist that have different characteristics in terms of caries development. Therefore, we introduce a novel method to cluster the correlated outcomes of dependent observations while selecting influential independent variables to unearth latent groupings within this dataset and reveal their association in each group. This paper describes the discovery of three heterogeneous clusters in the dataset, each with its own unique mother-child outcome trend, as well as identifying several microbial factors that contribute to ECC. Significantly, the three identified clusters represent three typical clinical conditions in which mother-child dyads have typical (cluster 1), high-low (cluster 2), and low-high caries experiences (cluster 3) compared to the overall trend of mother-child caries status. Intriguingly, the variables identified as the driving attributes of each cluster, including specific taxa, have the potential to be used in the future as caries preventive measures.}, }
@article {pmid36980799, year = {2023}, author = {Singh, S and Sharma, P and Sarma, DK and Kumawat, M and Tiwari, R and Verma, V and Nagpal, R and Kumar, M}, title = {Implication of Obesity and Gut Microbiome Dysbiosis in the Etiology of Colorectal Cancer.}, journal = {Cancers}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/cancers15061913}, pmid = {36980799}, issn = {2072-6694}, abstract = {The complexity and variety of gut microbiomes within and among individuals have been extensively studied in recent years in connection to human health and diseases. Our growing understanding of the bidirectional communication between metabolic diseases and the gut microbiome has also highlighted the significance of gut microbiome dysbiosis in the genesis and development of obesity-related cancers. Therefore, it is crucial to comprehend the possible role of the gut microbiota in the crosstalk between obesity and colorectal cancer (CRC). Through the induction of gut microbial dysbiosis, gut epithelial barrier impairment, metabolomic dysregulation, chronic inflammation, or dysregulation in energy harvesting, obesity may promote the development of colorectal tumors. It is well known that strategies for cancer prevention and treatment are most effective when combined with a healthy diet, physical activity, and active lifestyle choices. Recent studies also suggest that an improved understanding of the complex linkages between the gut microbiome and various cancers as well as metabolic diseases can potentially improve cancer treatments and overall outcomes. In this context, we herein review and summarize the clinical and experimental evidence supporting the functional role of the gut microbiome in the pathogenesis and progression of CRC concerning obesity and its metabolic correlates, which may pave the way for the development of novel prognostic tools for CRC prevention. Therapeutic approaches for restoring the microbiome homeostasis in conjunction with cancer treatments are also discussed herein.}, }
@article {pmid36980779, year = {2023}, author = {Liu, J and Luo, F and Wen, L and Zhao, Z and Sun, H}, title = {Current Understanding of Microbiomes in Cancer Metastasis.}, journal = {Cancers}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/cancers15061893}, pmid = {36980779}, issn = {2072-6694}, abstract = {Cancer has been the first killer that threatens people's lives and health. Despite recent improvements in cancer treatment, metastasis continues to be the main reason for death from cancer. The functions of microbiome in cancer metastasis have been studied recently, and it is proved that microbiome can influence tumor metastasis, as well as positive or negative responses to therapy. Here, we summarize the mechanisms of microorganisms affecting cancer metastasis, which include epithelial-mesenchymal transition (EMT), immunity, fluid shear stress (FSS), and matrix metalloproteinases (MMPs). This review will not only give a further understanding of relationship between microbiome and cancer metastasis, but also provide a new perspective for the microbiome's application in cancer metastasis prevention, early detection, and treatment.}, }
@article {pmid36980501, year = {2023}, author = {Park, MG and Cho, S and Oh, MM}, title = {Menopausal Changes in the Microbiome-A Review Focused on the Genitourinary Microbiome.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/diagnostics13061193}, pmid = {36980501}, issn = {2075-4418}, abstract = {A balanced interaction between the host and its microbiome is crucial to health. Research regarding the significance of the gut and vaginal microbiomes in female health is substantial. However, less data regarding the urinary microbiome are available. Interactions between the gut, vaginal, and urinary microbiomes are also currently being researched. Hormone-induced dysbiosis after menopause is believed to have effects on physical changes and health consequences. Postmenopausal changes in the gut microbiome are associated with increased short-chain fatty acids and hydrogen sulfide levels. Increased vaginal pH caused by reduced estrogen alters the vaginal microbiome, resulting in reduced levels of Lactobacillus. Such changes influence the vaginal structure and functions, contributing to the onset of genitourinary syndrome of menopause. A dysbiosis of the urinary microbiome is associated with urgency and urinary incontinence and also related to interstitial cystitis/bladder pain syndrome and neuropathic bladder. As these diseases commonly affect postmenopausal women, hormone-induced changes in the microbiome may play a role. Menopause increases the alpha diversity of the urinary microbiome and lowers the percentage of Lactobacillus in urine, and such changes precede recurrent cystitis. More research regarding the effects of changes in the urinary microbiome due to menopause on urinary tract diseases is needed.}, }
@article {pmid36980164, year = {2023}, author = {Rossi, RE and Dispinzieri, G and Elvevi, A and Massironi, S}, title = {Interaction between Gut Microbiota and Celiac Disease: From Pathogenesis to Treatment.}, journal = {Cells}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/cells12060823}, pmid = {36980164}, issn = {2073-4409}, abstract = {Celiac disease (CD) is a common systemic disorder that results from an abnormal response of human immunity to gluten intake, affecting the small intestine. In individuals who carry a genetic susceptibility, CD is triggered by environmental factors, including viral infections and dysbiosis of the gut microbiota. The gut microbiome is essential in controlling the immune system, and recent findings indicate that changes in the gut microbiome may contribute to various chronic immune disorders, such as CD through mechanisms that still require further exploration. Some bacteria exhibit epitopes that mimic gliadin and may enhance an immune response in the host. Other bacteria, including Pseudomonas aeruginosa, may work in conjunction with gluten to trigger and escalate intestinal inflammation. The microbiota may also directly influence antigen development through the production of immunogenic or tolerogenic gluten peptides or directly influence intestinal permeability through the release of zonulin. Finally, the gut microbiome can impact intestinal inflammation by generating proinflammatory or anti-inflammatory cytokines and metabolites. It is crucial to consider the impact of genetic factors (specifically, HLA-DQ haplotypes), perinatal elements such as birth mode, type of infant feeding, and antibiotic and infection exposure on the composition of the early intestinal microbiome. According to the available studies, the gut microbiome alterations associated with CD tend to exhibit a decreased presence of beneficial bacteria, including some anti-inflammatory Bifidobacterium species. However, some controversy remains as some reports have found no significant differences between the gut microbiomes of individuals with and without CD. A better understanding of the gut microbiome's role in the development of CD would greatly benefit both prevention and treatment efforts, especially in complicated or treatment-resistant cases. Here, we have attempted to summarize the available evidence on the relationship between the gut microbiota and CD, with a particular focus on potential therapeutic targets.}, }
@article {pmid36980160, year = {2023}, author = {Parra-Llorca, A and Pinilla-Gonzlez, A and Torrejón-Rodríguez, L and Lara-Cantón, I and Kuligowski, J and Collado, MC and Gormaz, M and Aguar, M and Vento, M and Serna, E and Cernada, M}, title = {Effects of Sepsis on Immune Response, Microbiome and Oxidative Metabolism in Preterm Infants.}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/children10030602}, pmid = {36980160}, issn = {2227-9067}, abstract = {This is a narrative review about the mechanisms involved in bacterial sepsis in preterm infants, which is an illness with a high incidence, morbidity, and mortality. The role of the innate immune response and its relationship with oxidative stress in the pathogenesis are described as well as their potential implementation as early biomarkers. Moreover, we address the impact that all the mechanisms triggered by sepsis have on the dysbiosis and the changes on neonatal microbiota.}, }
@article {pmid36979819, year = {2023}, author = {Leitao Filho, FS and Monica Peters, C and Sheel, AW and Yang, J and Nislow, C and Lam, S and Leung, JM and Sin, DD}, title = {Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030841}, pmid = {36979819}, issn = {2227-9059}, abstract = {Lower airway dysbiosis contributes to disease pathogenesis in respiratory diseases. However, little is known regarding the microbiota of lower airways or the oral cavity of healthy young persons. To address this gap, 25 healthy persons (24.3 ± 3.3 years; 52% females; no current smokers) underwent bronchoscopy during which bronchial brushing (BB) and bronchoalveolar lavage (BAL) fluid were collected. Prior to the procedure, an oral wash (OW) sample was also obtained. Microbiome analyses (16S rRNA locus) were performed (alpha- and beta-diversity, taxa annotations, and predicted functional metagenomic profiles) according to the airway compartment (BB, BAL, and OW). The greatest microbial richness was observed in OW and the lowest in BB (p < 0.001). Microbial communities differed significantly across compartments (p < 0.001), especially between BB and OW. Taxa analyses showed a significantly higher abundance of Firmicutes (BB: 32.7%; BAL: 31.4%) compared to OW (20.9%) (p < 0.001). Conversely, Proteobacteria predominated in OW (27.9%) as opposed to BB (7.0%) and BAL (12.5%) (p < 0.001), mostly due to a greater abundance of the bacteria in the Haemophilus genus in the OW (p < 0.001). The lower airway microbiota (BB and BAL) is significantly different from the OW microbiota in healthy young persons with respect to microbial diversity, taxa profiles, and predicted function.}, }
@article {pmid36979806, year = {2023}, author = {Athanasopoulou, K and Adamopoulos, PG and Scorilas, A}, title = {Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030827}, pmid = {36979806}, issn = {2227-9059}, abstract = {Over 10[14] symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.}, }
@article {pmid36979761, year = {2023}, author = {Di Tucci, C and De Vito, I and Muzii, L}, title = {Immune-Onco-Microbiome: A New Revolution for Gynecological Cancers.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030782}, pmid = {36979761}, issn = {2227-9059}, abstract = {Despite significant advances in understanding the pathogenetic mechanisms underlying gynaecological cancers, these cancers still remain widespread. Recent research points to a possible link between microbiota and cancer, and the most recent attention is focusing on the relationship between the microbiome, the immune system, and cancer. The microbiome diversity can affect carcinogenesis and the patient's immune response, modulating the inflammatory cascade and the severity of adverse events. In this review, we presented the recent evidence regarding microbiome alterations in patients with gynaecological tumours to understand if the link that exists between microbiome, immunity, and cancer can guide the prophylactic, diagnostic, and therapeutic management of gynaecological cancers.}, }
@article {pmid36979756, year = {2023}, author = {Lee, J and Lee, S and Kim, H and Bae, J and Park, JS}, title = {Gut Microbial Profile Changes in Patients with Gallbladder Stones after UDCA/CDCA Treatment.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030777}, pmid = {36979756}, issn = {2227-9059}, abstract = {Background: Ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) are used to treat patients with asymptomatic or mildly symptomatic gallstone disease. This study was conducted to evaluate the efficacy of gallbladder (GB) stone dissolution by UDCA/CDCA and the impact of treatment on gut microbial profiles. Methods: Fifteen treatment-naive patients with GB stones were initially included, but two dropped out during the treatment period. UDCA/CDCA was administered for 6 months. Abdominal ultrasonography was performed to evaluate response to treatment. In addition, fecal samples were collected before and after treatment for gut microbiome profiling. Then, 16S ribosomal RNA gene sequencing was carried out on fecal samples obtained before and after treatment, and results were compared with those of forty healthy controls. Results: Eight (62%) of the thirteen evaluable patients treated with UDCA/CDCA responded to treatment (four achieved complete GB stone resolution and four partial dissolution). Taxonomic compositions of fecal samples at the phylum level showed a significantly lower relative abundance of the Proteobacteria phylum in the pre-UDCA/CDCA group than in the healthy control group (p = 0.024). At the genus level, the relative abundances of five bacteria (Faecalibacterium, Roseburia, Lachnospira, Streptococcus, and Alistipes) differed in the control and pre-UDCA/CDCA group. Interestingly, the abundance of Roseburia was restored after 6 months of UDCA/CDCA treatment. Conclusion: Gut microbial dysbiosis was observed in GB stone patients and partially reversed by UDCA/CDCA treatment, which also effectively dissolved GB stones.}, }
@article {pmid36979685, year = {2023}, author = {Piccioni, A and Rosa, F and Mannucci, S and Manca, F and Merra, G and Chiloiro, S and Candelli, M and Covino, M and Gasbarrini, A and Franceschi, F}, title = {Gut Microbiota, LADA, and Type 1 Diabetes Mellitus: An Evolving Relationship.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030707}, pmid = {36979685}, issn = {2227-9059}, abstract = {There is much evidence confirming the crucial role played by the gut microbiota in modulating the immune system in the onset of autoimmune diseases. In this article, we focus on the relationship between alterations in the microbiome and the onset of diabetes mellitus type 1 and LADA, in light of the latest evidence. We will then look at both how the role of the gut microbiota appears to be increasingly crucial in the pathogenesis of these disorders and how this aspect may be instrumental in the development of new potential therapeutic strategies that modulate the gut microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation.}, }
@article {pmid36979663, year = {2023}, author = {Russo, E and Di Gloria, L and Cerboneschi, M and Smeazzetto, S and Baruzzi, GP and Romano, F and Ramazzotti, M and Amedei, A}, title = {Facial Skin Microbiome: Aging-Related Changes and Exploratory Functional Associations with Host Genetic Factors, a Pilot Study.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030684}, pmid = {36979663}, issn = {2227-9059}, abstract = {In this exploratory study, we investigate the variation in the facial skin microbiome architecture through aging and their functional association with host genetic factors in a cohort of healthy women, living in the same area and without cutaneous diseases. Notably, facial skin microbiota (SM) samples were collected from a cohort of 15 healthy Caucasian females, firstly divided into three age groups (younger women aged 20-35 years old; middle aged women of 36-52 years old; and older women aged 53-68 years old). Then, the recruited cohort was divided into two groups based on their facial hydration level (dry and normal skin). The facial SM revealed a different composition in the three analyzed aging groups and between normal and dry skins. The middle-aged women also revealed functional variations associated with collagen biosynthesis and oxidative stress damage repair. Otherwise, the association between selected host SNPs (single nucleotide polymorphisms) and the facial SM profile showed significant associations, suggesting a negative correlation with collagen metabolism and ROS damage protection. Finally, the composition and functionality of the facial SM seemed to affect the aging process through the two aging-correlated pathways of host ROS damage repair and collagen metabolism. Our exploratory data could be useful for future studies characterizing the structure, function, and dynamics of the SM in the aging process to design personalized therapeutic agents focusing on potential genomic targets, microbes, and their metabolites.}, }
@article {pmid36979599, year = {2023}, author = {Nuñez, S and Barra, M and Garrido, D}, title = {Developing a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli.}, journal = {Biosensors}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/bios13030388}, pmid = {36979599}, issn = {2079-6374}, abstract = {L-Fucose is a monosaccharide abundant in mammalian glycoconjugates. In humans, fucose can be found in human milk oligosaccharides (HMOs), mucins, and glycoproteins in the intestinal epithelium. The bacterial consumption of fucose and fucosylated HMOs is critical in the gut microbiome assembly of infants, dominated by Bifidobacterium. Fucose metabolism is important for the production of short-chain fatty acids and is involved in cross-feeding microbial interactions. Methods for assessing fucose concentrations in complex media are lacking. Here we designed and developed a molecular quantification method of free fucose using fluorescent Escherichia coli. For this, low- and high-copy plasmids were evaluated with and without the transcription factor fucR and its respective fucose-inducible promoter controlling the reporter gene sfGFP. E. coli BL21 transformed with a high copy plasmid containing pFuc and fucR displayed a high resolution across increasing fucose concentrations and high fluorescence/OD values after 18 h. The molecular circuit was specific against other monosaccharides and showed a linear response in the 0-45 mM range. Adjusting data to the Hill equation suggested non-cooperative, simple regulation of FucR to its promoter. Finally, the biosensor was tested on different concentrations of free fucose and the supernatant of Bifidobacterium bifidum JCM 1254 supplemented with 2-fucosyl lactose, indicating the applicability of the method in detecting free fucose. In conclusion, a bacterial biosensor of fucose was validated with good sensitivity and precision. A biological method for quantifying fucose could be useful for nutraceutical and microbiological applications, as well as molecular diagnostics.}, }
@article {pmid36979494, year = {2023}, author = {Chandran, D and Warren, K and McKeone, D and Hicks, SD}, title = {The Association between Infant Colic and the Multi-Omic Composition of Human Milk.}, journal = {Biomolecules}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biom13030559}, pmid = {36979494}, issn = {2218-273X}, abstract = {Infant colic is a common condition with unclear biologic underpinnings and limited treatment options. We hypothesized that complex molecular networks within human milk (i.e., microbes, micro-ribonucleic acids (miRNAs), cytokines) would contribute to colic risk, while controlling for medical, social, and nutritional variables. This hypothesis was tested in a cohort of 182 breastfed infants, assessed with a modified Infant Colic Scale at 1 month. RNA sequencing was used to interrogate microbial and miRNA features. Luminex assays were used to measure growth factors and cytokines. Milk from mothers of infants with colic (n = 28) displayed higher levels of Staphylococcus (adj. p = 0.038, d = 0.30), miR-224-3p (adj. p = 0.023, d = 0.33), miR-125b-5p (adj. p = 0.028, d = 0.29), let-7a-5p (adj. p = 0.028, d = 0.27), and miR-205-5p (adj. p = 0.029, d = 0.26) compared to milk from non-colic mother-infant dyads (n = 154). Colic symptom severity was directly associated with milk hepatocyte growth factor levels (R = 0.21, p = 0.025). A regression model involving let-7a-5p, miR-29a-3p, and Lactobacillus accurately modeled colic risk (X[2] = 16.7, p = 0.001). Molecular factors within human milk may impact colic risk, and provide support for a dysbiotic/inflammatory model of colic pathophysiology.}, }
@article {pmid36979425, year = {2023}, author = {Contreras-Correa, ZE and Messman, RD and Swanson, RM and Lemley, CO}, title = {Melatonin in Health and Disease: A Perspective for Livestock Production.}, journal = {Biomolecules}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biom13030490}, pmid = {36979425}, issn = {2218-273X}, abstract = {Mounting evidence in the literature indicates an important role of endogenous and exogenous melatonin in driving physiological and molecular adaptations in livestock. Melatonin has been extensively studied in seasonally polyestrous animals whereby supplementation studies have been used to adjust circannual rhythms in herds of animals under abnormal photoperiodic conditions. Livestock undergo multiple metabolic and physiological adaptation processes throughout their production cycle which can result in decreased immune response leading to chronic illness, weight loss, or decreased production efficiency; however, melatonin's antioxidant capacity and immunostimulatory properties could alleviate these effects. The cardiovascular system responds to melatonin and depending on receptor type and localization, melatonin can vasodilate or vasoconstrict several systemic arteries, thereby controlling whole animal nutrient partitioning via vascular resistance. Increased incidences of non-communicable diseases in populations exposed to circadian disruption have uncovered novel pathways of neurohormones, such as melatonin, influence health, and disease. Perturbations in immune function can negatively impact the growth and development of livestock which has been examined following melatonin supplementation. Specifically, melatonin can influence nutrient uptake, circulating nutrient profiles, and endocrine profiles controlling economically important livestock growth and development. This review focuses on the physiological, cellular, and molecular implications of melatonin on the health and disease of domesticated food animals.}, }
@article {pmid36979134, year = {2023}, author = {Chen, W and Yin, C and Li, J and Sun, W and Li, Y and Wang, C and Pi, Y and Cordero, G and Li, X and Jiang, X}, title = {Stimbiotics Supplementation Promotes Growth Performance by Improving Plasma Immunoglobulin and IGF-1 Levels and Regulating Gut Microbiota Composition in Weaned Piglets.}, journal = {Biology}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/biology12030441}, pmid = {36979134}, issn = {2079-7737}, abstract = {This study was conducted to investigate the effects of dietary supplementation with stimbiotics (STB) on growth performance, diarrhoea incidence, plasma antioxidant capacity, immunoglobulin concentration and hormone levels, and faecal microorganisms in weaned piglets. Compared with the control (CT) group, the addition of STB improved the body weight (BW) of piglets on days 28 and 42 (p < 0.05) and increased daily weight gain and daily feed intake from days 14-28 and throughout the trial period (p < 0.05). Correspondingly, the plasma insulin-like growth factor 1 (IGF-1) level on day 42 was significantly improved by STB (p < 0.05). VistaPros (VP) group levels of immunoglobulin (Ig) A and G were significantly higher on days 14 and 42 (p < 0.05) than the CT group levels. In addition, the activity of plasma catalase tended to be increased on day 14 (p = 0.053) in the VP group, as for superoxide dismutase, glutathione peroxidase, and malondialdehyde, STB did not significantly affect their levels (p > 0.05). Moreover, dietary STB increased the relative abundance of beneficial bacteria, including norank_f_Muribaculaceae, Rikenellaceae_RC9_gut_group, Parabacteroides, and unclassified_f__Oscillospiraceae. In summary, STB improved the immunity and IGF-1 levels in the plasma of weaned piglets and consequently promoted the growth performance of weaned piglets.}, }
@article {pmid36978962, year = {2023}, author = {Zou, X and Yokoyama, W and Liu, X and Wang, K and Hong, H and Luo, Y and Tan, Y}, title = {Milk Fat Globule Membrane Relieves Fatigue via Regulation of Oxidative Stress and Gut Microbiota in BALB/c Mice.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030712}, pmid = {36978962}, issn = {2076-3921}, abstract = {Milk fat globule membranes (MFGMs) are complex structures that incorporate bioactive proteins and lipids to assist in infant development. However, the antifatigue and antioxidant potentials of MFGM have not been investigated. In this study, repeated force swimming measured fatigue in male BALB/c mice fed MFGM and saline for 18 weeks. The MFGM supplementation increased the time to exhaustion by 42.7% at 6 weeks and 30.6% at 14 weeks (p < 0.05). Fatigue and injury-related biomarkers, including blood glucose, lactic acid, and lactate dehydrogenase, were ameliorated after free swimming (p < 0.05). The activity of antioxidant enzymes in blood serum increased at 18 weeks, while malondialdehyde (MDA) content decreased by 45.0% after the MFGM supplementation (p < 0.05). The Pearson correlation analysis showed a high correlation between fatigue-related indices and antioxidant levels. The increased protein expression of hepatic Nrf2 reduced the protein expression of Caspase-3 in the gastrocnemius muscle (p < 0.05). Moreover, the MFGM supplementation increased the relative abundance of Bacteroides, Butyricimonas, and Anaerostipes. Our results demonstrate that MFGM may maintain redox homeostasis to relieve fatigue, suggesting the potential application of MFGM as an antifatigue and antioxidant dietary supplement.}, }
@article {pmid36978958, year = {2023}, author = {Lauritano, C and Montuori, E and De Falco, G and Carrella, S}, title = {In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030710}, pmid = {36978958}, issn = {2076-3921}, abstract = {Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.}, }
@article {pmid36978911, year = {2023}, author = {Melrose, J}, title = {The Potential of Flavonoids and Flavonoid Metabolites in the Treatment of Neurodegenerative Pathology in Disorders of Cognitive Decline.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030663}, pmid = {36978911}, issn = {2076-3921}, abstract = {Flavonoids are a biodiverse family of dietary compounds that have antioxidant, anti-inflammatory, antiviral, and antibacterial cell protective profiles. They have received considerable attention as potential therapeutic agents in biomedicine and have been widely used in traditional complimentary medicine for generations. Such complimentary medical herbal formulations are extremely complex mixtures of many pharmacologically active compounds that provide a therapeutic outcome through a network pharmacological effects of considerable complexity. Methods are emerging to determine the active components used in complimentary medicine and their therapeutic targets and to decipher the complexities of how network pharmacology provides such therapeutic effects. The gut microbiome has important roles to play in the generation of bioactive flavonoid metabolites retaining or exceeding the antioxidative and anti-inflammatory properties of the intact flavonoid and, in some cases, new antitumor and antineurodegenerative bioactivities. Certain food items have been identified with high prebiotic profiles suggesting that neutraceutical supplementation may be beneficially employed to preserve a healthy population of bacterial symbiont species and minimize the establishment of harmful pathogenic organisms. Gut health is an important consideration effecting the overall health and wellbeing of linked organ systems. Bioconversion of dietary flavonoid components in the gut generates therapeutic metabolites that can also be transported by the vagus nerve and systemic circulation to brain cell populations to exert a beneficial effect. This is particularly important in a number of neurological disorders (autism, bipolar disorder, AD, PD) characterized by effects on moods, resulting in depression and anxiety, impaired motor function, and long-term cognitive decline. Native flavonoids have many beneficial properties in the alleviation of inflammation in tissues, however, concerns have been raised that therapeutic levels of flavonoids may not be achieved, thus allowing them to display optimal therapeutic effects. Dietary manipulation and vagal stimulation have both yielded beneficial responses in the treatment of autism spectrum disorders, depression, and anxiety, establishing the vagal nerve as a route of communication in the gut-brain axis with established roles in disease intervention. While a number of native flavonoids are beneficial in the treatment of neurological disorders and are known to penetrate the blood-brain barrier, microbiome-generated flavonoid metabolites (e.g., protocatechuic acid, urolithins, γ-valerolactones), which retain the antioxidant and anti-inflammatory potency of the native flavonoid in addition to bioactive properties that promote mitochondrial health and cerebrovascular microcapillary function, should also be considered as potential biotherapeutic agents. Studies are warranted to experimentally examine the efficacy of flavonoid metabolites directly, as they emerge as novel therapeutic options.}, }
@article {pmid36978820, year = {2023}, author = {Segers, C and Mysara, M and Coolkens, A and Wouters, S and Baatout, S and Leys, N and Lebeer, S and Verslegers, M and Mastroleo, F}, title = {Limnospira indica PCC 8005 Supplementation Prevents Pelvic Irradiation-Induced Dysbiosis but Not Acute Inflammation in Mice.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030572}, pmid = {36978820}, issn = {2076-3921}, abstract = {Pelvic irradiation-induced mucositis secondarily leads to dysbiosis, which seriously affects patients' quality of life after treatment. No safe and effective radioprotector or mitigator has yet been approved for clinical therapy. Here, we investigated the potential protective effects of fresh biomass of Limnospira indica PCC 8005 against ionizing irradiation-induced mucositis and dysbiosis in respect to benchmark probiotic Lacticaseibacillus rhamnosus GG ATCC 53103. For this, mice were supplemented daily before and after 12 Gy X-irradiation of the pelvis. Upon sacrifice, food supplements' efficacy was assessed for intestinal barrier protection, immunomodulation and changes in the microbiota composition. While both could not confer barrier protection or significant immunomodulatory effects, 16S microbial profiling revealed that L. indica PCC 8005 and L. rhamnosus GG could prevent pelvic irradiation-induced dysbiosis. Altogether, our data show that-besides benchmarked L. rhamnosus GG-L. indica PCC 8005 is an interesting candidate to further explore as a radiomitigator counteracting pelvic irradiation-induced dysbiosis in the presented in vivo irradiation-gut-microbiota platform.}, }
@article {pmid36978795, year = {2023}, author = {Wang, Z and Jiang, Q and Li, P and Shi, P and Liu, C and Wang, W and Huang, K and Yin, Y and Huang, P}, title = {The Water Extract of Ampelopsis grossedentata Alleviates Oxidative Stress and Intestinal Inflammation.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030547}, pmid = {36978795}, issn = {2076-3921}, abstract = {Oxidative stress is recognized as a significant contributor to the development and progression of inflammation and disruptions in the balance of gut microflora, commonly referred to as intestinal dysbiosis. It is crucial that safe and effective antioxidant and anti-inflammatory agents are identified to address these conditions. Ampelopsis grossedentata, a natural plant abundant in flavonoids and primarily found in southern China, has demonstrated potent antioxidant properties. However, the extent to which flavonoids in A. grossedentata impact intestinal inflammation and alter the composition of the gut microbiome remains to be fully understood. The purpose of this study was to explore the potential benefits of using A. grossedentata as an antioxidant and anti-inflammatory agent in the context of intestinal inflammation, both in vitro and in vivo. We first conducted an initial comparison of the effects of dihydromyricetin (DMY), an alcohol extract of A. grossedentata (AEA, 82% total flavonoids), and a water extract of A. grossedentata (WEA, 57% total flavonoids) on the cell viability and intestinal barrier integrity of porcine epithelial cells IPEC-J2. Although the total flavonoid content is much lower in WEA than in AEA, the results show that they have similar effects. Subsequently, the antioxidant properties of WEA were compared with those of commonly utilized antioxidants in vitro. Lastly, the antioxidant and anti-inflammatory properties of WEA, as well as its impacts on gut microbiota, were evaluated in animal models, including mice and Drosophila. In summary, the results of our study indicate that WEA, due to its antioxidant properties, exhibits a protective effect on the intestinal barrier function in porcine epithelial cell line IPEC-J2. Additionally, WEA demonstrates a positive correlation with DPPH, ABTS radical scavenging rate, FRAP, and reducing power under in vitro settings. Furthermore, WEA was shown to effectively alleviate oxidative stress in animal models by reducing the levels of pro-inflammatory cytokines and increasing the antioxidant enzyme activity in the liver, as well as by activating the Nrf2 signaling pathway in the duodenum. Additionally, WEA was able to regulate gut microbiota, promoting the growth of beneficial bacteria and inhibiting harmful microbes, as well as extending the lifespan of Drosophila. Overall, these findings suggest that WEA may serve as a valuable dietary supplement for addressing oxidative stress and inflammation through its anti-inflammatory and prebiotic effects, which are conferred via the Nrf2/Keap1 pathway.}, }
@article {pmid36978609, year = {2023}, author = {Cardoso, PG and Gonçalves, O and Cavalheri, T and Amorim, VE and Cao, W and Alexandrino, DAM and Jia, Z and Carvalho, MF and Vaz-Pires, P and Ozório, ROA}, title = {Combined Effects of Temperature and Dietary Lipid Level on Body Composition, Growth, and Freshness Profile in European Seabass, Dicentrarchus labrax.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/ani13061068}, pmid = {36978609}, issn = {2076-2615}, abstract = {A fish trial was carried out to evaluate the combined effects of temperature and dietary lipid level on the body composition, growth performance, and freshness profile of the European seabass (Dicentrarchus labrax). Fish were kept for 56 days at 20 °C and 24 °C and fed on two diets, with 16% and 20% lipid. At the end of the trial, fish were euthanized at two temperature conditions (0.6 °C or -0.6 °C) and kept on ice for 10 days at 4 °C to evaluate their freshness condition. Findings demonstrated that fish reared at 24 °C presented a lower lipid level and a higher daily growth index than those at 20 °C. Additionally, sensory analysis (Quality Index Method-QIM) and microbiological analysis revealed that fish reared at 24 °C showed better freshness conditions than those at 20 °C. However, the 16S rRNA metabarcoding analyses revealed a higher proliferation of genera associated with fish-spoiling bacteria in the skin microbiome of fish reared at 24 °C, i.e., Vibrio and Acinetobacter, which was not observed in the skin microbiome of fish reared at 20 °C. Nevertheless, the dietary lipid level did not have any influence on fish freshness. Therefore, our data suggest that the increase in temperature to 24 °C is beneficial for the growth and freshness profile (lower QIM and lower CFUs/cm[2]) of this particular species. Additionally, the lower euthanasia temperature (-0.6 °C) seems to lead to higher fish freshness than the normal temperature (0.6 °C).}, }
@article {pmid36978603, year = {2023}, author = {Song, J and Ma, Y and Zhang, H and Wang, L and Zhang, Y and Zhang, G}, title = {Fermented Total Mixed Ration Alters Rumen Fermentation Parameters and Microbiota in Dairy Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/ani13061062}, pmid = {36978603}, issn = {2076-2615}, abstract = {This study aimed to determine changes and interactions of ruminal microbiota and chemical parameters in dairy cows fed FTMR. Twelve multiparous Holstein dairy cows (Body weight = 616 ± 13.4 kg; day in milk = 106 ± 7.55 d; and parity = 2.31 ± 0.49; mean ± standard deviation) were divided randomly into two treatments depending on the day in milk, milk production, and parity. The two treatments were: (1) total mixed ration (TMR) and (2) FTMR. Illumina MiSeq sequencing was used to explore the changes in the ruminal microbiota. The results revealed that the bacterial and fungal diversity of the FTMR group were significantly higher than the TMR group. The predominant microbiota phyla in the bacteria and fungi showed significant differences between TMR and FTMR, as follows: Verrucomicrobia (p = 0.03) and Tenericutes (p = 0.01), Ascomycota (p = 0.04) and Basidiomycota (p = 0.04). The dominant bacterial genera in the bacteria, fungi, protozoan, and archaea that showed significant differences between TMR and FTMR were Unclassified_Bacteroidales (p = 0.02), Unclassified_RFP12 (p = 0.03), Candida (p = 0.0005), Bullera (p = 0.002), Cryptococcus (p = 0.007), and Ostracodinium (p = 0.01). LefSe analysis was performed to reveal the biomarker genera of the rumen microbiota community (bacteria, fungi, protozoan, and archaea) in the TMR and FTMR were the genera Shuttleworthia, Ruminococcus, Cryptococcus, Mycosphaerella, Bullera, Candida, and Ostracodinium. NH3-N concentration (p < 0.0001), total VFA concentration (p = 0.003), and molar proportion in total VFA of acetate (p = 0.01) were higher for the cows fed FTMR compared with the cows fed the TMR. Several bacterial genera showed significant correlations with rumen fermentation parameters. The genus Unclassified_Bacteroidales and Bullera were positively correlated with total volatile fatty acids (VFA) and acetate, whereas Candida and Ostracodinium showed negative correlations. Meanwhile, propionate was positively correlated with Candida and negatively correlated with Bullera. The PICRUSt functional profile prediction indicated that the xenobiotics biodegradation and metabolism, the lipid, amino acid, terpenoids, and polyketides metabolisms of the FTMR group were significantly higher than that of the TMR group. The results imply that FTMR can increase lipid and amino acid metabolism, and modulate the rumen microbiome and improve ruminal fermentation.}, }
@article {pmid36978593, year = {2023}, author = {Chen, W and Lv, X and Cao, X and Yuan, Z and Wang, S and Getachew, T and Mwacharo, JM and Haile, A and Quan, K and Li, Y and Sun, W}, title = {Integration of the Microbiome, Metabolome and Transcriptome Reveals Escherichia coli F17 Susceptibility of Sheep.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/ani13061050}, pmid = {36978593}, issn = {2076-2615}, abstract = {Escherichia coli (E. coli) F17 is one of the most common pathogens causing diarrhea in farm livestock. In the previous study, we accessed the transcriptomic and microbiomic profile of E. coli F17-antagonism (AN) and -sensitive (SE) lambs; however, the biological mechanism underlying E. coli F17 infection has not been fully elucidated. Therefore, the present study first analyzed the metabolite data obtained with UHPLC-MS/MS. A total of 1957 metabolites were profiled in the present study, and 11 differential metabolites were identified between E. coli F17 AN and SE lambs (i.e., FAHFAs and propionylcarnitine). Functional enrichment analyses showed that most of the identified metabolites were related to the lipid metabolism. Then, we presented a machine-learning approach (Random Forest) to integrate the microbiome, metabolome and transcriptome data, which identified subsets of potential biomarkers for E. coli F17 infection (i.e., GlcADG 18:0-18:2, ethylmalonic acid and FBLIM1); furthermore, the PCCs were calculated and the interaction network was constructed to gain insight into the crosstalk between the genes, metabolites and bacteria in E. coli F17 AN/SE lambs. By combing classic statistical approaches and a machine-learning approach, our results revealed subsets of metabolites, genes and bacteria that could be potentially developed as candidate biomarkers for E. coli F17 infection in lambs.}, }
@article {pmid36978536, year = {2023}, author = {Wang, M and Ren, C and Wang, P and Cheng, X and Chen, Y and Huang, Y and Chen, J and Sun, Z and Wang, Q and Zhang, Z}, title = {Microbiome-Metabolome Reveals the Contribution of the Gut-Testis Axis to Sperm Motility in Sheep (Ovis aries).}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/ani13060996}, pmid = {36978536}, issn = {2076-2615}, abstract = {A close association exists among testicular function, gut microbiota regulation, and organismal metabolism. In this study, serum and seminal plasma metabolomes, and the rumen microbiome of sheep with significant differences in sperm viability, were explored. Serum and seminal plasma metabolomes differed significantly between high-motility (HM) and low-motility (LM) groups of sheep, and 39 differential metabolites closely related to sperm motility in sheep were found in seminal plasma metabolomes, while 35 were found in serum samples. A 16S rRNA sequence analysis showed that the relative abundance of HM and LM rumen microorganisms, such as Ruminococcus and Quinella, was significantly higher in the HM group, whereas genera such as Rikenellaceae_RC9_gut_group and Lactobacillus were enriched in the mid-LM group. Serum hormone assays revealed that serum follicle-stimulating hormone (FSH) and MT levels were significantly lower in the LM group than in the HM group, whereas serum glucocorticoid (GC) levels were higher in the LM group than in the HM group, and they all affected sperm motility in sheep. Ruminococcus and other rumen microorganisms were positively correlated with sperm motility, whereas Lactobacillus was negatively correlated with FSH and GCs levels. Our findings suggest that rumen microbial activity can influence the host metabolism and hormone levels associated with fertility in sheep.}, }
@article {pmid36978455, year = {2023}, author = {Brzozowska, E and Lipiński, T and Korzeniowska-Kowal, A and Filik, K and Górski, A and Gamian, A}, title = {Detection and Level Evaluation of Antibodies Specific to Environmental Bacteriophage I11mO19 and Related Coliphages in Non-Immunized Human Sera.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030586}, pmid = {36978455}, issn = {2079-6382}, abstract = {Bacteriophages (phages) are viruses infecting bacteria. They are widely present in the environment, food, and normal microflora. The human microbiome is a mutually interdependent network of bacteria, bacteriophages, and human cells. The stability of these tri-kingdom interactions may be essential for maintaining immunologic and metabolic health. Phages, as with each other's antigens, may evoke an immune response during a human's lifetime and induce specific antibody generation. In this manuscript, we labeled these antibodies as naturally generated. Naturally generated antibodies may be one of the most important factors limiting the efficacy of phage therapy. Herein, we attempted to determine the physiological level of these antibodies specific to a population bacteriophage named I11mO19 in human sera, using an ELISA-based assay. First, we purified the phage particles and assessed the immunoreactivity of phage proteins. Then, affinity chromatography was performed on columns with immobilized phage proteins to obtain a fraction of human polyclonal anti-phage antibodies. These antibodies were used as a reference to elaborate an immunoenzymatic test that was used to determine the level of natural anti-phage antibodies. We estimated the average level of anti-I11mO19 phage antibodies at 190 µg per one milliliter of human serum. However, immunoblotting revealed that cross-reactivity occurs between some proteins of I11mO19 and two other coliphages: T4 and ΦK1E. The antigens probably share common epitopes, suggesting that the determined level of anti-I11mO19 phage might be overestimated and reflects a group of antibodies reactive to a broad range of other E. coli phages. Anti-I11mO19 antibodies did not react with Pseudomonas bacteriophage F8, confirming specificity to the coliphage group. In this work, we wanted to show whether it is possible to determine the presence and level of anti-phage antibodies in nontargeted-immunized sera, using an immunoenzymatic assay. The conclusion is that it is possible, and specific antibodies can be determined. However, the specificity refers to a broader coliphage group of phages, not only the single phage strain.}, }
@article {pmid36978453, year = {2023}, author = {Dugot, M and Merzon, E and Ashkenazi, S and Vinker, S and Green, I and Golan-Cohen, A and Israel, A}, title = {The Association between Previous Antibiotic Consumption and SARS-CoV-2 Infection: A Population-Based Case-Control Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030587}, pmid = {36978453}, issn = {2079-6382}, abstract = {Background: The susceptibility to SARS-CoV-2 infection is complex and not yet fully elucidated, being related to many variables; these include human microbiome and immune status, which are both affected for a long period by antibiotic use. We therefore aimed to examine the association of previous antibiotic consumption and SARS-CoV-2 infection in a large-scale population-based study with control of known confounders. Methods: A matched case-control study was performed utilizing the electronic medical records of a large Health Maintenance Organization. Cases were subjects with confirmed SARS-CoV-2 infection (n = 31,260), matched individually (1:4 ratio) to controls without a positive SARS-CoV-2 test (n = 125,039). The possible association between previous antibiotic use and SARS-CoV-2 infection was determined by comparing antibiotic consumption in the previous 6 and 12 months between the cases and controls. For each antibiotic consumed we calculated the odds ratio (OR) for documented SARS-CoV-2 infection, 95% confidence interval (CI), and p-value using univariate and multivariate analyses. Results: The association between previous antibiotic consumption and SARS-CoV-2 infection was complex and bi-directional. In the multivariate analysis, phenoxymethylpenicillin was associated with increased rate of SARS-CoV-2 infection (OR 1.110, 95% CI: 1.036-1.191) while decreased rates were associated with previous consumption of trimethoprim-sulfonamides (OR 0.783, 95% CI: 0.632-0.971) and azithromycin (OR 0.882, 95% CI: 0.829-0.938). Fluroquinolones were associated with decreased rates (OR 0.923, 95% CI: 0.861-0.989) only in the univariate analysis. Previous consumption of other antibiotics had no significant association with SARS-CoV-2 infection. Conclusions: Previous consumption of certain antibiotic agents has an independent significant association with increased or decreased rates of SARS-CoV-2 infection. Plausible mechanisms, that should be further elucidated, are mainly antibiotic effects on the human microbiome and immune modulation.}, }
@article {pmid36978384, year = {2023}, author = {Nadvornik, C and Kallab, M and Hommer, N and Schlatter, A and Stengel, T and Garhöfer, G and Zeitlinger, M and Eberl, S and Klymiuk, I and Trajanoski, S and Nehr, M and Makristathis, A and Schmidl, D and Nussbaumer-Proell, A}, title = {Effect of Antibiotic Eye Drops on the Nasal Microbiome in Healthy Subjects-A Pilot Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030517}, pmid = {36978384}, issn = {2079-6382}, abstract = {BACKGROUND: Antibiotic eye drops are frequently used in clinical practice. Due to the anatomical connection via the nasolacrimal duct, it seems possible that they have an influence on the nasal/pharyngeal microbiome. This was investigated by using two different commonly used antibiotic eye drops.<br><br>METHODS: 20 subjects were randomized to four groups of five subjects receiving eye drops containing gentamicin, ciprofloxacin, or, as controls, unpreserved povidone or benzalkonium chloride-preserved povidone. Nasal and pharyngeal swabs were performed before and after the instillation period. Swabs were analyzed by Illumina next-generation sequencing (NGS)-based 16S rRNA analysis. Bacterial culture was performed on solid media, and bacterial isolates were identified to the species level by MALDI-TOF MS. Species-dependent antimicrobial susceptibility testing was performed using single isolates and pools of isolates.<br><br>RESULTS: Bacterial richness in the nose increased numerically from 163 &#xb1; 30 to 243 &#xb1; 100 OTUs (gentamicin) and from 114 &#xb1; 17 to 144 &#xb1; 45 OTUs (ciprofloxacin). Phylogenetic diversity index (pd) of different bacterial strains in the nasal microbiome increased from 12.4 &#xb1; 1.0 to 16.9 &#xb1; 5.6 pd (gentamicin) and from 10.2 &#xb1; 1.4 to 11.8 &#xb1; 3.1 pd (ciprofloxacin). Unpreserved povidone eye drops resulted in minimal changes in bacterial counts. Preservative-containing povidone eye drops resulted in no change. A minor increase (1-2-fold) in the minimal inhibitory concentration (MIC) was observed in single streptococcal isolates.<br><br>CONCLUSIONS: Antibiotic eye drops could affect the nasal microbiome. After an instillation period of seven days, an increase in the diversity and richness of bacterial strains in the nasal microbiome was observed.}, }
@article {pmid36978365, year = {2023}, author = {García-García, J and Diez-Echave, P and Yuste, ME and Chueca, N and García, F and Cabeza-Barrera, J and Fernández-Varón, E and Gálvez, J and Colmenero, M and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Morón, R}, title = {Gut Microbiota Composition Can Predict Colonization by Multidrug-Resistant Bacteria in SARS-CoV-2 Patients in Intensive Care Unit: A Pilot Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030498}, pmid = {36978365}, issn = {2079-6382}, abstract = {The SARS-CoV-2 infection has increased the number of patients entering Intensive Care Unit (ICU) facilities and antibiotic treatments. Concurrently, the multi-drug resistant bacteria (MDRB) colonization index has risen. Considering that most of these bacteria are derived from gut microbiota, the study of its composition is essential. Additionally, SARS-CoV-2 infection may promote gut dysbiosis, suggesting an effect on microbiota composition. This pilot study aims to determine bacteria biomarkers to predict MDRB colonization risk in SARS-CoV-2 patients in ICUs. Seventeen adult patients with an ICU stay >48 h and who tested positive for SARS-CoV-2 infection were enrolled in this study. Patients were assigned to two groups according to routine MDRB colonization surveillance: non-colonized and colonized. Stool samples were collected when entering ICUs, and microbiota composition was determined through Next Generation Sequencing techniques. Gut microbiota from colonized patients presented significantly lower bacterial diversity compared with non-colonized patients (p < 0.05). Microbiota in colonized subjects showed higher abundance of Anaerococcus, Dialister and Peptoniphilus, while higher levels of Enterococcus, Ochrobactrum and Staphylococcus were found in non-colonized ones. Moreover, LEfSe analysis suggests an initial detection of Dialister propionicifaciens as a biomarker of MDRB colonization risk. This pilot study shows that gut microbiota profile can become a predictor biomarker for MDRB colonization in SARS-CoV-2 patients.}, }
@article {pmid36978337, year = {2023}, author = {Rovira, P}, title = {Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030470}, pmid = {36978337}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.}, }
@article {pmid36978215, year = {2023}, author = {Nitschke, AS and do Valle, HA and Vallance, BA and Bickford, C and Ip, A and Lanphear, N and Lanphear, B and Weikum, W and Oberlander, TF and Hanley, GE}, title = {Association between prenatal antibiotic exposure and autism spectrum disorder among term births: A population-based cohort study.}, journal = {Paediatric and perinatal epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ppe.12972}, pmid = {36978215}, issn = {1365-3016}, support = {/CAPMC/CIHR/Canada ; }, abstract = {BACKGROUND: Prenatal antibiotic exposure induces changes in the maternal microbiome, which could influence the development of the infant's microbiome-gut-brain axis.<br><br>OBJECTIVES: We assessed whether prenatal antibiotic exposure is associated with an increased risk of autism spectrum disorder (ASD) in offspring born at term.<br><br>METHODS: This population-based retrospective cohort study included everyone who delivered a live singleton-term infant in British Columbia, Canada between April 2000 and December 2014. Exposure was defined as filling antibiotic prescriptions during pregnancy. The outcome was an ASD diagnosis from the British Columbia Autism Assessment Network, with a follow-up to December 2016. To examine the association among pregnant individuals treated for the same indication, we studied a sub-cohort diagnosed with urinary tract infections. Cox proportional hazards models were used to estimate unadjusted and adjusted hazard ratios (HR). The analysis was stratified by sex, trimester, cumulative duration of exposure, class of antibiotic, and mode of delivery. We ran a conditional logistic regression of discordant sibling pairs to control for unmeasured environmental and genetic confounding.<br><br>RESULTS: Of the 569,953 children included in the cohort, 8729 were diagnosed with ASD (1.5%) and 169,922 were exposed to prenatal antibiotics (29.8%). Prenatal antibiotic exposure was associated with an increased risk of ASD (HR 1.10, 95% confidence interval [CI] 1.05, 1.15), particularly for exposure during the first and second trimesters (HR 1.11, 95% CI 1.04, 1.18 and HR 1.09, 95% CI 1.03, 1.16, respectively), and exposure lasting &#x2265;15&#x2009;days (HR 1.13, 95% CI 1.04, 1.23). No sex differences were observed. The association was attenuated in the sibling analysis (adjusted odds ratio 1.04, 95% CI 0.92, 1.17).<br><br>CONCLUSIONS: Prenatal antibiotic exposure was associated with a small increase in the risk of ASD in offspring. Given the possibility of residual confounding, these results should not influence clinical decisions regarding antibiotic use during pregnancy.}, }
@article {pmid36978146, year = {2023}, author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Iwayama, K and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H}, title = {Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {63}, pmid = {36978146}, issn = {2049-2618}, abstract = {BACKGROUND: Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes.<br><br>METHODS: We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure.<br><br>RESULTS: We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics.<br><br>CONCLUSIONS: The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.}, }
@article {pmid36978130, year = {2023}, author = {Yang, X and Wang, Z and Niu, J and Zhai, R and Xue, X and Wu, G and Fang, Y and Meng, G and Yuan, H and Zhao, L and Zhang, C}, title = {Pathobionts from chemically disrupted gut microbiota induce insulin-dependent diabetes in mice.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {62}, pmid = {36978130}, issn = {2049-2618}, abstract = {BACKGROUND: Dysbiotic gut microbiome, genetically predisposed or chemically disrupted, has been linked with insulin-dependent diabetes (IDD) including autoimmune type 1 diabetes (T1D) in both humans and animal models. However, specific IDD-inducing gut bacteria remain to be identified and their casual role in disease development demonstrated via experiments that can fulfill Koch's postulates.<br><br>RESULTS: Here, we show that novel gut pathobionts in the Muribaculaceae family, enriched by a low-dose dextran sulfate sodium (DSS) treatment, translocated to the pancreas and caused local inflammation, beta cell destruction and IDD in C57BL/6 mice. Antibiotic removal and transplantation of gut microbiota showed that this low DSS disrupted gut microbiota was both necessary and sufficient to induce IDD. Reduced butyrate content in the gut and decreased gene expression levels of an antimicrobial peptide in the pancreas allowed for the enrichment of selective members in the Muribaculaceae family in the gut and their translocation to the pancreas. Pure isolate of one such members induced IDD in wildtype germ-free mice on normal diet either alone or in combination with normal gut microbiome after gavaged into stomach and translocated to pancreas. Potential human relevance of this finding was shown by the induction of pancreatic inflammation, beta cell destruction and IDD development in antibiotic-treated wildtype mice via transplantation of gut microbiome from patients with IDD including autoimmune T1D.<br><br>CONCLUSION: The pathobionts that are chemically enriched in dysbiotic gut microbiota are sufficient to induce insulin-dependent diabetes after translocation to the pancreas. This indicates that IDD can be mainly a microbiome-dependent disease, inspiring the need to search for novel pathobionts for IDD development in humans. Video Abstract.}, }
@article {pmid36978107, year = {2023}, author = {Sun, S and Wang, D and Dong, D and Xu, L and Xie, M and Wang, Y and Ni, T and Jiang, W and Zhu, X and Ning, N and Sun, Q and Zhao, S and Li, M and Chen, P and Yu, M and Li, J and Chen, E and Zhao, B and Peng, Y and Mao, E}, title = {Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis.}, journal = {Critical care (London, England)}, volume = {27}, number = {1}, pages = {127}, pmid = {36978107}, issn = {1466-609X}, abstract = {BACKGROUND: The gut microbiome plays a pivotal role in the progression of sepsis. However, the specific mechanism of gut microbiota and its metabolites involved in the process of sepsis remains elusive, which limits its translational application.<br><br>METHOD: In this study, we used a combination of the microbiome and untargeted metabolomics to analyze stool samples from patients with sepsis enrolled at admission, then microbiota, metabolites, and potential signaling pathways that might play important roles in disease outcome were screened out. Finally, the above results were validated by the microbiome and transcriptomics analysis in an animal model of sepsis.<br><br>RESULTS: Patients with sepsis showed destruction of symbiotic flora and elevated abundance of Enterococcus, which were validated in animal experiments. Additionally, patients with a high burden of Bacteroides, especially B. vulgatus, had higher Acute Physiology and Chronic Health Evaluation II scores and longer stays in the intensive care unit. The intestinal transcriptome in CLP rats illustrated that Enterococcus and Bacteroides had divergent profiles of correlation with differentially expressed genes, indicating distinctly different roles for these bacteria in sepsis. Furthermore, patients with sepsis exhibited disturbances in gut amino acid metabolism compared with healthy controls; namely, tryptophan metabolism was tightly related to an altered microbiota and the severity of sepsis.<br><br>CONCLUSION: Alterations in microbial and metabolic features in the gut corresponded with the progression of sepsis. Our findings may help to predict the clinical outcome of patients in the early stage of sepsis and provide a translational basis for exploring new therapies.}, }
@article {pmid36977964, year = {2023}, author = {Balzano, T}, title = {Active Clinical Trials in Hepatic Encephalopathy: Something Old, Something New and Something Borrowed.}, journal = {Neurochemical research}, volume = {}, number = {}, pages = {}, pmid = {36977964}, issn = {1573-6903}, abstract = {Hepatic encephalopathy (HE) is a potentially reversible neurocognitive syndrome that occurs in patients with acute or chronic liver disease. Currently, most of the therapies for HE aim to reduce ammonia production or increase its elimination. To date, only two agents have been approved as treatments for HE: lactulose and rifaximin. Many other drugs have also been used, but data to support their use are limited, preliminary or lacking. The aim of this review is to provide an overview and discussion of the current development of treatments for HE. Data from ongoing clinical trials in HE were obtained from the ClinicalTrials.gov website, and a breakdown analysis of studies that were active on August 19th, 2022, was performed. Seventeen registered and ongoing clinical trials for therapeutics targeting HE were identified. More than 75% of these agents are in phase II (41.2%) or in phase III (34.7%). Among them, there are many old acquaintances in the field, such as lactulose and rifaximin, some new entries such as fecal microbiota transplantation and equine anti-thymocyte globulin, an immunosuppressive agent, but also some therapies borrowed from other conditions, such as rifamycin SV MMX and nitazoxanide, two antimicrobial agents FDA approved for the treatment of some types of diarrheas or VE303 and RBX7455, two microbiome restoration therapies, currently used as treatment of high-risk Clostridioides difficile infections. If working, some of these drugs could soon be used as valid alternatives to current therapies when ineffective or be approved as novel therapeutic approaches to improve the quality of life of HE patients.}, }
@article {pmid36977954, year = {2023}, author = {Mahiddine, FY and You, I and Park, H and Kim, MJ}, title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.}, journal = {Veterinary research communications}, volume = {}, number = {}, pages = {}, pmid = {36977954}, issn = {1573-7446}, abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.}, }
@article {pmid36977576, year = {2023}, author = {Hu, J and Cyle, KT and Miller, G and Shi, W}, title = {Water Deficits Shape the Microbiome of Bermudagrass Roots to be Actinobacteria Rich.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad036}, pmid = {36977576}, issn = {1574-6941}, abstract = {There is increasing evidence that microbes can help ameliorate plant growth under environmental stress. Still, it is largely unknown what microbes and potential functions are involved in sustaining turfgrass, the major component of urban/suburban landscapes, under drought. We examined microbial responses to water deficits in bulk soil, rhizosphere, and root endosphere of bermudagrass by applying evapotranspiration (ET)-based dynamic irrigation twice per week during the growing season to create six treatments (0, 40, 60, 80, 100, and 120% ET) and respective drought-stressed soil conditions. Bacterial and fungal communities were analyzed via marker gene amplicon sequencing and thereafter drought-reshaped potential functions of the bacterial community were projected. Slight yet significant microbial responses to irrigation treatments were observed in all three microhabitats. The root endophytic bacterial community was most responsive to water stress. No-irrigation primarily increased the relative abundance of root endophytic Actinobacteria, especially the genus Streptomyces. Irrigation at ≤ 40% ET increased the relative abundances of PICRUSt2-predicted functional genes encoding 1-aminocyclopropane-1-carboxylic acid deaminase, superoxide dismutase, and chitinase in root endosphere. Our data suggest that the root endophytic Actinobacteria are likely the key players to improve bermudagrass fitness under drought by modulating phytohormone ethylene production, scavenging reactive oxygen species, or ameliorating nutrient acquisition.}, }
@article {pmid36977462, year = {2023}, author = {Ney, LM and Wipplinger, M and Grossmann, M and Engert, N and Wegner, VD and Mosig, AS}, title = {Short chain fatty acids: key regulators of the local and systemic immune response in inflammatory diseases and infections.}, journal = {Open biology}, volume = {13}, number = {3}, pages = {230014}, doi = {10.1098/rsob.230014}, pmid = {36977462}, issn = {2046-2441}, abstract = {The human intestinal microbiome substantially affects human health and resistance to infections in its dynamic composition and varying release of microbial-derived metabolites. Short-chain fatty acids (SCFA) produced by commensal bacteria through fermentation of indigestible fibres are considered key regulators in orchestrating the host immune response to microbial colonization by regulating phagocytosis, chemokine and central signalling pathways of cell growth and apoptosis, thereby shaping the composition and functionality of the intestinal epithelial barrier. Although research of the last decades provided valuable insight into the pleiotropic functions of SCFAs and their capability to maintain human health, mechanistic details on how SCFAs act across different cell types and other organs are not fully understood. In this review, we provide an overview of the various functions of SCFAs in regulating cellular metabolism, emphasizing the orchestration of the immune response along the gut-brain, the gut-lung and the gut-liver axes. We discuss their potential pharmacological use in inflammatory diseases and infections and highlight new options of relevant human three-dimensional organ models to investigate and validate their biological functions in more detail.}, }
@article {pmid36977440, year = {2023}, author = {Dang, Z and Gao, M and Wang, L and Wu, J and Guo, Y and Zhu, Z and Huang, H and Kang, G}, title = {Synthetic bacterial therapies for intestinal diseases based on quorum- sensing circuits.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108142}, doi = {10.1016/j.biotechadv.2023.108142}, pmid = {36977440}, issn = {1873-1899}, abstract = {Bacterial therapy has become a key strategy against intestinal infectious diseases in recent years. Moreover, regulating the gut microbiota through traditional fecal microbiota transplantation and supplementation of probiotics faces controllability, efficacy, and safety challenges. The infiltration and emergence of synthetic biology and microbiome provide an operational and safe treatment platform for live bacterial biotherapies. Synthetic bacterial therapy can artificially manipulate bacteria to produce and deliver therapeutic drug molecules. This method has the advantages of solid controllability, low toxicity, strong therapeutic effects, and easy operation. As an essential tool for dynamic regulation in synthetic biology, quorum sensing (QS) has been widely used for designing complex genetic circuits to control the behavior of bacterial populations and achieve predefined goals. Therefore, QS-based synthetic bacterial therapy might become a new direction for the treatment of diseases. The pre-programmed QS genetic circuit can achieve a controllable production of therapeutic drugs on particular ecological niches by sensing specific signals released from the digestive system in pathological conditions, thereby realizing the integration of diagnosis and treatment. Based on this as well as the modular idea of synthetic biology, QS-based synthetic bacterial therapies are divided into an environmental signal sensing module (senses gut disease physiological signals), a therapeutic molecule producing module (plays a therapeutic role against diseases), and a population behavior regulating module (QS system). This review article summarized the structure and function of these three modules and discussed the rational design of QS gene circuits as a novel intervention strategy for intestinal diseases. Moreover, the application prospects of QS-based synthetic bacterial therapy were summarized. Finally, the challenges faced by these methods were analyzed to make the targeted recommendations for developing a successful therapeutic strategy for intestinal diseases.}, }
@article {pmid36977254, year = {2023}, author = {Becker, AAMJ and Munden, S and McCabe, E and Hurley, D and Fanning, S and Chapwanya, A and Butaye, P}, title = {The Endometrial Microbiota-16S rRNA Gene Sequence Signatures in Healthy, Pregnant and Endometritis Dairy Cows.}, journal = {Veterinary sciences}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/vetsci10030215}, pmid = {36977254}, issn = {2306-7381}, abstract = {Endometritis is one of the most important causes of infertility in dairy cows, resulting in high economic losses in the dairy industry. Though the presence of a commensal uterine microbiota is now well established, the complex role of these bacteria in genital health, fertility, and susceptibility to uterine diseases remains unclear. In this study, we explore the endometrial microbiota through 16S rRNA gene profiling from cytobrush samples taken ex vivo from healthy, pregnant, and endometritis cows. There were no significant differences between healthy and pregnant cows, whose uterine microbiota were dominated by Streptococcus, Pseudomonas, Fusobacterium, Lactococcus and Bacteroides. Compared to pregnant and clinically healthy cows, the uterine bacterial community of endometritis cows was significantly decreased in species diversity (p < 0.05), reflecting uneven community composition in different patterns with either dominance of Escherichia-Shigella, Histophilus, Bacteroides and Porphyromonas or Actinobacteria.}, }
@article {pmid36977046, year = {2023}, author = {Rashid, F and Dubinkina, V and Ahmad, S and Maslov, S and Irudayaraj, JMK}, title = {Gut Microbiome-Host Metabolome Homeostasis upon Exposure to PFOS and GenX in Male Mice.}, journal = {Toxics}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/toxics11030281}, pmid = {36977046}, issn = {2305-6304}, abstract = {Alterations of the normal gut microbiota can cause various human health concerns. Environmental chemicals are one of the drivers of such disturbances. The aim of our study was to examine the effects of exposure to perfluoroalkyl and polyfluoroalkyl substances (PFAS)-specifically, perfluorooctane sulfonate (PFOS) and 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy) propanoic acid (GenX)-on the microbiome of the small intestine and colon, as well as on liver metabolism. Male CD-1 mice were exposed to PFOS and GenX in different concentrations and compared to controls. GenX and PFOS were found to have different effects on the bacterial community in both the small intestine and colon based on 16S rRNA profiles. High GenX doses predominantly led to increases in the abundance of Clostridium sensu stricto, Alistipes, and Ruminococcus, while PFOS generally altered Lactobacillus, Limosilactobacillus, Parabacteroides, Staphylococcus, and Ligilactobacillus. These treatments were associated with alterations in several important microbial metabolic pathways in both the small intestine and colon. Untargeted LC-MS/MS metabolomic analysis of the liver, small intestine, and colon yielded a set of compounds significantly altered by PFOS and GenX. In the liver, these metabolites were associated with the important host metabolic pathways implicated in the synthesis of lipids, steroidogenesis, and in the metabolism of amino acids, nitrogen, and bile acids. Collectively, our results suggest that PFOS and GenX exposure can cause major perturbations in the gastrointestinal tract, aggravating microbiome toxicity, hepatotoxicity, and metabolic disorders.}, }
@article {pmid36976797, year = {2023}, author = {Sandle, GI and Herod, MR and Fontana, J and Lippiat, JD and Stockley, PG}, title = {Is intestinal transport dysfunctional in COVID-19-related diarrhea?.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00021.2023}, pmid = {36976797}, issn = {1522-1547}, abstract = {Diarrhea, often severe, is a recognised and frequently early symptom during acute COVID-19 infection and may persist or develop for the first time in patients with long-COVID, with socio-economic consequences. Diarrheal mechanisms in these cases are poorly understood. There is evidence for disruption of intestinal epithelial barrier function, and also for changes in the gut microbiome which is critical for gut immunity and metabolism. Whether the SARS-CoV-2 virus has adverse effects on intestinal transport proteins is unclear. However, the ability of the virus to inhibit expression and activity of an aldosterone-regulated epithelial sodium (Na[+]) channel (ENaC) present in human distal colon, which is responsible for Na[+] and water salvage, points to possible disruption of other intestinal transport proteins during COVID-19 infection. In this Perspective, we develop this idea by highlighting possible intestinal transport protein targets for the SARS-CoV-2 virus and discuss how their interactions might be explored in the laboratory.}, }
@article {pmid36976399, year = {2023}, author = {Siemsen, W and Halske, C and Behrens, HM and Krüger, S and Becker-Pauly, C and Röcken, C}, title = {The putative pleiotropic functions of meprin β in gastric cancer.}, journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association}, volume = {}, number = {}, pages = {}, pmid = {36976399}, issn = {1436-3305}, abstract = {BACKGROUND: The gastric microbiome and inflammation play a key role in gastric cancer (GC) by regulating the immune response in a complex manner and by inflammatory events supporting carcinogenesis. Meprin β is a zinc endopeptidase and participates in tissue homeostasis, intestinal barrier function and immunological processes. It influences local inflammatory processes, dysbiosis and the microbiome. Here, we tested the hypothesis that meprin β is expressed in GC and of tumor biological significance.<br><br>PATIENTS AND METHODS: Four hundred forty whole mount tissue sections of patients with therapy-naive GC were stained with an anti-meprin &#x3b2; antibody. The histoscore and staining pattern were analyzed for each case. Following dichotomization at the median histoscore into a "low" and "high" group, the expression was correlated with numerous clinicopathological patient characteristics.<br><br>RESULTS: Meprin &#x3b2; was found intracellularly and at the cell membrane of GC. Cytoplasmic expression correlated with the phenotype according to Lauren, microsatellite instability and PD-L1 status. Membranous expression correlated with intestinal phenotype, mucin-1-, E-cadherin-, &#x3b2;-catenin status, mucin typus, microsatellite instability, KRAS mutation and PD-L1-positivity. Patients with cytoplasmic expression of meprin &#x3b2; showed a better overall and tumor-specific survival.<br><br>CONCLUSIONS: Meprin &#x3b2; is differentially expressed in GC and has potential tumor biological relevance. It might function as a tumor suppressor or promotor depending on histoanatomical site and context.}, }
@article {pmid36976283, year = {2023}, author = {Hamilton, F and Wright, WF and Lee, TC}, title = {Extended Follow-up of Microbiome Therapeutic SER-109 for Recurrent Clostridioides difficile Infection.}, journal = {JAMA}, volume = {329}, number = {12}, pages = {1032-1033}, doi = {10.1001/jama.2023.0497}, pmid = {36976283}, issn = {1538-3598}, }
@article {pmid36976280, year = {2023}, author = {Cohen, SH and Louie, TJ and McGovern, BH}, title = {Extended Follow-up of Microbiome Therapeutic SER-109 for Recurrent Clostridioides difficile Infection-Reply.}, journal = {JAMA}, volume = {329}, number = {12}, pages = {1033-1034}, doi = {10.1001/jama.2023.0496}, pmid = {36976280}, issn = {1538-3598}, }
@article {pmid36975854, year = {2023}, author = {Roager, L and Sonnenschein, EC and Gram, L}, title = {Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0340822}, doi = {10.1128/spectrum.03408-22}, pmid = {36975854}, issn = {2165-0497}, abstract = {The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The I. galbana microbiome was dominated by the genus Alteromonas, whereas the microbiome associated with T. suecica was dominated by Marinobacteraceae and Rhodobacteraceae family members. While these two families were also prevalent in the microbiome associated with C. weissflogii, Flavobacteriaceae and Cryomorphaceae were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes. IMPORTANCE Microalgae are very important as primary producers in the ocean, but also as forthcoming sustainable producers of biotechnologically interesting compounds. Accordingly, the bacterial microbiomes associated with microalgae are attracting increasing attention due to their effects on the growth and health of microalgae. Since most members of these microbiomes cannot be cultured, knowledge about community composition is best obtained using sequencing-based methods. This study evaluates the impact of DNA extraction methods on DNA quantity and quality along with sequence-based characterization of the bacterial microbiome composition of three microalgae: Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii.}, }
@article {pmid36975828, year = {2023}, author = {Sheng, D and Yue, K and Li, H and Zhao, L and Zhao, G and Jin, C and Zhang, L}, title = {The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0354922}, doi = {10.1128/spectrum.03549-22}, pmid = {36975828}, issn = {2165-0497}, abstract = {Microbiota can influence the occurrence, development, and therapeutic response of a wide variety of cancer types by modulating immune responses to tumors. Recent studies have demonstrated the existence of intratumor bacteria inside ovarian cancer (OV). However, whether intratumor microbes are associated with tumor microenvironment (TME) and prognosis of OV still remains unknown. The RNA-sequencing data and clinical and survival data of 373 patients with OV in The Cancer Genome Atlas (TCGA) were collected and downloaded. According to the knowledge-based functional gene expression signatures (Fges), OV was classified into two subtypes, termed immune-enriched and immune-deficient subtypes. The immune-enriched subtype, which had higher immune infiltration enriched with CD8[+] T cells and the M1 type of macrophages (M1) and higher tumor mutational burden, exhibited a better prognosis. Based on the Kraken2 pipeline, the microbiome profiles were explored and found to be significantly different between the two subtypes. A prediction model consisting of 32 microbial signatures was constructed using the Cox proportional-hazard model and showed great prognostic value for OV patients. The prognostic microbial signatures were strongly associated with the hosts' immune factors. Especially, M1 was strongly associated with five species (Achromobacter deleyi and Microcella alkaliphila, Devosia sp. strain LEGU1, Ancylobacter pratisalsi, and Acinetobacter seifertii). Cell experiments demonstrated that Acinetobacter seifertii can inhibit macrophage migration. Our study demonstrated that OV could be classified into immune-enriched and immune-deficient subtypes and that the intratumoral microbiota profiles were different between the two subtypes. Furthermore, the intratumoral microbiome was closely associated with the tumor immune microenvironment and OV prognosis. IMPORTANCE Recent studies have demonstrated the existence of intratumoral microorganisms. However, the role of intratumoral microbes in the development of ovarian cancer and their interaction with the tumor microenvironment are largely unknown. Our study demonstrated that OV could be classified into immune-enriched and -deficient subtypes and that the immune enrichment subtype had a better prognosis. Microbiome analysis showed that intratumor microbiota profiles were different between the two subtypes. Furthermore, the intratumor microbiome was an independent predictor of OV prognosis that could interact with immune gene expression. Especially, M1 was closely associated with intratumoral microbes, and Acinetobacter seifertii could inhibit macrophage migration. Together, the findings of our study highlight the important roles of intratumoral microbes in the TME and prognosis of OV, paving the way for further investigation into its underlying mechanisms.}, }
@article {pmid36975809, year = {2023}, author = {Falardeau, J and Yildiz, E and Yan, Y and Castellarin, SD and Wang, S}, title = {Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0200422}, doi = {10.1128/aem.02004-22}, pmid = {36975809}, issn = {1098-5336}, abstract = {Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10[3] CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.}, }
@article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0100322}, doi = {10.1128/msystems.01003-22}, pmid = {36975801}, issn = {2379-5077}, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, }
@article {pmid36975538, year = {2023}, author = {Szewczyk, A and Andres-Mach, M and Zagaja, M and Kaczmarczyk-Ziemba, A and Maj, M and Szala-Rycaj, J}, title = {The Effect of a Diet Enriched with Jerusalem artichoke, Inulin, and Fluoxetine on Cognitive Functions, Neurogenesis, and the Composition of the Intestinal Microbiota in Mice.}, journal = {Current issues in molecular biology}, volume = {45}, number = {3}, pages = {2561-2579}, pmid = {36975538}, issn = {1467-3045}, abstract = {The aim of the study was to assess the effect of long-term administration of natural prebiotics: Jerusalem artichoke (topinambur, TPB) and inulin (INU) as well as one of the most popular antidepressants, fluoxetine (FLU), on the proliferation of neural stem cells, learning and memory functions, and the composition of the intestinal microbiota in mice. Cognitive functions were assessed using the Morris Water Maze (MWM)Test. Cells were counted using a confocal microscope and ImageJ software. We performed 16S rRNA sequencing to assess changes in the gut microbiome of the mice. The obtained results showed that the 10-week supplementation with TPB (250 mg/kg) and INU (66 mg/kg) stimulates the growth of probiotic bacteria, does not affect the learning and memory process, and does not disturb the proliferation of neural stem cells in the tested animals. Based on this data, we can assume that both TPB and INU seem to be safe for the proper course of neurogenesis. However, 2-week administration of FLU confirmed an inhibitory impact on Lactobacillus growth and negatively affected behavioral function and neurogenesis in healthy animals. The above studies suggest that the natural prebiotics TPB and INU, as natural supplements, may have the potential to enrich the diversity of intestinal microbiota, which may be beneficial for the BGM axis, cognitive functions, and neurogenesis.}, }
@article {pmid36974685, year = {2023}, author = {Skeen, HR and Willard, DE and Jones, AW and Winger, BM and Gyllenhaal, EF and Tsuru, BR and Hackett, SJ and Novembre, J}, title = {Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16915}, pmid = {36974685}, issn = {1365-294X}, abstract = {Seasonal migration of Nearctic-Neotropical passerine birds may have profound effects on the diversity and abundance of their host-associated microbiota. Migratory birds experience seasonal change in environments and diets throughout the course of the annual cycle that, along with recurrent biological events such as reproduction, may significantly impact their microbiota. In this study, we characterize the intestinal microbiota of four closely related species of migratory Catharus thrushes at three time points of their migratory cycle: during spring migration, on the summer breeding territories and during fall migration. Using observations replicated over 3 years, we determined that microbial community diversity of Catharus thrushes was significantly different across distinct time periods of the annual cycle, whereas community composition was more similar within than across years. Elevated alpha diversity in the summer birds compared to either migratory period indicated that birds may harbour a reduced microbiota during active migration. We also found that community composition of the microbiota did not substantially differ between host species. Finally, we recovered two phyla, Cyanobacteria and Planctomycetota, which are not commonly described from birds, that were in relatively high abundance in specific years. This study contributes to our growing understanding of how microbiota in wild birds vary throughout disparate ecological conditions and reveals potential axes across which an animal's microbial flexibility adapts to variable environments and recurrent biological conditions throughout the annual cycle.}, }
@article {pmid36974462, year = {2023}, author = {Zhang, S and Li, S and Huang, J and Ding, X and Qiu, Y and Luo, X and Meng, J and Hu, Y and Zhou, H and Fan, H and Cao, Y and Gao, F and Xue, Y and Zou, M}, title = {Gram-negative bacteria and lipopolysaccharides as risk factors for the occurrence of diabetic foot.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgad178}, pmid = {36974462}, issn = {1945-7197}, abstract = {CONTEXT: Imbalance of the skin microbial community could impair skin immune homeostasis and thus trigger skin lesions. Dysbiosis of skin microbiome may be involved in the early pathogenesis of diabetic foot (DF). However, the potential mechanism remains unclear.<br><br>OBJECTIVE: To investigate the dynamic composition and function of the foot skin microbiome with risk stratification for DF and assess whether dysbiosis of the skin microbiome induces diabetic skin lesions.<br><br>METHODS: We enrolled 90 consecutive subjects who were divided into five groups based on DF risk stratification: very low, low, moderate and high risk for ulcers and a healthy control group. Integrated analysis of 16S rRNA and metagenomic sequencing of cotton swab samples was applied to identify the foot skin microbiome composition and functions in subjects. Then, a mouse model of microbiota transplantation was used to evaluate the effects of the skin microbiome on diabetic skin lesions.<br><br>RESULTS: The results demonstrated that, with the progression of diabetic complications, the proportion of gram-negative bacteria in plantar skin increased. At the species level, metagenome sequencing analyses showed Moraxella osloensis to be a representative core strain in the high-risk group. The major microbial metabolites affecting diabetic skin lesions were increased amino acid metabolites, and antibiotic resistance genes in microorganisms were abundant. Skin microbiota from high-risk patients induced more inflammatory cell infiltration, similar to the lipopolysaccharide (LPS)-stimulated response, which was inhibited by Toll-like receptor 4 (TLR4) antagonists.<br><br>CONCLUSIONS: The skin microbiome in patients with diabetes undergoes dynamic changes at taxonomic and functional levels with the progression of diabetic complications. The increase in gram-negative bacteria on the skin surface through LPS-TLR4 signal transduction could induce inflammatory response in early diabetic skin lesions.}, }
@article {pmid36974413, year = {2023}, author = {Manolis, AA and Manolis, TA and Melita, H and Manolis, AS}, title = {Features of a Balanced Healthy Diet With Cardiovascular and Other Benefits.}, journal = {Current vascular pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/1570161121666230327135916}, pmid = {36974413}, issn = {1875-6212}, abstract = {BACKGROUND: Cardiovascular (CV) disease (CVD) remains the leading cause of death globally. Besides lack of exercise, obesity, smoking, and other risk factors, poor nutrition and unhealthy/unbalanced diets play an important role in CVD.<br><br>OBJECTIVE: This review examined data on all issues of the CV-health benefits of a balanced diet, with tabulation of nutritional data and health-authority recommendations and pictorial illustration of the main features of a CV-healthy diet.<br><br>METHODS: PubMed and Google Scholar were searched for relevant studies and reviews on diet and CV health.<br><br>RESULTS: For a long time, there has been evidence, corroborated by recent findings, that pro-vegetarian diets have a beneficial influence on serum lipid levels, markers of inflammation and endothelial function, prooxidant-antioxidant balance, and gut microbiome, all probably contributing to reduced CV risk. Worries about the nutritional adequacy of vegetarian diets are circumvented by obtaining certain nutrients lacking or found in lower amounts in plants than in animal foods, by consuming a wide variety of healthy plant foods and through intake of oral supplements or fortified foods. Well-balanced diets, such as the Mediterranean or the Dietary-Approaches-to-Stop-Hypertension diets, provide CV-health benefits. Nevertheless, a broad variety of plant-based diets with low/minimal animal food intake may allow for the personalized and culturally adjusted application of dietary recommendations contributing to the maintenance of CV health.<br><br>CONCLUSION: Universal adoption of a balanced CV-healthy diet can reduce global, CV and other mortality by ~20%. This requires world-wide programs of information for and education of the public, starting with school children and expanding to all groups, sectors, and levels.}, }
@article {pmid36974227, year = {2023}, author = {Hennessy, M and Kristula, M and Cady, S and Smith, B and Indugu, N and Vecchiarelli, B and Pitta, D}, title = {Acidification of colostrum affects the fecal microbiota of preweaning dairy calves.}, journal = {JDS communications}, volume = {4}, number = {2}, pages = {80-85}, pmid = {36974227}, issn = {2666-9102}, abstract = {Calf diarrhea is a leading cause of death in preweaning calves and it causes major economic losses to producers. Acidified milk has been shown to have beneficial effects on health and growth parameters in calves but there is little research into its effects on the microbiota, and few studies on the use of acidified colostrum. The purpose of this study was to compare how feeding acidified colostrum to calves at birth affects fecal microbiota from birth through 8 wk of age compared with calves fed nonacidified colostrum. In this study, 5 calves received acidified colostrum (treated group) and 5 calves received nonacidified colostrum (control group) at birth and at 12 h of age. All calves were subsequently fed acidified whole milk until weaning at 8 wk of age and had access to starter grain starting at d 3 and throughout the study. Fecal samples were collected at 24 h, 48 h, and at 1, 2, 3, 4, 5, 6, 7, and 8 wk of age. Samples were extracted for genomic DNA, PCR-amplified for the V1-V2 region of the 16S rRNA bacteria gene, sequenced, and analyzed using QIIME2. Bacterial richness (estimated by number of observed species) and bacterial diversity (estimated by Shannon diversity index) differed between time points but not between treatment groups, and both increased over time. Weighted and unweighted UniFrac analysis showed differences between bacterial communities across time points and treatments. Across all time points (lmer test), 6 bacterial genera were different between treatments: Faecalibacterium and unclassified Clostridiaceae were more abundant, whereas Atopobium, Collinsella, CF231, and unclassified Veillonellaceae were less abundant in treated versus control calves. Faecalibacterium is a butyrate-producing bacterium that has been linked to decreased prevalence of diarrhea in calves. Our results indicate that there is considerable flux in the calf microbiome through the neonatal period and weaning transition but that feeding acidified colostrum followed by acidified whole milk allowed early colonization of Faecalibacterium. Further studies are needed to verify the positive benefits of promoting Faecalibacterium on improving the health of preweaning calves.}, }
@article {pmid36973820, year = {2023}, author = {Su, J and Wang, Y and Bai, M and Peng, T and Li, H and Xu, HJ and Guo, G and Bai, H and Rong, N and Sahu, SK and He, H and Liang, X and Jin, C and Liu, W and Strube, ML and Gram, L and Li, Y and Wang, E and Liu, H and Wu, H}, title = {Soil conditions and the plant microbiome boost the accumulation of monoterpenes in the fruit of Citrus reticulata 'Chachi'.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {61}, pmid = {36973820}, issn = {2049-2618}, mesh = {*Citrus ; Fruit ; Rhizosphere ; *Microbiota ; Terpenes ; }, abstract = {BACKGROUND: The medicinal material quality of Citrus reticulata 'Chachi' differs depending on the bioactive components influenced by the planting area. Environmental factors, such as soil nutrients, the plant-associated microbiome and climatic conditions, play important roles in the accumulation of bioactive components in citrus. However, how these environmental factors mediate the production of bioactive components of medicinal plants remains understudied.<br><br>RESULTS: Here, a multi-omics approach was used to clarify the role of environmental factors such as soil nutrients and the root-associated microbiome on the accumulation of monoterpenes in the peel of C. reticulata 'Chachi' procured from core (geo-authentic product region) and non-core (non-geo-authentic product region) geographical regions. The soil environment (high salinity, Mg, Mn and K) enhanced the monoterpene content by promoting the expression of salt stress-responsive genes and terpene backbone synthase in the host plants from the core region. The microbial effects on the monoterpene accumulation of citrus from the core region were further verified by synthetic community (SynCom) experiments. Rhizosphere microorganisms activated terpene synthesis and promoted monoterpene accumulation through interactions with the host immune system. Endophyte microorganisms derived from soil with the potential for terpene synthesis might enhance monoterpene accumulation in citrus by providing precursors of monoterpenes.<br><br>CONCLUSIONS: Overall, this study demonstrated that both soil properties and the soil microbiome impacted monoterpene production in citrus peel, thus providing an essential basis for increasing fruit quality via reasonable fertilization and precision microbiota management. Video Abstract.}, }
@article {pmid36973807, year = {2023}, author = {Zhang, Y and Wang, Y and Tang, M and Zhou, J and Zhang, T}, title = {The microbial dark matter and "wanted list" in worldwide wastewater treatment plants.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {59}, pmid = {36973807}, issn = {2049-2618}, abstract = {BACKGROUND: Wastewater treatment plants (WWTPs) are one of the largest biotechnology applications in the world and are of critical importance to modern urban societies. An accurate evaluation of the microbial dark matter (MDM, microorganisms whose genomes remain uncharacterized) proportions in WWTPs is of great value, while there is no such research yet. This study conducted a global meta-analysis of MDM in WWTPs with 317,542 prokaryotic genomes from the Genome Taxonomy Database and proposed a "wanted list" for priority targets in further investigations of activated sludge.<br><br>RESULTS: Compared with the Earth Microbiome Project data, WWTPs had relatively lower genome-sequenced proportions of prokaryotes than other ecosystems, such as the animal related environments. Analysis showed that the median proportions of the genome-sequenced cells and taxa (100% identity and 100% coverage in 16S rRNA gene region) in WWTPs reached 56.3% and 34.5% for activated sludge, 48.6% and 28.5% for aerobic biofilm, and 48.3% and 28.5% for anaerobic digestion sludge, respectively. This result meant MDM had high proportions in WWTPs. Besides, all of the samples were occupied by a few predominant taxa, and the majority of the sequenced genomes were from pure cultures. The global-scale "wanted list" for activated sludge contained four phyla that have few representatives and 71 operational taxonomic units with the majority of them having no genome or isolate yet. Finally, several genome mining methods were verified to successfully recover genomes from activated sludge such as hybrid assembly of the second- and third-generation sequencing.<br><br>CONCLUSIONS: This work elucidated the proportion of MDM in WWTPs, defined the "wanted list" of activated sludge for future investigations, and certified potential genome recovery methods. The proposed methodology of this study can be applied to other ecosystems and improve understanding of ecosystem structure across diverse habitats. Video Abstract.}, }
@article {pmid36973710, year = {2023}, author = {Li, H and Wang, H and Ju, H and Lv, J and Yang, S and Zhang, W and Lu, H}, title = {Comparison of gut viral communities in children under 5 years old and newborns.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {52}, pmid = {36973710}, issn = {1743-422X}, abstract = {OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique.<br><br>METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group.<br><br>RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity.<br><br>CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.}, }
@article {pmid36973599, year = {2023}, author = {Li, Y and Liu, LH and Jian, ZY and Li, PH and Jin, X and Li, H and Wang, KJ}, title = {Association between antibiotic exposure and adverse outcomes of children and pregnant women: evidence from an umbrella review.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, pmid = {36973599}, issn = {1867-0687}, abstract = {BACKGROUND: Antibiotics are widely prescribed among children and pregnant women, but their safety profile is controversial. This study aimed to summarize and appraise current evidence for the potential impact of antibiotic exposure on pregnancy outcomes and children's health.<br><br>METHODS: PubMed, Embase, Web of Science and the Cochrane Database of Systematic Reviews were searched from inception to June 2022. Meta-analyses of any study design comparing the impact of antibiotic exposure with nonexposure among children, pregnant women and prepregnant women on adverse health outcomes of children and pregnancy were retrieved. The quality of evidence was assessed by a Measurement Tool to Assess Systematic Reviews 2 (AMSTAR2) and the Grading of Recommendations, Assessment, Development and Evaluation (GRADE). Data were reanalyzed, and the credibility of the evidence was determined.<br><br>RESULTS: Out of 2956 studies identified, 19 articles with 39 associations were included. Totally 19 of the associations (48.72%) were statistically significant with a P value&#x2009;&#x2264;&#x2009;0.05, while only six were supported by highly suggestive evidence. Children with postnatal antibiotic exposure had a higher risk of developing asthma odds ratio (OR): 1.95, 95% confidence interval (CI): 1.76-2.17, wheezing (OR: 1.81, 95% CI 1.65-1.97) and allergic rhinoconjunctivitis (OR: 1.66, 95% CI 1.51-1.83), with prediction intervals excluding the nulls. Quality assessed by both AMSTAR2 and GRADE of included meta-analyses were very low in general.<br><br>CONCLUSIONS: Antibiotic exposure in early life was associated with children's long-term health, especially in cases of allergic diseases. Prenatal exposure might also influence children's health in some aspects but requires more high-quality evidence. Potential adverse effects of antibiotics on pregnancy outcomes were not observed in our study. Studies with higher quality and better quantification of antibiotic exposure are needed in the future.}, }
@article {pmid36973411, year = {2023}, author = {DeFilipp, Z and Maus, MV}, title = {Linking the microbiome to CAR-T cell responses.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {36973411}, issn = {1546-170X}, }
@article {pmid36973353, year = {2023}, author = {Fackelmann, G and Pham, CK and Rodríguez, Y and Mallory, ML and Provencher, JF and Baak, JE and Sommer, S}, title = {Current levels of microplastic pollution impact wild seabird gut microbiomes.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {36973353}, issn = {2397-334X}, abstract = {Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways. A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. Here, we investigated if microplastics are associated with changes in proventricular and cloacal microbiomes in two seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters. The amount of microplastics in the gut was significantly correlated with gut microbial diversity and composition: microplastics were associated with decreases in commensal microbiota and increases in (zoonotic) pathogens and antibiotic-resistant and plastic-degrading microbes. These results illustrate that environmentally relevant microplastic concentrations and mixtures are associated with changes in gut microbiomes in wild seabirds.}, }
@article {pmid36973329, year = {2023}, author = {Bhandari, R and Sanz-Saez, A and Leisner, CP and Potnis, N}, title = {Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {24}, pmid = {36973329}, issn = {2730-6151}, abstract = {While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.}, }
@article {pmid36972851, year = {2023}, author = {Wang, X and Eguchi, A and Fujita, Y and Wan, X and Chang, L and Yang, Y and Shan, J and Qu, Y and Ma, L and Shirayama, Y and Mori, C and Yang, J and Hashimoto, K}, title = {Abnormal compositions of gut microbiota and metabolites are associated with susceptibility versus resilience in rats to inescapable electric stress.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jad.2023.03.073}, pmid = {36972851}, issn = {1573-2517}, abstract = {BACKGROUND: Increasing evidence suggests the role of gut microbiota in resilience versus vulnerability after stress. However, the role of gut microbiota and microbiome-derived metabolites in resilience versus susceptibility in rodents exposed to stress remains unclear.<br><br>METHODS: Adult male rats were exposed to inescapable electric stress under the learned helplessness (LH) paradigm. The composition of gut microbiota and metabolites in the brain and blood from control (no stress) rats, LH resilient rats, and LH susceptible rats were examined.<br><br>RESULTS: At the genus level, the relative abundances of Asaccharobacter, Eisenbergiella, and Klebsiella in LH susceptible rats were significantly higher than that of LH resilient rats. At the species level, the relative abundances of several microbiome were significantly altered between LH susceptible rats and LH resilient rats. Furthermore, there were several metabolites in the brain and blood altered between LH susceptible rats and LH resilient rats. A network analysis showed correlations between the abundance of several microbiome and metabolites in the brain (or blood).<br><br>LIMITATIONS: Detailed roles of microbiome and metabolites are unclear.<br><br>CONCLUSIONS: These findings suggest that abnormal compositions of the gut microbiota and metabolites might contribute to susceptibility versus resilience in rats subjected to inescapable electric foot shock.}, }
@article {pmid36972800, year = {2023}, author = {Wood, E and Hein, S and Mesnage, R and Fernandes, F and Abhayaratne, N and Xu, Y and Zhang, Z and Bell, L and Williams, C and Rodriguez-Mateos, A}, title = {Wild Blueberry (Poly)phenols can Improve Vascular Function And Cognitive Performance In Healthy Older Males And Females: A Double-Blind Randomized Controlled Trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2023.03.017}, pmid = {36972800}, issn = {1938-3207}, abstract = {BACKGROUND: Evidence suggests that intake of blueberry (poly)phenols is associated with improvements in vascular function and cognitive performance. Whether these cognitive effects are linked to increases in cerebral and vascular blood flow or changes in the gut microbiota is currently unknown.<br><br>METHODS: A double-blind, parallel randomized controlled trial was conducted in 61 healthy older individuals aged 65-80 y. Participants received either 26g of freeze-dried wild blueberry (WBB) powder (302 mg anthocyanins) or a matched placebo (0 mg anthocyanins). Endothelial function measured by flow-mediated dilation (FMD), cognitive function, arterial stiffness, blood pressure (BP), cerebral blood flow (CBF), gut microbiome and blood parameters were measured at baseline and 12 weeks following daily consumption. Plasma and urinary (poly)phenol metabolites were analyzed using micro-elution solid phase-extraction coupled with LC-MS.<br><br>RESULTS: A significant increase in FMD and reduction in 24 h ambulatory systolic BP were found in the WBB group compared to placebo (0.86%; 95% CI 0.56, 1.17, p<0.001; -3.59 mmHg; 95% CI -6.95, -0.23, p=0.037; respectively). Enhanced immediate recall on the auditory verbal learning task, alongside better accuracy on a task-switch task were also found following WBB treatment compared to placebo (p<0.05). Total 24 h urinary (poly)phenol excretion increased significantly in the WBB group compared to placebo. No changes in CBF or gut microbiota composition were found.<br><br>CONCLUSIONS: Daily intake of WBB powder, equivalent to 178 g fresh weight, improves vascular and cognitive function, and decreases 24h ambulatory systolic BP in healthy older individuals. This suggests that WBB (poly)phenols may reduce future cardiovascular disease (CVD) disease risk in an older population, and may improve episodic memory processes and executive functioning in older adults at risk of cognitive decline. CLINICAL TRIAL REGISTRATION NUMBER IN CLINICALTRIALS.GOV: NCT04084457.}, }
@article {pmid36972797, year = {2023}, author = {Li, Y and Xie, G and Zha, Y and Ning, K}, title = {GAN-GMHI: a generative adversarial network with high discriminative power for microbiome-based disease prediction.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2023.03.009}, pmid = {36972797}, issn = {1673-8527}, }
@article {pmid36972763, year = {2023}, author = {Prentice, RE and Wright, EK and Flanagan, E and Hunt, RW and Moore, GT and Nold-Petry, CA and Bell, SJ and Nold, MF and Goldberg, R}, title = {Review: The effect of in-utero exposure to maternal inflammatory bowel disease and immunomodulators on infant immune system development and function.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2023.03.005}, pmid = {36972763}, issn = {2352-345X}, abstract = {Autoimmune and inflammatory disorders, including inflammatory bowel disease (IBD), commonly affect women of childbearing age, warranting the use of immunomodulatory agents at a time where pregnancy may be desired. In-utero exposure to pro-inflammatory mediators from maternal IBD, IBD-associated intestinal dysbiosis, and immunomodulatory drug use may impact neonatal immune system development during what is considered to be a critical period, with potential long-lasting impacts on susceptibility to disease. Both the innate and adaptative immune systems of the neonatal differ to that of the adult in terms of both cellular composition and sensitivity to antigenic and innate stimulation. The infant immune system gradually develops to more closely resemble that of the adult. Exposure to maternal inflammation in-utero may aberrantly impact this period of infant immune system development, with maternal autoimmune and inflammatory disorders shown to affect the physiologic changes in serum cytokine abundance observed during pregnancy. The maternal and neonatal intestinal microbiome greatly influence infant mucosal and peripheral immune system development, and thereby impact the susceptibility to short term inflammatory diseases, the adequacy of vaccine response and later life risk of atopic and inflammatory disorders. Maternal disease, mode of delivery, method of feeding, time of weaning to include solid foods in the diet and neonatal antibiotic exposure all influence the composition of the infant microbiome, and thereby infant immune system maturation. How exposure to specific immunosuppressive medications in-utero alters infant immune cell phenotype and response to stimulation has been explored, but with existing studies limited by the time at which samples are performed, heterogenicity in methods, and small sample size. Furthermore, the impact of more recently introduced biologic agents have not been explored. Evolving knowledge in this field may influence therapeutic preferences for individuals with IBD planning to conceive, particularly if substantive differences in the risk of infant infection and childhood immune disease are identified.}, }
@article {pmid36972423, year = {2023}, author = {Murali, A and Giri, V and Zickgraf, FM and Ternes, P and Cameron, HJ and Sperber, S and Haake, V and Driemert, P and Kamp, H and Funk-Weyer, D and Sturla, SJ and Rietjens, IMCM and van Ravenzwaay, B}, title = {Connecting Gut Microbial Diversity with Plasma Metabolome and Fecal Bile Acid Changes Induced by the Antibiotics Tobramycin and Colistin Sulfate.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.2c00316}, pmid = {36972423}, issn = {1520-5010}, abstract = {The diversity of microbial species in the gut has a strong influence on health and development of the host. Further, there are indications that the variation in expression of gut bacterial metabolic enzymes is less diverse than the taxonomic profile, underlying the importance of microbiome functionality, particularly from a toxicological perspective. To address these relationships, the gut bacterial composition of Wistar rats was altered by a 28 day oral treatment with the antibiotics tobramycin or colistin sulfate. On the basis of 16S marker gene sequencing data, tobramycin was found to cause a strong reduction in the diversity and relative abundance of the microbiome, whereas colistin sulfate had only a marginal impact. Associated plasma and fecal metabolomes were characterized by targeted mass spectrometry-based profiling. The fecal metabolome of tobramycin-treated animals had a high number of significant alterations in metabolite levels compared to controls, particularly in amino acids, lipids, bile acids (BAs), carbohydrates, and energy metabolites. The accumulation of primary BAs and significant reduction of secondary BAs in the feces indicated that the microbial alterations induced by tobramycin inhibit bacterial deconjugation reactions. The plasma metabolome showed less, but still many alterations in the same metabolite groups, including reductions in indole derivatives and hippuric acid, and furthermore, despite marginal effects of colistin sulfate treatment, there were nonetheless systemic alterations also in BAs. Aside from these treatment-based differences, we also uncovered interindividual differences particularly centering on the loss of Verrucomicrobiaceae in the microbiome, but with no apparent associated metabolite alterations. Finally, by comparing the data set from this study with metabolome alterations in the MetaMapTox database, key metabolite alterations were identified as plasma biomarkers indicative of altered gut microbiomes resulting from a wide activity spectrum of antibiotics.}, }
@article {pmid36971925, year = {2023}, author = {Capuco, A and Urits, I and Hasoon, J and Chun, R and Gerald, B and Wang, JK and Ngo, AL and Simopoulos, T and Kaye, AD and Colontonio, MM and Parker-Actlis, TQ and Fuller, MC and Viswanath, O}, title = {Retraction Note: Gut Microbiome Dysbiosis and Depression: A Comprehensive Review.}, journal = {Current pain and headache reports}, volume = {}, number = {}, pages = {}, pmid = {36971925}, issn = {1534-3081}, }
@article {pmid36971593, year = {2023}, author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ}, title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0073822}, doi = {10.1128/msystems.00738-22}, pmid = {36971593}, issn = {2379-5077}, abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.}, }
@article {pmid36971568, year = {2023}, author = {Amat, S and Timsit, E and Workentine, M and Schwinghamer, T and van der Meer, F and Guo, Y and Alexander, TW}, title = {A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota: a Pilot Study.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0101622}, doi = {10.1128/msystems.01016-22}, pmid = {36971568}, issn = {2379-5077}, abstract = {To address the emergence of antimicrobial-resistant pathogens in livestock, microbiome-based strategies are increasingly being sought to reduce antimicrobial use. Here, we describe the effects of intranasal application of bacterial therapeutics (BTs) on the bovine respiratory microbiota and used structural equation modeling to investigate the causal networks after BT application. Beef cattle received (i) an intranasal cocktail of previously characterized BT strains, (ii) an injection of metaphylactic antimicrobial (tulathromycin), or (iii) intranasal saline. Despite being transient colonizers, inoculated BT strains induced longitudinal modulation of the nasopharyngeal bacterial microbiota while showing no adverse effect on animal health. The BT-mediated changes in bacteria included reduced diversity and richness and strengthened cooperative and competitive interactions. In contrast, tulathromycin increased bacterial diversity and antibiotic resistance and disrupted bacterial interactions. Overall, a single intranasal dose of BTs can modulate the bovine respiratory microbiota, highlighting that microbiome-based strategies have potential in being utilized to mitigate bovine respiratory disease in feedlot cattle. IMPORTANCE Bovine respiratory disease (BRD) remains the most significant health challenge affecting the North American beef cattle industry and results in $3 billion in economic losses yearly. Current BRD control strategies mainly rely on antibiotics, with metaphylaxis commonly employed to mitigate BRD incidence in commercial feedlots. However, the emergence of multidrug-resistant BRD pathogens threatens to reduce the efficacy of antimicrobials. Here, we investigated the potential use of novel bacterial therapeutics (BTs) to modulate the nasopharyngeal microbiota in beef calves, which are commonly administered metaphylactic antibiotics to mitigate BRD when sourced from auction markets. By direct comparison of the BTs with an antibiotic commonly used for BRD metaphylaxis in feedlots, this study conveyed the potential use of the BTs to modulate respiratory microbiome and thereby improve resistance against BRD in feedlot cattle.}, }
@article {pmid36971560, year = {2023}, author = {Enaud, R and Lussac-Sorton, F and Charpentier, E and Velo-Suárez, L and Guiraud, J and Bui, S and Fayon, M and Schaeverbeke, T and Nikolski, M and ,  and Burgel, PR and Héry-Arnaud, G and Delhaes, L}, title = {Effects of Lumacaftor-Ivacaftor on Airway Microbiota-Mycobiota and Inflammation in Patients with Cystic Fibrosis Appear To Be Linked to Pseudomonas aeruginosa Chronic Colonization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0225122}, doi = {10.1128/spectrum.02251-22}, pmid = {36971560}, issn = {2165-0497}, abstract = {Lumacaftor-ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) modulator combination approved for patients with cystic fibrosis (CF) who are homozygous for the F508del allele. This treatment showed significant clinical improvement; however, few studies have addressed the evolution of the airway microbiota-mycobiota and inflammation in patients receiving lumacaftor-ivacaftor treatment. Seventy-five patients with CF aged 12 years or older were enrolled at the initiation of lumacaftor-ivacaftor therapy. Among them, 41 had spontaneously produced sputa collected before and 6 months after treatment initiation. Airway microbiota and mycobiota analyses were performed via high-throughput sequencing. Airway inflammation was assessed by measuring the calprotectin levels in sputum; the microbial biomass was evaluated via quantitative PCR (qPCR). At baseline (n = 75), bacterial alpha-diversity was correlated with pulmonary function. After 6 months of lumacaftor-ivacaftor treatment, a significant improvement in the body mass index and a decreased number of intravenous antibiotic courses were noted. No significant changes in bacterial and fungal alpha- and beta-diversities, pathogen abundances, or calprotectin levels were observed. However, for patients not chronically colonized with Pseudomonas aeruginosa at treatment initiation, calprotectin levels were lower, and a significant increase in bacterial alpha-diversity was observed at 6 months. This study shows that the evolution of the airway microbiota-mycobiota in CF patients depends on the patient's characteristics at lumacaftor-ivacaftor treatment initiation, notably chronic colonization with P. aeruginosa. IMPORTANCE The management of cystic fibrosis has been transformed recently by the advent of CFTR modulators, including lumacaftor-ivacaftor. However, the effects of such therapies on the airway ecosystem, particularly on the microbiota-mycobiota and local inflammation, which are involved in the evolution of pulmonary damage, are unclear. This multicenter study of the evolution of the microbiota under protein therapy supports the notion that CFTR modulators should be started as soon as possible, ideally before the patient is chronically colonized with P. aeruginosa. (This study has been registered at ClinicalTrials.gov under identifier NCT03565692).}, }
@article {pmid36971547, year = {2023}, author = {Etienne-Mesmin, L and Meslier, V and Uriot, O and Fournier, E and Deschamps, C and Denis, S and David, A and Jegou, S and Morabito, C and Quinquis, B and Thirion, F and Plaza Oñate, F and Le Chatelier, E and Ehrlich, SD and Blanquet-Diot, S and Almeida, M}, title = {In Vitro Modelling of Oral Microbial Invasion in the Human Colon.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0434422}, doi = {10.1128/spectrum.04344-22}, pmid = {36971547}, issn = {2165-0497}, abstract = {Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.}, }
@article {pmid36971136, year = {2023}, author = {Cinza-Sanjurjo, S and González-Juanatey, JR}, title = {Role of microbiome in the cardiovascular continuum. Relationship diet-microbiome and cardiovascular risk.}, journal = {European journal of preventive cardiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurjpc/zwad093}, pmid = {36971136}, issn = {2047-4881}, }
@article {pmid36970974, year = {2023}, author = {Horniblow, RD and Pathak, P and Eshrati, M and Latunde-Dada, GO and Tselepis, C}, title = {Intestinal iron bio-accessibility changes by Lignin and the subsequent impact on cell metabolism and intestinal microbiome communities.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d2fo03807b}, pmid = {36970974}, issn = {2042-650X}, abstract = {The detrimental effects of high concentrations of colonic iron have been linked to intestinal inflammation and microbial dysbiosis. Exploiting chelation against this luminal pool of iron may restore intestinal health and have beneficial impacts on microbial communities. This study aimed to explore whether lignin, a heterogenous polyphenolic dietary component, has iron-binding affinity and can sequester iron within the intestine and thus, potentially modulate the microbiome. Within in vitro cell-culture models, the treatment of RKO and Caco-2 cells with lignin almost abolished intracellular iron import (96% and 99% reduction of iron acquisition respectively) with corresponding changes in iron metabolism proteins (ferritin and transferrin receptor-1) and reductions in the labile-iron pool. In a Fe-59 supplemented murine model, intestinal iron absorption was significantly inhibited by 30% when lignin was co-administered compared to the control group with the residual iron lost in the faeces. The supplementation of lignin into a microbial bioreactor colonic model increased the solubilisation and bio-accessibility of iron present by 4.5-fold despite lignin-iron chelation previously restricting intracellular iron absorption in vitro and in vivo. The supplementation of lignin in the model increased the relative abundance of Bacteroides whilst levels of Proteobacteria decreased which could be attributed to the changes in iron bio-accessibility due to iron chelation. In summary, we demonstrate that lignin is an effective luminal iron chelator. Iron chelation leads to the limitation of intracellular iron import whilst, despite increasing iron solubility, favouring the growth of beneficial bacteria.}, }
@article {pmid36970947, year = {2023}, author = {Ermolenko, E and Sitkin, S and Vakhitov, T and Solovyeva, O and Karaseva, A and Morozova, A and Kotyleva, M and Shumikhina, I and Lavrenova, N and Demyanova, E and Dmitriev, A and Suvorov, A}, title = {Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-12}, doi = {10.3920/BM2022.0053}, pmid = {36970947}, issn = {1876-2891}, abstract = {Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.}, }
@article {pmid36970862, year = {2023}, author = {Salekeen, R and Lustgarten, MS and Islam, KMD}, title = {Model organism life extending therapeutics modulate diverse nodes in the drug-gene-microbe tripartite human longevity interactome.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07391102.2023.2192823}, pmid = {36970862}, issn = {1538-0254}, abstract = {Advances in antiaging drug/lead discovery in animal models constitute a large body of literature on novel senotherapeutics and geroprotectives. However, with little direct evidence or mechanism of action in humans-these drugs are utilized as nutraceuticals or repurposed supplements without proper testing directions, appropriate biomarkers, or consistent in-vivo models. In this study, we take previously identified drug candidates that have significant evidence of prolonging lifespan and promoting healthy aging in model organisms, and simulate them in human metabolic interactome networks. Screening for drug-likeness, toxicity, and KEGG network correlation scores, we generated a library of 285 safe and bioavailable compounds. We interrogated this library to present computational modeling-derived estimations of a tripartite interaction map of animal geroprotective compounds in the human molecular interactome extracted from longevity, senescence, and dietary restriction-associated genes. Our findings reflect previous studies in aging-associated metabolic disorders, and predict 25 best-connected drug interactors including Resveratrol, EGCG, Metformin, Trichostatin A, Caffeic Acid and Quercetin as direct modulators of lifespan and healthspan-associated pathways. We further clustered these compounds and the functionally enriched subnetworks therewith to identify longevity-exclusive, senescence-exclusive, pseudo-omniregulators and omniregulators within the set of interactome hub genes. Additionally, serum markers for drug-interactions, and interactions with potentially geroprotective gut microbial species distinguish the current study and present a holistic depiction of optimum gut microbial alteration by candidate drugs. These findings provide a systems level model of animal life-extending therapeutics in human systems, and act as precursors for expediting the ongoing global effort to find effective antiaging pharmacological interventions.Communicated by Ramaswamy H. Sarma.}, }
@article {pmid36970711, year = {2023}, author = {Berard, A and Lajoie, J and Herrera, C}, title = {Editorial: Inflammation in the female genital tract.}, journal = {Frontiers in reproductive health}, volume = {5}, number = {}, pages = {1161839}, pmid = {36970711}, issn = {2673-3153}, }
@article {pmid36970687, year = {2023}, author = {Peng, X and Yao, S and Huang, J and Zhao, Y and Chen, H and Chen, L and Yu, Z}, title = {Alterations in bacterial community dynamics from noncancerous to Gastric cancer.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138928}, pmid = {36970687}, issn = {1664-302X}, abstract = {Gastric microbiome has been shown to contribute to gastric carcinogenesis, understanding how alterations in gastric microbiome is helpful to the prevention and treatment of gastric cancer (GC). However, few studies have focused on the change of microbiome during the gastric carcinogenesis. In this study, the microbiome of gastric juice samples from healthy control (HC), gastric precancerous lesions (GPL) and gastric cancer (GC) was investigated by 16S rRNA gene sequencing. Our results showed that the alpha diversity of patients with GC was significantly lower than other groups. Compared to other groups, some genera in GC group were shown to be up-regulated (e.g., Lautropia and Lactobacillus) and down-regulated (e.g., Peptostreptococcus and Parvimonas). More importantly, the emergence of Lactobacillus was closely related to the occurrence and development of GC. Moreover, the microbial interactions and networks in GPL exhibited higher connectivity, complexity and lower clustering property, while GC showed the opposite trend. Taken together, we suggest that changes in the gastric microbiome are associated with GC and perform a key function in maintaining the tumor microenvironment. Therefore, our findings will provide new ideas and references for the treatment of GC.}, }
@article {pmid36970682, year = {2023}, author = {Cao, R and Zhang, Y and Ju, Y and Wang, W and Zhao, Y and Liu, N and Zhang, G and Wang, X and Xie, X and Dai, C and Liu, Y and Yin, H and Shi, K and He, C and Wang, W and Zhao, L and Jeon, CO and Hao, L}, title = {Exopolysaccharide-producing bacteria enhanced Pb immobilization and influenced the microbiome composition in rhizosphere soil of pakchoi (Brassica chinensis L.).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117312}, pmid = {36970682}, issn = {1664-302X}, abstract = {Lead (Pb) contamination of planting soils is increasingly serious, leading to harmful effects on soil microflora and food safety. Exopolysaccharides (EPSs) are carbohydrate polymers produced and secreted by microorganisms, which are efficient biosorbent materials and has been widely used in wastewater treatment to remove heavy metals. However, the effects and underlying mechanism of EPS-producing marine bacteria on soil metal immobilization, plant growth and health remain unclear. The potential of Pseudoalteromonas agarivorans Hao 2018, a high EPS-producing marine bacterium, to produce EPS in soil filtrate, immobilize Pb, and inhibit its uptake by pakchoi (Brassica chinensis L.) was studied in this work. The effects of strain Hao 2018 on the biomass, quality, and rhizospheric soil bacterial community of pakchoi in Pb-contaminated soil were further investigated. The results showed that Hao 2018 reduced the Pb concentration in soil filtrate (16%-75%), and its EPS production increased in the presence of Pb[2+]. When compared to the control, Hao 2018 remarkably enhanced pakchoi biomass (10.3%-14.3%), decreased Pb content in edible tissues (14.5%-39.2%) and roots (41.3%-41.9%), and reduced the available Pb content (34.8%-38.1%) in the Pb-contaminated soil. Inoculation with Hao 2018 raised the pH of the soil, the activity of several enzymes (alkaline phosphatase, urease, and dehydrogenase), the nitrogen content (NH4 [+]-N and NO3 [-]-N), and the pakchoi quality (Vc and soluble protein content), while also raising the relative abundance of bacteria that promote plant growth and immobilize metals, such as Streptomyces and Sphingomonas. In conclusion, Hao 2018 reduced the available Pb in soil and pakchoi Pb absorption by increasing the pH and activity of multiple enzymes and regulating microbiome composition in rhizospheric soil.}, }
@article {pmid36970673, year = {2023}, author = {He, S and Zhao, C and Guo, Y and Zhao, J and Xu, X and Hu, Y and Lian, B and Ye, H and Wang, N and Luo, L and Liu, Q}, title = {Alterations in the gut microbiome and metabolome profiles of septic mice treated with Shen FuHuang formula.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111962}, pmid = {36970673}, issn = {1664-302X}, abstract = {Sepsis has a high mortality rate, and treating sepsis remains a significant challenge worldwide. In former studies, our group found that traditional Chinese medicine, Shen FuHuang formula (SFH), is a promising medicine in treating coronavirus disease 2019 (COVID-19) patients with the septic syndrome. However, the underlying mechanisms remain elusive. In the present study, we first investigated the therapeutic effects of SFH on septic mice. To investigate the mechanisms of SFH-treated sepsis, we identified the gut microbiome profile and exploited untargeted metabolomics analyses. The results demonstrated that SFH significantly enhanced the mice's 7-day survival rate and hindered the release of inflammatory mediators, i.e., TNF-α, IL-6, and IL-1β. 16S rDNA sequencing further deciphered that SFH decreased the proportion of Campylobacterota and Proteobacteria at the phylum level. LEfSe analysis revealed that the treatment of SFH enriched Blautia while decreased Escherichia_Shigella. Furthermore, serum untargeted metabolomics analysis indicated that SFH could regulate the glucagon signaling pathway, PPAR signaling pathway, galactose metabolism, and pyrimidine metabolism. Finally, we found the relative abundance of Bacteroides, Lachnospiraceae_NK4A136_group, Escherichia_Shigella, Blautia, Ruminococcus, and Prevotella were closely related to the enrichment of the metabolic signaling pathways, including L-tryptophan, uracil, glucuronic acid, protocatechuic acid, and gamma-Glutamylcysteine. In conclusion, our study demonstrated that SFH alleviated sepsis by suppressing the inflammatory response and hence reduced mortality. The mechanism of SFH for treating sepsis may be ascribed to the enrichment of beneficial gut flora and modulation in glucagon signaling pathway, PPAR signaling pathway, galactose metabolism, and pyrimidine metabolism. To sum up, these findings provide a new scientific perspective for the clinical application of SFH in treating sepsis.}, }
@article {pmid36970665, year = {2023}, author = {Gong, R and Song, S and Ai, Y and Wang, S and Dong, X and Ren, Z and Xie, H and Jiang, B and Zhao, L}, title = {Exploring the growing forest musk deer (Moschus berezovskii) dietary protein requirement based on gut microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1124163}, pmid = {36970665}, issn = {1664-302X}, abstract = {It is necessary to assess the appropriate dietary protein level of the forest musk deer (FMD), as nutritional needs are unclear. The microbiome in gastrointestinal tracts plays an important role in regulating nutrient utilization, absorption and host growth or development. Thus, we aimed to evaluate growth performance, nutrient digestibility and fecal microbiome of growing FMD supplied with different protein levels of diets. Eighteen 6-month-old male FMD with an initial weight 5.0 ± 0.2 kg were used in a 62-day trial. The animals were randomly distributed to three groups, the dietary crude protein (CP) level was 11.51% (L), 13.37% (M), and 15.48% (H). The results showed that the CP digestibility decreased as dietary CP level increased (p < 0.01). Compared with group L and H, FMD in M group has higher average daily gain, feed efficiency and neutral detergent fiber digestibility. For the fecal bacterial community, the percentage of Firmicutes was increased, Bacteroidetes was decreased and the diversity of microbiota significantly reduced (p < 0.05) with the increasing of dietary protein. The proportion of Ruminococcaceae_005, Ruminococcaceae_UCG-014 and uncultured_bacterium_f_Lachnospiraceae were significantly increased wtih rising CP, the proportions of Bacteroides and Rikenellaceae_RC9_gut_group were significantly decrease nevertheless at the genus level. The higher abundance of f_Prevotellaceae and g_Prevotellaceae_UCG_004 were found at M group by LEfSe analysis. The relative abundance of uncultured_bacterium_f_Ruminococcaceae was positively correlated with the average daily gain and feed conversion ratio (p < 0.05), whereas Family_XIII_AD3011_group was negatively correlated with feed conversion ratio (p < 0.05). The UPGMA tree showed L and M groups were closer in clustering relationship, while H group was clustered separately into a branch, which indicated that the bacterial structure had changed greatly with protein level increased from 13.37 to 15.48%. Overall, our results indicated that the optimum dietary CP for the growing FMD was 13.37%.}, }
@article {pmid36970663, year = {2023}, author = {Zhong, X and Zhao, Y and Huang, L and Liu, J and Wang, K and Gao, X and Zhao, X and Wang, X}, title = {Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140498}, pmid = {36970663}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbial community, which can be disturbed or repaired by changes in the internal environment, contributes to the development of acute myocardial infarction (AMI). Gut probiotics play a role in microbiome remodeling and nutritional intervention post-AMI. A newly isolated Lactobacillus johnsonii strain EU03 has shown potential as a probiotic. Here, we investigated the cardioprotective function and mechanism of L. johnsonii through gut microbiome remodeling in AMI rats.<br><br>METHODS: A rat model of left anterior descending coronary artery ligation (LAD)-mediated AMI was assessed with echocardiography, histology, and serum cardiac biomarkers to evaluate the beneficial effects of L. johnsonii. The immunofluorescence analysis was utilized to visualize the intestinal barrier changes. Antibiotic administration model was used for assessing the gut commensals' function in the improvement of cardiac function post-AMI. The underlying beneficial mechanism through L. johnsonii enrichment was further investigated by metagenomics and metabolomics analysis.<br><br>RESULTS: A 28-day treatment with L. johnsonii protected cardiac function, delayed cardiac pathology, suppressed myocardial injury cytokines, and improved gut barrier integrity. The microbiome composition was reprogrammed by enhancing the abundance of L. johnsonii. Microbiome dysbiosis by antibiotics abrogated the improvement of cardiac function post-AMI by L. johnsonii. L. johnsonii enrichment caused remodeling of gut microbiome by increasing the abundance of Muribaculaceae, Lactobacillus, and decreasing Romboutsia, Clostridia UCG-014, which were correlated with cardiac traits and serum metabolic biomarkers 16,16-dimethyl-PGA2, and Lithocholate 3-O-glucuronide.<br><br>CONCLUSION: These findings reveal that gut microbiome remodeling by L. johnsonii ameliorates the cardiac function post-AMI and might advance microbiome-targeted nutritional intervention.Graphical Abstract.}, }
@article {pmid36970590, year = {2023}, author = {Dan, WY and Yang, YS and Peng, LH and Sun, G and Wang, ZK}, title = {Gastrointestinal microbiome and cholelithiasis: Current status and perspectives.}, journal = {World journal of gastroenterology}, volume = {29}, number = {10}, pages = {1589-1601}, pmid = {36970590}, issn = {2219-2840}, abstract = {Cholelithiasis is a common digestive disease affecting 10% to 15% of adults. It imposes significant global health and financial burdens. However, the pathogenesis of cholelithiasis involves several factors and is incompletely elucidated. In addition to genetic predisposition and hepatic hypersecretion, the pathogenesis of cholelithiasis might involve the gastrointestinal (GI) microbiome, consisting of microorganisms and their metabolites. High-throughput sequencing studies have elucidated the role of bile, gallstones, and the fecal microbiome in cholelithiasis, associating microbiota dysbiosis with gallstone formation. The GI microbiome may drive cholelithogenesis by regulating bile acid metabolism and related signaling pathways. This review examines the literature implicating the GI microbiome in cholelithiasis, specifically gallbladder stones, choledocholithiasis, and asymptomatic gallstones. We also discuss alterations of the GI microbiome and its influence on cholelithogenesis.}, }
@article {pmid36970461, year = {2023}, author = {Cui, X and Guo, Y and Liu, Q}, title = {Qingfei Jiedu Granules fight influenza by regulating inflammation, immunity, metabolism, and gut microbiota.}, journal = {Journal of traditional and complementary medicine}, volume = {13}, number = {2}, pages = {170-182}, pmid = {36970461}, issn = {2225-4110}, abstract = {BACKGROUND AND AIM: Qingfei Jiedu Granules (QFJD) are a new Traditional Chinese Medicine (TCM) which has been clinically used against coronavirus pneumonia in China. In this study, the therapeutic effect and the underlying mechanisms of QFJD against influenza were investigated.<br><br>EXPERIMENTAL PROCEDURE: Pneumonia mice were induced by influenza A virus. Survival rate, weight loss, lung index and lung pathology were measured to evaluate the therapeutic effect of QFJD. The expression of inflammatory factors and lymphocytes was used to assess anti-inflammatory and immunomodulatory effect of QFJD. Gut microbiome analysis was performed to decipher the potential effect of QFJD on intestinal microbiota. Metabolomics approach was conducted to explore the overall metabolic regulation of QFJD.<br><br>RESULT AND CONCLUSION: QFJD shows a significant therapeutic effect on the treatment of influenza and the expression of many pro-inflammatory cytokines were obviously inhibited. QFJD also markedly modulates the level of T and B lymphocytes. The high-dose QFJD has shown similar therapeutic efficiency compared to positive drugs. QFJD profoundly enriched Verrucomicrobia and maintained the balance between Bacteroides and Firmicutes. QFJD associated with 12 signaling pathways in metabolomics study, 9 of which were the same as the model group and were closely related to citrate cycle and amino acid metabolism.To sum up, QFJD is a novel and promising drug against influenza. It can regulate inflammation, immunity, metabolism, and gut microbiota to fight influenza. Verrucomicrobia shows great potential to improve influenza infection and may be an important target.}, }
@article {pmid36970454, year = {2023}, author = {Kwandee, P and Somnuk, S and Wanikorn, B and Nakphaichit, M and Tunsagool, P}, title = {Efficacy of Triphala extracts on the changes of obese fecal microbiome and metabolome in the human gut model.}, journal = {Journal of traditional and complementary medicine}, volume = {13}, number = {2}, pages = {207-217}, pmid = {36970454}, issn = {2225-4110}, abstract = {Triphala is a mixture of tree fruits obtained from Terminalia chebula, Terminalia bellerica, and Phyllanthus emblica. It is one of the Ayurveda medicinal recipes used to treat health diseases such as obesity. The chemical composition analysis of Triphala extracts obtained from an equal portion of three fruits was performed. The contents of total phenolic compounds (62.87 ± 0.21 mg gallic acid equivalent/mL), total flavonoids (0.24 ± 0.01 mg catechin equivalent/mL), hydrolyzable tannins (177.27 ± 10.09 mg gallotannin equivalent/mL), and condensed tannins (0.62 ± 0.11 mg catechin equivalent/mL) were observed in Triphala extracts. The 1 mg/mL of Triphala extracts was applied to batch culture fermentation which contained the feces from voluntarily obese female adults (body mass index of 35.0-40.0 kg/m[2]) for 24 h. The extraction of DNA and metabolites was each conducted on the samples obtained from batch culture fermentation within and without Triphala extracts treatment. The 16S rRNA gene sequencing and untargeted metabolomic analysis were carried out. There was no statistically significant difference between Triphala extracts and control treatments on the changes in microbial profiles (p-value <0.05). While the metabolomic analysis showed statistically significant differences of 305 up-regulated and 23 down-regulated metabolites in the treatment of Triphala extracts when compared with the control (p-value <0.05 and fold-change ≥2) belonging to 60 pathways. The pathway analysis revealed that Triphala extracts play an important role in the activation of phenylalanine, tyrosine and tryptophan biosynthesis. In this study, phenylalanine and tyrosine were identified metabolites which involve in the regulation of energy metabolism. The treatment of Triphala extracts possesses the induction of phenylalanine, tyrosine and tryptophan biosynthesis in fecal batch culture fermentation of obese adults and therefore it can be suggested as a probable herbal medicinal recipe for obesity treatment.}, }
@article {pmid36970450, year = {2023}, author = {Tanelian, A and Nankova, B and Cheriyan, A and Arens, C and Hu, F and Sabban, EL}, title = {Differences in gut microbiota associated with stress resilience and susceptibility to single prolonged stress in female rodents.}, journal = {Neurobiology of stress}, volume = {24}, number = {}, pages = {100533}, pmid = {36970450}, issn = {2352-2895}, abstract = {Exposure to traumatic stress is a major risk factor for the development of neuropsychiatric disorders in a subpopulation of individuals, whereas others remain resilient. The determinants of resilience and susceptibility remain unclear. Here, we aimed to characterize the microbial, immunological, and molecular differences between stress-susceptible and stress-resilient female rats before and after exposure to a traumatic experience. Animals were randomly divided into unstressed controls (n = 10) and experimental groups (n = 16) exposed to Single Prolonged Stress (SPS), an animal model of PTSD. Fourteen days later, all rats underwent a battery of behavioral tests and were sacrificed the following day to collect different organs. Stool samples were collected before and after SPS. Behavioral analyses revealed divergent responses to SPS. The SPS treated animals were further subdivided into SPS-resilient (SPS-R) and SPS-susceptible (SPS-S) subgroups. Comparative analysis of fecal 16S sequencing before and after SPS exposure indicated significant differences in the gut microbial composition, functionality, and metabolites of the SPS-R and SPS-S subgroups. In line with the observed distinct behavioral phenotypes, the SPS-S subgroup displayed higher blood-brain barrier permeability and neuroinflammation relative to the SPS-R and/or controls. These results indicate, for the first time, pre-existing and trauma-induced differences in the gut microbial composition and functionality of female rats that relate to their ability to cope with traumatic stress. Further characterization of these factors will be crucial for understanding susceptibility and fostering resilience, especially in females, who are more likely than males to develop mood disorders.}, }
@article {pmid36970332, year = {2023}, author = {Cui, X and Su, Y and Huang, X and Chen, J and Ma, J and Liao, P and He, X}, title = {Combined analysis of plasma metabolome and intestinal microbiome sequencing to explore jiashen prescription and its potential role in changing intestine-heart axis and effect on chronic heart failure.}, journal = {Frontiers in cardiovascular medicine}, volume = {10}, number = {}, pages = {1147438}, pmid = {36970332}, issn = {2297-055X}, abstract = {BACKGROUND: Heart failure (HF) is a syndrome with global clinical and socioeconomic burden worldwide owing to its poor prognosis. Jiashen Prescription (JSP), a traditional Chinese medicine (TCM) formula, exhibits unambiguous effects on treating HF. Previously, we have reported that underlying mechanisms of JSP by an untargeted metabolomics approach, but the contribution of gut microbiota and metabolic interaction to the cardioprotective efficacy of JSP remains to be elucidated.<br><br>MATERIALS AND METHODS: Firstly, the rat model of heart failure was established by the permanent ligation of the left anterior descending coronary artery. The efficacy evaluation of JSP in treating HF rats was per-formed by left ventricular ejection fraction (LVEF). Then, 16S rRNA gene sequencing and LC/MS-based metabolomic analysis were utilized to explore the characteristics of cecal-contents microecology and plasma metabolic profile, respectively. After that, the correlation between intestinal micro-ecological characteristics and plasma metabolic characteristics was analyzed to explore the potential mechanism of the JSP treatment in HF.<br><br>RESULTS: JSP could improve the cardiac function of heart failure rats and thus ameliorate heart failure via enhancing rat LVEF. Results of intestinal flora analysis revealed that JSP not only adjusted gut microbiota disturbances by enriching species diversity, reducing the abundance of pathogenic bacteria (such as Allobaculum, Brevinema), as well as increasing the abundance of beneficial bacteria (such as Lactobacillus, Lachnospiraceae_NK4A136_group), but also improved metabolic disorders by reversing metabolite plasma levels to normality. Through the conjoint analysis of 8 metabolites and the OTUs relative abundance data in the 16srRNA sequencing results by WGCNA method, 215 floras significantly related to the eight compounds were identified. The results of the correlation analysis demonstrated a significant association between intestinal microbiota and plasma metabolic profile, especially the significant correlation of Ruminococcaceae_UCG-014 and Protoporphyrin IX, Ruminococcaceae_UCG-005, Christensenellaceae_R-7_group and nicotinamide, dihydrofolic acid.<br><br>CONCLUSION: The present study illustrated the underlying mechanism of JSP to treat heart failure by affecting intestinal flora and plasma metabolites, provide a potential therapeutic strategy against heart failure.}, }
@article {pmid36970136, year = {2023}, author = {Munley, JA and Nagpal, R and Hanson, NC and Mirzaie, A and Laquian, L and Mohr, AM and Efron, PA and Arnaoutakis, DJ and Cooper, MA}, title = {Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization.}, journal = {Journal of vascular surgery cases and innovative techniques}, volume = {9}, number = {2}, pages = {101084}, pmid = {36970136}, issn = {2468-4287}, abstract = {OBJECTIVE: Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period.<br><br>METHODS: We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14&#xa0;days after surgery, and postoperatively at the clinic at >30&#xa0;days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P&#xa0;< .05 was considered statistically significant.<br><br>RESULTS: Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71&#xa0;years). Nine healthy controls were also analyzed (78% men; average age, 55&#xa0;years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P&#xa0;= .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P&#xa0;= .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period.<br><br>CONCLUSIONS: The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.}, }
@article {pmid36970065, year = {2023}, author = {Bloodworth, JC and Hoji, A and Wolff, G and Mandal, RK and Schmidt, NW and Deshane, JS and Morrow, CD and Kloepfer, KM and Cook-Mills, JM}, title = {Dysbiotic lung microbial communities of neonates from allergic mothers confer neonate responsiveness to suboptimal allergen.}, journal = {Frontiers in allergy}, volume = {4}, number = {}, pages = {1135412}, pmid = {36970065}, issn = {2673-6101}, abstract = {In humans and animals, offspring of allergic mothers have increased responsiveness to allergens. This is blocked in mice by maternal supplementation with α-tocopherol (αT). Also, adults and children with allergic asthma have airway microbiome dysbiosis with increased Proteobacteria and may have decreased Bacteroidota. It is not known whether αT alters neonate development of lung microbiome dysbiosis or whether neonate lung dysbiosis modifies development of allergy. To address this, the bronchoalveolar lavage was analyzed by 16S rRNA gene analysis (bacterial microbiome) from pups of allergic and non-allergic mothers with a basal diet or αT-supplemented diet. Before and after allergen challenge, pups of allergic mothers had dysbiosis in lung microbial composition with increased Proteobacteria and decreased Bacteroidota and this was blocked by αT supplementation. We determined whether intratracheal transfer of pup lung dysbiotic microbial communities modifies the development of allergy in recipient pups early in life. Interestingly, transfer of dysbiotic lung microbial communities from neonates of allergic mothers to neonates of non-allergic mothers was sufficient to confer responsiveness to allergen in the recipient pups. In contrast, neonates of allergic mothers were not protected from development of allergy by transfer of donor lung microbial communities from either neonates of non-allergic mothers or neonates of αT-supplemented allergic mothers. These data suggest that the dysbiotic lung microbiota is dominant and sufficient for enhanced neonate responsiveness to allergen. Importantly, infants within the INHANCE cohort with an anti-inflammatory profile of tocopherol isoforms had an altered microbiome composition compared to infants with a pro-inflammatory profile of tocopherol isoforms. These data may inform design of future studies for approaches in the prevention or intervention in asthma and allergic disease early in life.}, }
@article {pmid36969858, year = {2023}, author = {Liu, X and Dun, M and Jian, T and Sun, Y and Wang, M and Zhang, G and Ling, J}, title = {Cordyceps militaris extracts and cordycepin ameliorate type 2 diabetes mellitus by modulating the gut microbiota and metabolites.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1134429}, pmid = {36969858}, issn = {1663-9812}, abstract = {Introduction: Cordyceps militaris, which has many potential medicinal properties, has rarely been reported to alleviate type 2 diabetes mellitus (T2DM). Methods: The effects of C. militaris extracts (CE) and cordycepin (CCS) on high-fat diet and streptozotocin (STZ) induced T2DM mice were analysed by gut microbiome and metabolomics methods in this study. Results: The results demonstrated that glucose and lipid metabolism parameters, oxidative stress biomarkers and inflammation cytokines were down-regulated in the CCS and CE groups. A comparative analysis of the fecal samples from mice in the model and experimental groups showed that experimental groups resulted in a higher abundance of Firmicutes/Bacteroidetes. Conclusion: This study provides evidence that C. militaris can be used as a food supplement to relieve T2DM, which provides a promising prospect for new functional food in it.}, }
@article {pmid36969828, year = {2023}, author = {Zhou, X and Ma, L and Dong, L and Li, D and Chen, F and Hu, X}, title = {Bamboo shoot dietary fiber alleviates gut microbiota dysbiosis and modulates liver fatty acid metabolism in mice with high-fat diet-induced obesity.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1161698}, pmid = {36969828}, issn = {2296-861X}, abstract = {INTRODUCTION: Obesity is a common nutritional disorder characterized by an excessive fat accumulation. In view of the critical role of gut microbiota in the development of obesity and metabolic diseases, novel dietary therapies have been developed to manage obesity by targeting the gut microbiome. In this study, we investigated anti-obesity effects of bamboo shoot dietary fiber (BSDF) and the potential mechanisms.<br><br>METHODS: After 12 weeks of intervention with BSDF in high-fat mice, we detected obesity-related phenotypic indicators, and made transcriptomic analysis of liver tissue. Then we analyzed the changes of gut microbiota using 16S rRNA gene sequencing, explored the effect of BSDF on gut microbiota metabolites, and finally verified the importance of gut microbiota through antibiotic animal model.<br><br>RESULTS AND DISCUSSION: We found that BSDF was effective in reducing lipid accumulation in liver and adipose tissue and alleviating dyslipidemia and insulin resistance. Liver transcriptome analysis results showed that BSDF could improve lipid metabolism and liver injury by modulating peroxisome proliferator-activated receptor (PPAR) and fatty acid metabolic pathways. The 16S rRNA gene sequencing analysis of gut microbiota composition showed that BSDF significantly enriched beneficial bacteria such as Bifidobacterium, Akkermansia, Dubosiella, and Alloprevotella. Analysis of fecal metabolomics and gut microbiota metabolites revealed that BSDF increased the levels of several short-chain fatty acids and enriched bile acids, which may be important for improving lipid metabolism. Notably, the obesity-related metabolic disorders were abrogated after the abrogation of gut microbiota, suggesting that gut microbiota is a key factor in the beneficial effects of BSDF.<br><br>CONCLUSION: Our study suggests that BSDF as a prebiotic supplement has the potential to improve obesity by improving gut microbiota and modulating host PPAR and fatty acid metabolic pathways.}, }
@article {pmid36969811, year = {2023}, author = {Chichlowski, M and van Diepen, JA and Prodan, A and Olga, L and Ong, KK and Kortman, GAM and Dunger, DB and Gross, G}, title = {Early development of infant gut microbiota in relation to breastfeeding and human milk oligosaccharides.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1003032}, pmid = {36969811}, issn = {2296-861X}, abstract = {BACKGROUND: Infant gut microbiota composition is influenced by various factors early in life. Here, we investigate associations between infant gut microbiome development, infant age, breastfeeding duration, and human milk oligosaccharides (HMO) composition in breastmilk.<br><br>METHODS: A total of 94 mother-infant pairs were recruited as part of the Cambridge Baby Growth and Breastfeeding Study (CBGS-BF) (Cambridge, UK). Infant stool samples (n = 337) were collected at 2 week, 6 week, 3 month, and 6 month of age. The 16S rRNA V3-V4 rRNA region was sequenced using MiSeq Illumina to determine microbiota composition and diversity. Mother's hindmilk samples were collected at birth, 2 week, 6 week, 3 month, and 6 month postpartum. Concentrations of five neutral [2'FL, 3'FL, lacto-N-fucopentaose 1 (LNFP1), LNnT, LNT] and two acidic (3'SL, and 6'SL) HMOs were measured in all milk samples using High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD). We explored the associations between infant gut microbiome parameters and age, duration of exclusive breastfeeding (EBF), and levels of individual HMOs.<br><br>RESULTS: Bifidobacterium was the most abundant genus in infant stool at all-time points, irrespective of breastfeeding duration, with an overall mean relative abundance of 70%. The relative abundance of B. bifidum in stool from infants who were breastfed for longer than 6 months was significantly higher compared to the infant breastfed up to 3 months (p = 0.0285). Alpha-diversity (both Shannon and ASV-level Richness) of infant gut microbiota showed a biphasic change with infant age, decreasing from 2 weeks until 3 months and then increasing until 6 months of age. Bifidobacterium relative abundance was associated with higher concentrations of 2'FL and LNFP1 in breastmilk across all time-points (p = 0.049 and 0.017, respectively), with trends toward a higher abundance of B. longum species. No significant association with Bifidobacterium was found for breastmilk LNnT, 3'SL, and 6'SL levels.<br><br>CONCLUSION: Our study is in line with previous data demonstrating that EBF duration in the first months of life impacts infant gut microbiota composition. The observed links between specific HMOs in breastmilk and bacteria in infant stool provide evidence of how mother's milk affects infant microbiome development.}, }
@article {pmid36969810, year = {2023}, author = {Abdolmaleky, HM and Sheng, Y and Zhou, JR}, title = {Bioactive nutraceuticals oligo-lactic acid and fermented soy extract alleviate cognitive decline in mice in part via anti-neuroinflammation and modulation of gut microbiota.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1116278}, pmid = {36969810}, issn = {2296-861X}, abstract = {INTRODUCTION: Cognition decline is associated with aging and certain diseases, such as neurodegenerative or neuropsychiatric disorders, diabetes and chronic kidney disease. Inflammation/neuroinflammation is considered an important causal factor, and experimental evidence suggests that anti-inflammatory natural compounds may effectively prevent cognitive decline. The goal of this study was to evaluate the effects of two natural bioactive agents, oligo-lactic acid (LAP) and fermented soy extract (ImmunBalance, IMB), on cognition in an adenine-induced cognitive impairment mouse model and to investigate the modulation of related biomarkers.<br><br>METHODS: Male C57 black mice were randomly assigned into the following experimental groups and received the corresponding treatments for 2 weeks before the use of adenine for model development: (1) negative control; (2) model control: injection of adenine at 50&#x2009;mg/kg daily for 4 weeks; (3, 4) IMB groups: adenine injection and IMB oral gavage at 250 and 1,000&#x2009;mg/kg BW, respectively; and (5) LAP group: adenine injection and LAP oral gavage at 1,000&#x2009;mg/kg BW. One week after the model was developed, mice were evaluated for cognitive performances by using Y maze test, novel object recognition test, open field test, and Barnes maze tests. At the end of the experiment, brain tissues and cecum fecal samples were collected for analysis of gene expression and gut microbiota.<br><br>RESULTS: Mice treated with LAP or IMB had significantly improved spatial working memory, spatial recognition memory (LAP only), novel object recognition, and spatial learning and memory, compared with those in the model group. Gene expression analysis showed that, among a panel of cognition related genes, six of them (ELOVL2, GLUT4, Nestein, SNCA, TGFB1, and TGFB2) were significantly altered in the model group. LAP treatment significantly reversed expression levels of inflammatory/neuroinflammatory genes (SNCA, TGFB1), and IMB significantly reversed expression levels of genes related to inflammation/neuroinflammation, neurogenesis, and energy metabolism (ELOVL2, GLUT4, Nestin, TGFB1, and TGFB2). The altered microbiome was attenuated only by IMB.<br><br>DISCUSSION: In conclusion, our data showed that LAP improved cognition associated with regulating biomarkers related to neuroinflammation and energy metabolism, whereas IMB improved cognition associated with regulating biomarkers related to neuroinflammation, energy metabolism, and neurogenesis, and modulating gut microbiota. Our results suggest that LAP and IMB may improve cognitive performance in mice via distinct mechanisms of action.}, }
@article {pmid36969543, year = {2023}, author = {Parr McQueen, J and Gattoni, K and Gendron, EMS and Schmidt, SK and Sommers, P and Porazinska, DL}, title = {External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment.}, journal = {Journal of nematology}, volume = {55}, number = {1}, pages = {20230004}, pmid = {36969543}, issn = {0022-300X}, abstract = {Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.}, }
@article {pmid36969243, year = {2023}, author = {Ancona, G and Alagna, L and Alteri, C and Palomba, E and Tonizzo, A and Pastena, A and Muscatello, A and Gori, A and Bandera, A}, title = {Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1080043}, pmid = {36969243}, issn = {1664-3224}, abstract = {The gut microbiota plays a crucial role in human health and disease. Gut dysbiosis is known to be associated with increased susceptibility to respiratory diseases and modifications in the immune response and homeostasis of the lungs (the so-called gut-lung axis). Furthermore, recent studies have highlighted the possible role of dysbiosis in neurological disturbances, introducing the notion of the "gut-brain axis." During the last 2 years, several studies have described the presence of gut dysbiosis during coronavirus disease 2019 (COVID-19) and its relationship with disease severity, SARS-CoV-2 gastrointestinal replication, and immune inflammation. Moreover, the possible persistence of gut dysbiosis after disease resolution may be linked to long-COVID syndrome and particularly to its neurological manifestations. We reviewed recent evidence on the association between dysbiosis and COVID-19, investigating the possible epidemiologic confounding factors like age, location, sex, sample size, the severity of disease, comorbidities, therapy, and vaccination status on gut and airway microbial dysbiosis in selected studies on both COVID-19 and long-COVID. Moreover, we analyzed the confounding factors strictly related to microbiota, specifically diet investigation and previous use of antibiotics/probiotics, and the methodology used to study the microbiota (α- and β-diversity parameters and relative abundance tools). Of note, only a few studies focused on longitudinal analyses, especially for long-term observation in long-COVID. Lastly, there is a lack of knowledge regarding the role of microbiota transplantation and other therapeutic approaches and their possible impact on disease progression and severity. Preliminary data seem to suggest that gut and airway dysbiosis might play a role in COVID-19 and in long-COVID neurological symptoms. Indeed, the development and interpretation of these data could have important implications for future preventive and therapeutic strategies.}, }
@article {pmid36969224, year = {2023}, author = {Ma, Y and Kerkar, N}, title = {Editorial: The association between HLA genes and autoimmune liver diseases.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1175342}, doi = {10.3389/fimmu.2023.1175342}, pmid = {36969224}, issn = {1664-3224}, }
@article {pmid36969214, year = {2023}, author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X}, title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1117726}, pmid = {36969214}, issn = {1664-3224}, abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.<br><br>MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.<br><br>RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.<br><br>CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.}, }
@article {pmid36969207, year = {2023}, author = {Chancharoenthana, W and Kamolratanakul, S and Visitchanakun, P and Sontidejkul, S and Cheibchalard, T and Somboonna, N and Settachaimongkon, S and Leelahavanichkul, A}, title = {Lacticaseibacilli attenuated fecal dysbiosis and metabolome changes in Candida-administered bilateral nephrectomy mice.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1131447}, pmid = {36969207}, issn = {1664-3224}, abstract = {The impacts of metabolomic changes (reduced short-chain-fatty acids; SCFAs) in uremic condition is not fully understood. Once daily Candida gavage with or without probiotics (different times of administration) for 1 week prior to bilateral nephrectomy (Bil Nep) in 8-week-old C57BL6 mice as the possible models more resemble human conditions were performed. Candida-administered Bil Nep mice demonstrated more severe conditions than Bil Nep alone as indicated by mortality (n = 10/group) and other 48 h parameters (n = 6-8/group), including serum cytokines, leaky gut (FITC-dextran assay, endotoxemia, serum beta-glucan, and loss of Zona-occludens-1), and dysbiosis (increased Enterobacteriaceae with decreased diversity in microbiome analysis) (n = 3/group for fecal microbiome) without the difference in uremia (serum creatinine). With nuclear magnetic resonance metabolome analysis (n = 3-5/group), Bil Nep reduced fecal butyric (and propionic) acid and blood 3-hydroxy butyrate compared with sham and Candida-Bil Nep altered metabolomic patterns compared with Bil Nep alone. Then, Lacticaseibacillus rhamnosus dfa1 (SCFA-producing Lacticaseibacilli) (n = 8/group) attenuated the model severity (mortality, leaky gut, serum cytokines, and increased fecal butyrate) of Bil Nep mice (n = 6/group) (regardless of Candida). In enterocytes (Caco-2 cells), butyrate attenuated injury induced by indoxyl sulfate (a gut-derived uremic toxin) as indicated by transepithelial electrical resistance, supernatant IL-8, NFκB expression, and cell energy status (mitochondria and glycolysis activities by extracellular flux analysis). In conclusion, the reduced butyrate by uremia was not enhanced by Candida administration; however, the presence of Candida in the gut induced a leaky gut that was attenuated by SCFA-producing probiotics. Our data support the use of probiotics in uremia.}, }
@article {pmid36969184, year = {2023}, author = {Wang, C and Yu, X and Lin, H and Wang, G and Liu, J and Gao, C and Qi, M and Wang, D and Wang, F}, title = {Integrating microbiome and metabolome revealed microbe-metabolism interactions in the stomach of patients with different severity of peptic ulcer disease.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1134369}, pmid = {36969184}, issn = {1664-3224}, abstract = {BACKGROUND: Peptic ulcer disease (PUD) is a multi-cause illness with an unknown role for gastric flora and metabolism in its pathogenesis. In order to further understand the pathogenesis of gastric flora and metabolism in PUD, this study used histological techniques to analyze the microbiome and metabolome of gastric biopsy tissue. In this paper, our work described the complex interactions of phenotype-microbial-metabolite-metabolic pathways in PUD patients at different pathological stages.<br><br>METHODS: Gastric biopsy tissue samples from 32 patients with chronic non-atrophic gastritis, 24 patients with mucosal erosions, and 8 patients with ulcers were collected for the microbiome. UPLC-MS metabolomics was also used to detect gastric tissue samples. These datasets were analyzed individually and integrated using various bioinformatics methods.<br><br>RESULTS: Our work found reduced diversity of gastric flora in patients with PUD. PUD patients at different pathological stages presented their own unique flora, and there were significant differences in flora phenotypes. Coprococcus_2, Phenylobacterium, Candidatus_Hepatoplasma, and other bacteria were found in the flora of people with chronic non-atrophic gastritis (HC). The representative flora of mucosal erosion (ME) had uncultured_bacterium_c_Subgroup_6, Sphingomonadaceae, Xanthobacteraceae, and uncultured_bacterium_f_Xanthobacteraceae. In comparison, the characteristic flora of the PUD group was the most numerous and complex, including Ruminococcus_2, Agathobacter, Alistipes, Helicobacter, Bacteroides and Faecalibacterium. Metabolomics identified and annotated 66 differential metabolites and 12 significantly different metabolic pathways. The comprehensive analysis correlated microorganisms with metabolites at different pathological stages and initially explored the complex interactions of phenotype-microbial-metabolite-metabolic pathways in PUD patients at different pathological stages.<br><br>CONCLUSION: Our research results provided substantial evidence to support some data on the analysis of the microbial community and its metabolism in the stomach, and they demonstrated many specific interactions between the gastric microbiome and the metabolome. Our study can help reveal the pathogenesis of PUD and indicate plausible disease-specific mechanisms for future studies from a new perspective.}, }
@article {pmid36969182, year = {2023}, author = {Yamamoto, A and Kambara, Y and Fujiwara, H}, title = {Impact of oral microbiota on pathophysiology of GVHD.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1132983}, pmid = {36969182}, issn = {1664-3224}, abstract = {Allogeneic transplantation of hematopoietic cells is the only curative therapy for several hematopoietic disease in which patients receive cytotoxic conditioning regimens followed by infusion of hematopoietic stem cells. Although the outcomes have improved over the past decades, graft-versus-host-disease (GVHD), the most common life-threatening complication, remains a major cause of non-relapse morbidity and mortality. Pathophysiology of acute GVHD characterized by host antigen-presenting cells after tissue damage and donor T-cells is well studied, and additionally the importance of recipient microbiota in the intestine is elucidated in the GVHD setting. Oral microbiota is the second most abundant bacterial flora in the body after the intestinal tract, and it is related to chronic inflammation and carcinogenesis. Recently, composition of the oral microbiome in GVHD related to transplantation has been characterized and several common patterns, dysbiosis and enrichment of the specific bacterial groups, have been reported. This review focuses on the role of the oral microbiota in the context of GVHD.}, }
@article {pmid36969178, year = {2023}, author = {Ling, Z and Cheng, Y and Gao, J and Lei, W and Yan, X and Hu, X and Shao, L and Liu, X and Kang, R}, title = {Alterations of the fecal and vaginal microbiomes in patients with systemic lupus erythematosus and their associations with immunological profiles.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1135861}, pmid = {36969178}, issn = {1664-3224}, abstract = {BACKGROUND: Exploring the human microbiome in multiple body niches is beneficial for clinicians to determine which microbial dysbiosis should be targeted first. We aimed to study whether both the fecal and vaginal microbiomes are disrupted in SLE patients and whether they are correlated, as well as their associations with immunological features.<br><br>METHODS: A group of 30 SLE patients and 30 BMI-age-matched healthy controls were recruited. Fecal and vaginal samples were collected, the 16S rRNA gene was sequenced to profile microbiomes, and immunological features were examined.<br><br>RESULTS: Distinct fecal and vaginal bacterial communities and decreased microbial diversity in feces compared with the vagina were found in SLE patients and controls. Altered bacterial communities were found in the feces and vaginas of patients. Compared with the controls, the SLE group had slightly lower gut bacterial diversity, which was accompanied by significantly higher bacterial diversity in their vaginas. The most predominant bacteria differed between feces and the vagina in all groups. Eleven genera differed in patients' feces; for example, Gardnerella and Lactobacillus increased, whereas Faecalibacterium decreased. Almost all the 13 genera differed in SLE patients' vaginas, showing higher abundances except for Lactobacillus. Three genera in feces and 11 genera in the vagina were biomarkers for SLE patients. The distinct immunological features were only associated with patients' vaginal microbiomes; for example, Escherichia-Shigella was negatively associated with serum C4.<br><br>CONCLUSIONS: Although SLE patients had fecal and vaginal dysbiosis, dysbiosis in the vagina was more obvious than that in feces. Additionally, only the vaginal microbiome interacted with patients' immunological features.}, }
@article {pmid36969036, year = {2023}, author = {Yang, X and An, H and He, Y and Fu, G and Jiang, Z}, title = {Comprehensive analysis of microbiota signature across 32 cancer types.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1127225}, pmid = {36969036}, issn = {2234-943X}, abstract = {Microbial communities significantly inhabit the human body. Evidence shows the interaction between the human microbiome and host cells plays a central role in multiple physiological processes and organ microenvironments. However, the majority of related studies focus on gut microbiota or specific tissues/organs, and the component signature of intratumor microbiota across various cancer types remains unclear. Here, we systematically analyzed the correlation between intratumor microbial signature with survival outcomes, genomic features, and immune profiles across 32 cancer types based on the public databases of Bacteria in Cancer (BIC) and The Cancer Genome Atlas (TCGA). Results showed the relative abundance of microbial taxa in tumors compared to normal tissues was observed as particularly noticeable. Survival analysis found that specific candidate microbial taxa were correlated with prognosis across various cancers. Then, a microbial-based scoring system (MS), which was composed of 64 candidate prognostic microbes, was established. Further analyses showed significant differences in survival status, genomic function, and immune profiles among the distinct MS subgroups. Taken together, this study reveals the diversity and complexity of microbiomes in tumors. Classifying cancer into different subtypes based on intratumor microbial signatures might reasonably reflect genomic characteristics, immune features, and survival status.}, }
@article {pmid36968415, year = {2023}, author = {Sharma, I and Kashyap, S and Agarwala, N}, title = {Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1132824}, pmid = {36968415}, issn = {1664-462X}, abstract = {Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.}, }
@article {pmid36968295, year = {2023}, author = {Lundtorp Olsen, C and Markvart, M and Vendius, VFD and Damgaard, C and Belstrøm, D}, title = {Short-term sugar stress induces compositional changes and loss of diversity of the supragingival microbiota.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2189770}, pmid = {36968295}, issn = {2000-2297}, abstract = {Frequent intake of free sugars is a major risk factor for dental caries, but the immediate influence of sugar intake on the supragingival microbiota remains unknown. We aim to characterize the effect of 14 days of sugar rinsing on the supragingival microbiota. Forty orally and systemically healthy participants rinsed their mouth with a 10% sucrose solution, 6-8 times a day, for 14 days, followed by 14 days without sugar stress. Supragingival plaque samples were collected at baseline, and after 14, and 28 days. The supragingival microbiota was analyzed using 16S rDNA sequencing. Taxonomic classification was performed using the Human Oral Microbiome Database. After 14 days of sugar stress induced by the daily sugar rinses, a significant loss of α-diversity (p = 0.02) and a significant increase in the relative abundance of Actinomyces (6.5% to 9.6%, p = 0.006) and Corynebacterium (6.2% to 9.1%, p = 0.03) species were recorded. In addition, a significant decrease in Streptococcus (10.3% to 6.1%, p = 0.001) species was observed. Sugar-mediated changes returned to baseline conditions 14 days after the last sugar rinse. The present study shows that temporary sugar stress induces loss of diversity and compositional changes to the supragingival microbiota, which are reversible if oral care is maintained.}, }
@article {pmid36968219, year = {2023}, author = {Um, CY and Peters, BA and Choi, HS and Oberstein, P and Beggs, DB and Usyk, M and Wu, F and Hayes, RB and Gapstur, SM and McCullough, ML and Ahn, J}, title = {Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation.}, journal = {Cancer research communications}, volume = {3}, number = {1}, pages = {43-53}, pmid = {36968219}, issn = {2767-9764}, abstract = {UNLABELLED: Although short-term feeding studies demonstrated effects of grains, fiber, and gluten on gut microbiome composition, the impact of habitual intake of these dietary factors is poorly understood. We examined whether habitual intakes of whole and refined grains, fiber, and gluten are associated with gut microbiota in a cross-sectional study. This study included 779 participants from the multi-ethnic Food and Microbiome Longitudinal Investigation study. Bacterial 16SV4 rRNA gene from baseline stool was amplified and sequenced using Illumina MiSeq. Read clustering and taxonomic assignment was performed using QIIME2. Usual dietary intake was assessed by a 137-item food frequency questionnaire. Association of diet with gut microbiota was assessed with respect to overall composition and specific taxon abundances. Whole grain intake was associated with overall composition, as measured by the Jensen-Shannon divergence (multivariable-adjusted P trend for quartiles = 0.03). The highest intake quartile was associated with higher abundance of Bacteroides plebeius, Faecalibacterium prausnitzii, Blautia producta, and Erysipelotrichaceae and lower abundance of Bacteroides uniformis. These bacteria also varied by dietary fiber intake. Higher refined grain and gluten intake was associated with lower Shannon diversity (P trend < 0.05). These findings suggest that whole grain and dietary fiber are associated with overall gut microbiome structure, largely fiber-fermenting microbiota. Higher refined grain and gluten intakes may be associated with lower microbial diversity.<br><br>SIGNIFICANCE: Regular consumption of whole grains and dietary fiber was associated with greater abundance of gut bacteria that may lower risk of colorectal cancer. Further research on the association of refined grains and gluten with gut microbial composition is needed to understand their roles in health and disease.}, }
@article {pmid36968117, year = {2023}, author = {Xiao, Y and Huang, S and Yu, W and Ni, Y and Lu, D and Wu, Q and Leng, Q and Yang, T and Ni, M and Xie, J and Zhang, X}, title = {Effects of emergency/nonemergency cervical cerclage on the vaginal microbiome of pregnant women with cervical incompetence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1072960}, pmid = {36968117}, issn = {2235-2988}, abstract = {BACKGROUND: Evaluation of the therapeutic effects of cerclage on preterm birth (PTB) caused by cervical incompetence remains challenging. The vaginal microbiome is associated with preterm births. Thus, this study aimed to analyse the vaginal microbiota of patients with cervical incompetence, explore the relationship between the composition of the vaginal microbiota before cervical cerclage and at term delivery, and assess the effect of cervical cerclage on the vaginal microbiota.<br><br>METHODS: Patients (n = 30) underwent cerclage performed by the same surgical team. Vaginal swabs were obtained pre-surgery and seven days post-surgery. A gestational age-matched cohort of healthy pregnant women (n = 20) (no particular abnormality during pregnancy, delivery at term) was used as the control group and sampled during a comparable pregnancy. All collected vaginal swabs were analysed by 16S rRNA gene sequencing.<br><br>RESULTS: When comparing the healthy control and cervical cerclage groups, the enriched microorganism in the healthy controls was G. Scardovia, and the enriched microorganism of the cerclage was G. Streptococcus. &#x3b1; diversity was significantly increased in patients who received cerclage with preterm delivery compared with those with full-term delivery, and the enriched microorganism was F. Enterococcus. A comparison before and after nonemergency cerclage suggested that the enriched microorganisms were G. Lactobacillus and F. Lactobacillaceae before surgery. After nonemergency cerclage, the enriched microorganisms were F. Enterobacteriaceae and C. Gammaproteobacteria. Vaginal microbiota diversity significantly increased, and the proportion of women with Lactobacillus spp.-depleted microbiomes increased after emergency cerclage. Significant differences in &#x3b2; diversity were found between the groups. Before the emergency cerclage, the enriched microorganisms were G. Lactobacillus, O. Alteromonadales, and P. Firmicutes. After emergency cerclage, the enriched microorganisms were P. Actinobacteria, C. Actinobacteria, P. Proteobacteria, F. Bifidobacteriaceae, O. Bifidobacteriales, G. Gardnerella, and G. Veillonella.<br><br>CONCLUSION: Cerclage (particularly emergency cerclage) may alter the vaginal microbiota by increasing microbiota diversity, decreasing vaginal Lactobacillus abundance, and increasing the abundance of pathogenic bacteria that are not conducive to pregnancy maintenance, thereby affecting surgical efficacy. Therefore, the role of the vaginal microbiome should be considered when developing treatment strategies for pregnant women with cervical incompetence.<br><br>CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn, identifier ChiCTR2100046305.}, }
@article {pmid36968114, year = {2023}, author = {Homayouni Rad, A and Pourjafar, H and Mirzakhani, E}, title = {A comprehensive review of the application of probiotics and postbiotics in oral health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1120995}, pmid = {36968114}, issn = {2235-2988}, abstract = {Oral diseases are among the most common diseases around the world that people usually suffer from during their lifetime. Tooth decay is a multifactorial disease, and the composition of oral microbiota is a critical factor in its development. Also, Streptococcus mutans is considered the most important caries-causing species. It is expected that probiotics, as they adjust the intestinal microbiota and reduce the number of pathogenic bacteria in the human intestine, can exert their health-giving effects, especially the anti-pathogenic effect, in the oral cavity, which is part of the human gastrointestinal tract. Therefore, numerous in vitro and in vivo studies have been conducted on the role of probiotics in the prevention of tooth decay. In this review, while investigating the effect of different strains of probiotics Lactobacillus and Bifidobacteria on oral diseases, including dental caries, candida yeast infections, periodontal diseases, and halitosis, we have also discussed postbiotics as novel non-living biological compounds derived from probiotics.}, }
@article {pmid36968080, year = {2023}, author = {Wang, M and Li, L and Qian, J and Wang, N and Bao, J and Lu, J and Chen, F and Li, Y and Zhang, Y and Yan, F}, title = {Periodontitis salivary microbiota exacerbates nonalcoholic fatty liver disease in high-fat diet-induced obese mice.}, journal = {iScience}, volume = {26}, number = {4}, pages = {106346}, pmid = {36968080}, issn = {2589-0042}, abstract = {Periodontitis may aggravate the development of nonalcoholic fatty liver disease (NAFLD); however, the precise mechanism is unknown. In this study, salivary microbiota collected from patients with periodontitis was transferred intragastrically to obese mice induced by high-fat diet. Microbiomics and metabolomics analysis were performed to assess the influence of periodontitis salivary microbiota on gut microbiome and liver metabolism. Periodontitis salivary microbiota altered gut microbiota composition and exacerbated intestinal barrier dysfunction in obese mice. Subsequently, the bacterial lipopolysaccharide transported to liver may activate the toll-like receptor 4 signaling and cause the release of pro-inflammatory factors. Moreover, the tryptophan-kynurenine-AhR signal axis was upregulated in liver, which may be related to aggravated hepatic steatosis and glucolipid metabolism dysregulation during NAFLD development. This study indicated that in the context of obesity, periodontitis salivary microbiota may aggravate the pathological progression of NAFLD, in which the tryptophan-AhR pathway may play a key role.}, }
@article {pmid36967532, year = {2023}, author = {You, X and Rani, A and Özcan, E and Lyu, Y and Sela, DA}, title = {Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192546}, doi = {10.1080/19490976.2023.2192546}, pmid = {36967532}, issn = {1949-0984}, abstract = {Human milk guides the structure and function of microbial commensal communities that colonize the nursing infant gut. Indigestible molecules dissolved in human milk establish a microbiome often dominated by bifidobacteria capable of utilizing these substrates. Interestingly, urea accounts for ~15% of total human milk nitrogen, representing a potential reservoir for microbiota that may be salvaged for critical metabolic operations during lactation and neonatal development. Accordingly, B. infantis strains are competent for urea nitrogen utilization, constituting a previously hypothetical phenotype in commensal bacteria hosted by humans. Urease gene expression, downstream nitrogen metabolic pathways, and enzymatic activity are induced during urea utilization to yield elevated ammonia concentrations. Moreover, biosynthetic networks relevant to infant nutrition and development are transcriptionally responsive to urea utilization including branched chain and other essential amino acids. Importantly, isotopically labeled urea nitrogen is broadly distributed throughout the expressed B. infantis proteome. This incisively demonstrates that the previously inaccessible urea nitrogen is incorporated into microbial products available for infant host utilization. In aggregate, B. infantis possesses the requisite phenotypic foundation to participate in human milk urea nitrogen recycling within its infant host and thus may be a key contributor to nitrogen homeostasis early in life.}, }
@article {pmid36967434, year = {2023}, author = {Ma, X and Jia, X and Peng, Y and Li, X and Wang, C and Yu, K}, title = {Gut microbiota disruption during sepsis and the influence of innate metabolites on sepsis prognosis.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {36967434}, issn = {1618-1905}, abstract = {Sepsis causes high mortality in intensive care units. Although there have been many studies on the gut microbiota in patients with sepsis, the impact of sepsis on the gut microbiota has not been directly determined because the treatment of sepsis also affects the gut microbiota. Therefore, we designed this animal experiment to explore gut microbiota alterations during sepsis. Mice were divided into two groups, mice that survived less than 3 days and mice that survived more than 3 days. Fecal samples collected on the day of cecal ligation and puncture (CLP), as well as on the 3rd and 7th days after CLP, were subjected to microbial community analysis and nontargeted metabolomics analysis. The results showed significantly lower bacterial diversity in fecal samples after CLP. At the genus level, the fecal samples obtained on the 3rd and 7th days after CLP exhibited significantly increased relative abundances of Bacteroides, Helicobacter, etc., and significantly decreased relative abundances of Alloprevotella, Prevotella, etc. Innate metabolite levels were significantly different in mice that survived less than 3 days and mice that survived more than 3 days. In conclusion, CLP-induced sepsis in mice changes the structure of the gut microbiome, and innate metabolites affect the prognosis of septic mice.}, }
@article {pmid36967379, year = {2023}, author = {Sun, Y and Zhang, X and Jin, C and Yue, K and Sheng, D and Zhang, T and Dou, X and Liu, J and Jing, H and Zhang, L and Yue, J}, title = {Prospective, longitudinal analysis of the gut microbiome in patients with locally advanced rectal cancer predicts response to neoadjuvant concurrent chemoradiotherapy.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {221}, pmid = {36967379}, issn = {1479-5876}, abstract = {BACKGROUND: Neoadjuvant concurrent chemoradiotherapy (nCCRT) is a standard treatment for locally advanced rectal cancer (LARC). The gut microbiome may be reshaped by radiotherapy through its effects on microbial composition, mucosal immunity, and the systemic immune system. We sought to clarify dynamic, longitudinal changes in the gut microbiome and blood immunomodulators throughout nCCRT and to explore the relationship of such changes with outcomes after nCCRT.<br><br>METHODS: A total of 39 patients with LARC were recruited for this study. Fecal samples and peripheral blood samples were collected from all 39 patients before nCCRT, during nCCRT (at week 3), and after nCCRT (at week 5). The gut microbiota and the microbial community structure were analyzed by 16S rRNA sequencing of the V3-V4 region. Levels of blood immunomodulatory proteins were measured with a Millipore HCKPMAG-11&#xa0;K kit and Luminex 200 platform (Luminex, USA).<br><br>RESULTS: Cross-sectional and longitudinal analyses revealed that the gut microbiome profile and enterotype exhibited characteristic variations that could distinguish patients with good response (AJCC TRG classification 0-1) vs poor response (TRG 2-3) to nCCRT. Sparse partial least squares regression and canonical correspondence analyses showed multivariate associations between specific microbial taxa, host immunomodulatory proteins, immune cells, and outcomes after nCCRT. An integrated model consisting of baseline Clostridium sensu stricto 1 levels, fold changes in Intestinimonas, blood levels of the herpesvirus entry mediator (HVEM/CD270), and lymphocyte counts could predict good vs poor outcome after nCCRT [area under the receiver-operating characteristics curve (AUC)=&#x2009;0.821; area under the precision-recall curve [AUPR]&#x2009;=&#x2009;0.911].<br><br>CONCLUSIONS: Our results showed that longitudinal variations in specific gut taxa, associated host immune cells, and immunomodulatory proteins before and during nCCRT could be useful for early predictions of the efficacy of nCCRT, which could guide the choice of individualized treatment for patients with LARC.}, }
@article {pmid36967101, year = {2023}, author = {Thanawala, SU and Kaplan, DE and Falk, GW and Beveridge, CA and Schaubel, D and Serper, M and Yang, YX}, title = {Antibiotic exposure is associated with a risk of esophageal adenocarcinoma.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cgh.2023.03.012}, pmid = {36967101}, issn = {1542-7714}, abstract = {BACKGROUND &amp; AIMS: Antibiotic exposure leads to changes in the gut microbiota. Our objective was to evaluate the association between antibiotic exposure and esophageal adenocarcinoma (EAC) risk.<br><br>METHODS: We performed a nested case-control study using data from the Veterans Health Administration from 2004 through 2020. Cases group consisted of patients who received an incident diagnosis of EAC. For each case, up to 20 matched controls were selected using incidence density sampling. Our primary exposure of interest was any oral or intravenous antibiotic use. Our secondary exposures included cumulative number of days of exposure and classification of antibiotics by various subgroups. Conditional logistic regression was used to estimate the crude and adjusted odds ratios (aOR) for the risk of EAC associated with antibiotic exposure.<br><br>RESULTS: The case-control analysis included 8,226 EAC cases and 140,670 matched controls. Exposure to any antibiotic was associated with an aOR for EAC of 1.74 (95% CI: 1.65-1.83) versus no antibiotic exposure. Compared to no antibiotic exposure, the aOR for EAC was 1.63 (95% CI:1.52-1.74, p<0.001) for cumulative exposure to any antibiotic for 1-15 days, 1.77 (95% CI 1.65-1.89, p<0.001) for 16-47 days, and 1.87 (95% CI 1.75-2.01, p<0.001) for &#x2265;48 days, respectively (p for trend <0.001).<br><br>CONCLUSION: Exposure to any antibiotic is associated with an increased risk of EAC, and this risk increases as the cumulative days of exposure increases. This novel finding is hypothesis-generating for potential mechanisms that may play a role in the development or progression of EAC.}, }
@article {pmid36967089, year = {2023}, author = {Cui, SS and Jiang, QW and Chen, SD}, title = {Sex difference in biological change and mechanism of Alzheimer's disease: from macro- to micro-landscape.}, journal = {Ageing research reviews}, volume = {}, number = {}, pages = {101918}, doi = {10.1016/j.arr.2023.101918}, pmid = {36967089}, issn = {1872-9649}, abstract = {Alzheimer's disease (AD) is the most common form of dementia and numerous studies reported a higher prevalence and incidence of AD among women. Although women have longer lifetime, longevity does not wholly explain the higher frequency and lifetime risk in women. It is important to understand sex differences in AD pathophysiology and pathogenesis, which could provide foundation for future clinical AD research. Here, we review the most recent and relevant literature on sex differences in biological change of AD from macroscopical neuroimaging to microscopical pathologic change (neuronal degeneration, synaptic dysfunction, amyloid-beta and tau accumulation). We also discussed sex differences in cellular mechanisms related to AD (neuroinflammation, mitochondria dysfunction, oxygen stress, apoptosis, autophagy, blood-brain-barrier dysfunction, gut microbiome alteration, bulk and single cell/nucleus omics) and possible causes underlying these differences including sex-chromosome, sex hormone and hypothalamic-pituitary- adrenal (HPA) axis effects.}, }
@article {pmid36966625, year = {2023}, author = {He, LX and He, LY and Gao, FZ and Zhang, M and Chen, J and Jia, WL and Ye, P and Jia, YW and Hong, B and Liu, SS and Liu, YS and Zhao, JL and Ying, GG}, title = {Mariculture affects antibiotic resistome and microbiome in the coastal environment.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131208}, doi = {10.1016/j.jhazmat.2023.131208}, pmid = {36966625}, issn = {1873-3336}, abstract = {Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The pollution, distribution, and characteristics of antibiotics, antibiotic resistance genes (ARGs) and microbiomes have been investigated in this study. Results showed that 20 antibiotics were detected in Chinese coastal environment, with predominance of erythromycin-H2O, enrofloxacin and oxytetracycline. In coastal mariculture sites, antibiotic concentrations were significantly higher than in control sites, and more types of antibiotics were detected in the South than in the North of China. Residues of enrofloxacin, ciprofloxacin and sulfadiazine posed high resistance selection risks. β-Lactam, multi-drug and tetracycline resistance genes were frequently detected with significantly higher abundance in the mariculture sites. Of the 262 detected ARGs, 10, 26, and 19 were ranked as high-risk, current-risk, future-risk, respectively. The main bacterial phyla were Proteobacteria and Bacteroidetes, of which 25 genera were zoonotic pathogens, with Arcobacter and Vibrio in particular ranking in the top10. Opportunistic pathogens were more widely distributed in the northern mariculture sites. Phyla of Proteobacteria and Bacteroidetes were the potential hosts of high-risk ARGs, while the conditional pathogens were associated with future-risk ARGs, indicating a potential threat to human health.}, }
@article {pmid36966280, year = {2023}, author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J}, title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {81}, pmid = {36966280}, issn = {1471-2180}, abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.}, }
@article {pmid36966246, year = {2023}, author = {Hall, MW and Wellappuli, NC and Huang, RC and Wu, K and Lam, DK and Glogauer, M and Beiko, RG and Senadheera, DB}, title = {Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {23}, pmid = {36966246}, issn = {2730-6151}, abstract = {Experimentally induced gingivitis is associated with inflammatory and microbiological changes in an otherwise healthy subject, demonstrating the impacts of discontinuing oral hygiene routines. Understanding the bacterial dynamics during the induction and resolution of gingival inflammation will aid in the development of bacterial prognostic tests and probiotics for severe oral disease. We profiled the bacterial community in 15 healthy subjects who suspended all oral-hygiene practices for three weeks. Saliva, tongue, subgingival, and supragingival plaque samples were collected over seven weeks and showed a return to community baseline after oral hygiene practices were resumed. Stronger temporal changes in subgingival and supragingival plaque suggest these sample types may be preferred over saliva or tongue plaque for future prognostics. Taxonomic groups spanning ten phyla demonstrated consistent abundance shifts, including a significant decrease in Streptococcus, Neisseria, and Actinomyces populations, and an increase in Prevotella, Fusobacterium, and Porphyromonas populations. With four distinct oral sites surveyed and results mapped to the Human Oral Microbiome Database reference set, this work provides a comprehensive taxonomic catalog of the bacterial shifts observed during the onset and resolution of gingival inflammation.}, }
@article {pmid36966207, year = {2023}, author = {Bickel, S and Or, D}, title = {Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {322}, pmid = {36966207}, issn = {2399-3642}, abstract = {Earth's diverse soil microbiomes host bacteria within dynamic and fragmented aqueous habitats that occupy complex pore spaces and restrict the spatial range of ecological interactions. Yet, the spatial distributions of bacterial cells in soil communities remain underexplored. Here, we propose a modelling framework representing submillimeter-scale distributions of soil bacteria based on physical constraints supported by individual-based model results and direct observations. The spatial distribution of bacterial cell clusters modulates various metabolic interactions and soil microbiome functioning. Dry soils with long diffusion times limit localized interactions of the sparse communities. Frequently wet soils enable long-range trophic interactions between dense cell clusters through connected aqueous pathways. Biomes with high carbon inputs promote large and dense cell clusters where anoxic microsites form even in aerated soils. Micro-geographic considerations of difficult-to-observe microbial processes can improve the interpretation of data from bulk soil samples.}, }
@article {pmid36965559, year = {2023}, author = {Jiang, S and Xu, H and Zhao, C and Zhong, F and Li, D}, title = {Oyster polysaccharides relieve DSS-induced colitis via anti-inflammatory and maintaining the physiological hypoxia.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {124150}, doi = {10.1016/j.ijbiomac.2023.124150}, pmid = {36965559}, issn = {1879-0003}, abstract = {Oyster polysaccharides (OPS) possess potent anti-inflammatory properties and mediate gut microbiome. The research aimed to investigate the beneficial effect of OPS on attenuating colitis. OPS administration decreased the disease activity index and suppressed the increase in colon length. Hematoxylin and eosin staining results displayed that OPS restored the DSS-induced histopathological damage. After oral administration of OPS, myeloperoxidase activity and pro-inflammatory cytokines (TNF-α) in colitis mice were inhibited, while IL-10 was elevated. Western blotting results revealed that OPS improved the expression of tight junction proteins (ZO-1, Claudin-4, and Occludin). Additionally, OPS stabilized the expression of hypoxia-inducible factor-1α (HIF-1α) and prevented the levels of bacterial endotoxin (lipopolysaccharides). OPS activated barrier-protective genes (intestinal trefoil factor) via mediating HIF-1α. These results indicated that OPS alleviated DSS-induced colitis by inhibiting inflammation and regulating HIF-1α. OPS would be a potential candidate to alleviate DSS-induced colitis.}, }
@article {pmid36965522, year = {2023}, author = {Luo, L and Chang, Y and Sheng, L}, title = {Gut-liver axis in the progression of nonalcoholic fatty liver disease: From the microbial derivatives-centered perspective.}, journal = {Life sciences}, volume = {}, number = {}, pages = {121614}, doi = {10.1016/j.lfs.2023.121614}, pmid = {36965522}, issn = {1879-0631}, abstract = {Nonalcoholic fatty liver disease (NAFLD) is one of the world's most common chronic liver diseases. However, its pathogenesis remains unclear. With the deepening of research, NAFLD is considered a metabolic syndrome associated with the environment, heredity, and metabolic disorders. Recently, the close relationship between the intestinal microbiome and NAFLD has been discovered, and the theory of the "gut-liver axis" has been proposed. In short, the gut bacteria directly reach the liver via the portal vein through the damaged intestinal wall or indirectly participate in the development of NAFLD through signaling pathways mediated by their components and metabolites. This review focuses on the roles of microbiota-derived lipopolysaccharide, DNA, peptidoglycan, bile acids, short-chain fatty acids, endogenous ethanol, choline and its metabolites, indole and its derivatives, and bilirubin and its metabolites in the progression of NAFLD, which may provide significative insights into the pathogenesis, diagnosis, and treatment for this highly prevalent liver disease.}, }
@article {pmid36965327, year = {2023}, author = {Lin, D and Medeiros, DM}, title = {The microbiome as a major function of the gastrointestinal tract and its implication in micronutrient metabolism and chronic diseases.}, journal = {Nutrition research (New York, N.Y.)}, volume = {112}, number = {}, pages = {30-45}, doi = {10.1016/j.nutres.2023.02.007}, pmid = {36965327}, issn = {1879-0739}, abstract = {The composition and function of microbes harbored in the human gastrointestinal lumen have been underestimated for centuries because of the underdevelopment of nucleotide sequencing techniques and the lack of humanized gnotobiotic models. Now, we appreciate that the gut microbiome is an integral part of the human body and exerts considerable roles in host health and diseases. Dietary factors can induce changes in the microbial community composition, metabolism, and function, thereby altering the host immune response, and consequently, may influence disease risks. An imbalance of gut microbiome homeostasis (i.e., dysbiosis) has been linked to several chronic diseases, such as inflammatory bowel diseases, obesity, and diabetes. Remarkable progress has recently been made in better understanding the extent to which the influence of the diet-microbiota interaction on host health outcomes in both animal models and human participants. However, the exact causality of the gut microbiome on the development of diseases is still controversial. In this review, we will briefly describe the general structure and function of the intestine and the process of nutrient absorption in humans. This is followed by a summarization of the recent updates on interactions between gut microbiota and individual micronutrients, including carotenoids, vitamin A, vitamin D, vitamin C, folate, iron, and zinc. In the opinion of the authors, these nutrients were identified as representative of vitamins and minerals with sufficient research on their roles in the microbiome. The host responses to the gut microbiome will also be discussed. Future direction in microbiome research, for example, precision microbiome, will be proposed.}, }
@article {pmid36965240, year = {2023}, author = {Cassotta, M and Cianciosi, D and De Giuseppe, R and Navarro-Hortal, MD and Armas Diaz, Y and Forbes-Hernández, TY and Pifarre, KT and Pascual Barrera, AE and Grosso, G and Xiao, J and Battino, M and Giampieri, F}, title = {Possible role of nutrition in the prevention of inflammatory bowel disease-related colorectal cancer: A focus on human studies.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {110}, number = {}, pages = {111980}, doi = {10.1016/j.nut.2023.111980}, pmid = {36965240}, issn = {1873-1244}, abstract = {Patients with inflammatory bowel disease (IBD) are at substantially high risk for colorectal cancer (CRC). IBD-associated CRC accounts for roughly 10% to 15% of the annual mortality in patients with IBD. IBD-related CRC also affects younger patients compared with sporadic CRC, with a 5-y survival rate of 50%. Regardless of medical therapies, the persistent inflammatory state characterizing IBD raises the risk for precancerous changes and CRC, with additional input from several elements, including genetic and environmental risk factors, IBD-associated comorbidities, intestinal barrier dysfunction, and gut microbiota modifications. It is well known that nutritional habits and dietary bioactive compounds can influence IBD-associated inflammation, microbiome abundance and composition, oxidative stress balance, and gut permeability. Additionally, in recent years, results from broad epidemiologic and experimental studies have associated certain foods or nutritional patterns with the risk for colorectal neoplasia. The present study aimed to review the possible role of nutrition in preventing IBD-related CRC, focusing specifically on human studies. It emerges that nutritional interventions based on healthy, nutrient-dense dietary patterns characterized by a high intake of fiber, vegetables, fruit, ω-3 polyunsaturated fatty acids, and a low amount of animal proteins, processed foods, and alcohol, combined with probiotic supplementation have the potential of reducing IBD-activity and preventing the risk of IBD-related CRC through different mechanisms, suggesting that targeted nutritional interventions may represent a novel promising approach for the prevention and management of IBD-associated CRC.}, }
@article {pmid36965002, year = {2023}, author = {Martiny, JBH and Martiny, AC and Brodie, E and Chase, AB and Rodríguez-Verdugo, A and Treseder, KK and Allison, SD}, title = {Investigating the eco-evolutionary response of microbiomes to environmental change.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.14209}, pmid = {36965002}, issn = {1461-0248}, abstract = {Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.}, }
@article {pmid36964865, year = {2023}, author = {Kitamura, N and Hashida, Y and Higuchi, T and Ohno, S and Sento, S and Sasabe, E and Murakami, I and Yamamoto, T and Daibata, M}, title = {Detection of Merkel cell polyomavirus in multiple primary oral squamous cell carcinomas.}, journal = {Odontology}, volume = {}, number = {}, pages = {}, pmid = {36964865}, issn = {1618-1255}, abstract = {Oral microbiome studies have mainly focussed on bacteria, with the relationship between viruses and oral cancers remaining poorly understood. Oral cancers can develop even in the absence of any history of daily smoking or drinking. Oral cancer patients frequently have multiple primary cancers in the oral cavity and other organs, such as the upper gastrointestinal tract. Merkel cell polyomavirus (MCPyV) is a novel oncovirus identified from a subtype of skin cancer in 2008. In this study, we investigated the potential involvement of MCPyV in the pathogenesis of oral squamous cell carcinoma (OSCC). Participants comprised 115 Japanese patients with OSCC (single primary: 109 tumours in 109 patients; multiple primaries: 16 tumours in 6 patients) treated in our department between 2014 and 2017. DNA was extracted from formalin-fixed paraffin-embedded specimens of primary lesions. MCPyV DNA copy counts were analysed by quantitative real-time polymerase chain reaction. Twenty-four of the 115 patients (20.9%) were positive for MCPyV DNA. No association was found between presence or absence of MCPyV DNA and clinical characteristics other than number of primary lesions. The MCPyV DNA-positive rate was significantly higher for multiple primary OSCCs (62.5%, 10/16 tumours) than for single primary OSCCs (16.5%, 18/109 tumours; P < 0.001). Furthermore, MCPyV DNA load was significantly higher for patients with multiple primaries (P < 0.05). MCPyV was observed more frequently and DNA load was significantly higher with multiple primary OSCCs than with single primary OSCC. MCPyV may play some role as an oncovirus for multiple primary OSCCs.}, }
@article {pmid36964623, year = {2023}, author = {Manabe, Y and Ishibashi, T and Asano, R and Tonomura, S and Maeda, Y and Motooka, D and Ueda, J and Yanagawa, M and Edamoto-Taira, Y and Chikaishi-Kirino, T and Masaki, T and Inagaki, T and Nakamura, S and Katada, Y and Okazawa, M and Narazaki, M and Ogo, T and Kumanogoh, A and Nakaoka, Y}, title = {Gut dysbiosis is associated with aortic aneurysm formation and progression in Takayasu arteritis.}, journal = {Arthritis research &amp; therapy}, volume = {25}, number = {1}, pages = {46}, pmid = {36964623}, issn = {1478-6362}, abstract = {BACKGROUND: Takayasu arteritis (TAK) is an autoimmune large vessel vasculitis that affects the aorta and its major branches, eventually leading to the development of aortic aneurysm and vascular stenosis or occlusion. This retrospective and prospective study aimed to investigate whether the gut dysbiosis exists in patients with TAK and to identify specific gut microorganisms related to aortic aneurysm formation/progression in TAK.<br><br>METHODS: We analysed the faecal microbiome of 76 patients with TAK and 56 healthy controls (HCs) using 16S ribosomal RNA sequencing. We examined the relationship between the composition of the gut microbiota and clinical parameters.<br><br>RESULTS: The patients with TAK showed an altered gut microbiota with a higher abundance of oral-derived bacteria, such as Streptococcus and Campylobacter, regardless of the disease activity, than HCs. This increase was significantly associated with the administration of a proton pump inhibitor used for preventing gastric ulcers in patients treated with aspirin and glucocorticoids. Among patients taking a proton pump inhibitor, Campylobacter was more frequently detected in those who underwent vascular surgeries and endovascular therapy for aortic dilatation than in those who did not. Among the genus of Campylobacter, Campylobacter gracilis in the gut microbiome was significantly associated with clinical events related to aortic aneurysm formation/worsening in patients with TAK. In a prospective analysis, patients with a gut microbiome positive for Campylobacter were significantly more likely to require interventions for aortic dilatation than those who were negative for Campylobacter. Furthermore, patients with TAK who were positive for C. gracilis by polymerase chain reaction showed a tendency to have severe aortic aneurysms.<br><br>CONCLUSIONS: A specific increase in oral-derived Campylobacter in the gut may be a novel predictor of aortic aneurysm formation/progression in patients with TAK.}, }
@article {pmid36964325, year = {2023}, author = {Gu, C and Zhang, F and Lu, K and Sun, X and Guo, W and Shao, Q}, title = {Response of microbial community in the soil of halophyte after contamination with tetrabromobisphenol A.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {36964325}, issn = {1678-4405}, abstract = {Coastal wetlands are subjected to increasing tetrabromobisphenol A (TBBPA) pollution, whereas knowledge of TBBPA degradation in marine environments is lacking. The changes of bacterial communities in TBBPA-polluted soil covered with halophytes were investigated. TBBPA could be degraded in the halophyte-covered saline-alkali soil in a microcosm experiment. Higher TBBPA removal occurred in the soil of Kandelia obovata compared with soils covered with Suaeda australis and Phragmites australis within 56 days of cultivation. The rhizosphere soils of S. australis, P. australis, and K. obovata mainly involved the classes of Bacteroidia, Gammaproteobacteria, Alphaproteobacteria, and Anaerolineae. Additionally, manganese oxidation, aerobic anoxygenic phototrophy, and fermentation functions were higher in the rhizosphere soil of K. obovata after TBBPA addition. This study supports that using suitable local halophytic plants is a promising approach for degrading TBBPA-contaminated coastal soil.}, }
@article {pmid36964264, year = {2023}, author = {Bélteky, M and Milletich, PL and Ahrens, AP and Triplett, EW and Ludvigsson, J}, title = {Infant gut microbiome composition correlated with type 1 diabetes acquisition in the general population: the ABIS study.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {36964264}, issn = {1432-0428}, abstract = {AIMS/HYPOTHESIS: While autoantibodies are traditional markers for type 1 diabetes development, we identified gut microbial biomarkers in 1-year-old infants associated with future type 1 diabetes up to 20 years before diagnosis.<br><br>METHODS: Infants enrolled in the longitudinal general population cohort All Babies In Southeast Sweden (ABIS) provided a stool sample at a mean age of 12.5 months. Samples (future type 1 diabetes, n=16; healthy controls, n=268) were subjected to 16S ribosomal RNA (rRNA) sequencing and quantitative PCR. Microbial differences at the taxonomic and core microbiome levels were assessed. PICRUSt was used to predict functional content from the 16S rRNA amplicons. Sixteen infants, with a future diagnosis of type 1 diabetes at a mean age of 13.3&#xb1;5.4 years, and one hundred iterations of 32 matched control infants, who remained healthy up to 20 years of age, were analysed.<br><br>RESULTS: Parasutterella and Eubacterium were more abundant in healthy control infants, while Porphyromonas was differentially more abundant in infants with future type 1 diabetes diagnosis. Ruminococcus was a strong determinant in differentiating both control infants and those with future type 1 diabetes using random forest analysis and had differing trends of abundance when comparing control infants and those with future type 1 diabetes. Flavonifractor and UBA1819 were the strongest factors for differentiating control infants, showing higher abundance in control infants compared with those with future type 1 diabetes. Alternatively, Alistipes (more abundant in control infants) and Fusicatenibacter (mixed abundance patterns when comparing case and control infants) were the strongest factors for differentiating future type 1 diabetes. Predicted gene content regarding butyrate production and pyruvate fermentation was differentially observed to be higher in healthy control infants.<br><br>CONCLUSIONS/INTERPRETATION: This investigation suggests that microbial biomarkers for type 1 diabetes may be present as early as 1 year of age, as reflected in the taxonomic and functional differences of the microbial communities. The possibility of preventing disease onset by altering or promoting a 'healthy' gut microbiome is appealing.<br><br>DATA AVAILABILITY: The forward and reverse 16S raw sequencing data generated in this study are available through the NCBI Sequence Read Archive under BioProject PRJNA875929. Associated sample metadata used for statistical comparison are available in the source data file. R codes used for statistical comparisons and figure generation are available at: https://github.com/PMilletich/T1D_Pipeline .}, }
@article {pmid36964135, year = {2023}, author = {McLaughlin, S and Zhalnina, K and Kosina, S and Northen, TR and Sasse, J}, title = {The core metabolome and root exudation dynamics of three phylogenetically distinct plant species.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1649}, pmid = {36964135}, issn = {2041-1723}, abstract = {Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.}, }
@article {pmid36964133, year = {2023}, author = {Ruze, R and Song, J and Yin, X and Chen, Y and Xu, R and Wang, C and Zhao, Y}, title = {Mechanisms of obesity- and diabetes mellitus-related pancreatic carcinogenesis: a comprehensive and systematic review.}, journal = {Signal transduction and targeted therapy}, volume = {8}, number = {1}, pages = {139}, pmid = {36964133}, issn = {2059-3635}, abstract = {Research on obesity- and diabetes mellitus (DM)-related carcinogenesis has expanded exponentially since these two diseases were recognized as important risk factors for cancers. The growing interest in this area is prominently actuated by the increasing obesity and DM prevalence, which is partially responsible for the slight but constant increase in pancreatic cancer (PC) occurrence. PC is a highly lethal malignancy characterized by its insidious symptoms, delayed diagnosis, and devastating prognosis. The intricate process of obesity and DM promoting pancreatic carcinogenesis involves their local impact on the pancreas and concurrent whole-body systemic changes that are suitable for cancer initiation. The main mechanisms involved in this process include the excessive accumulation of various nutrients and metabolites promoting carcinogenesis directly while also aggravating mutagenic and carcinogenic metabolic disorders by affecting multiple pathways. Detrimental alterations in gastrointestinal and sex hormone levels and microbiome dysfunction further compromise immunometabolic regulation and contribute to the establishment of an immunosuppressive tumor microenvironment (TME) for carcinogenesis, which can be exacerbated by several crucial pathophysiological processes and TME components, such as autophagy, endoplasmic reticulum stress, oxidative stress, epithelial-mesenchymal transition, and exosome secretion. This review provides a comprehensive and critical analysis of the immunometabolic mechanisms of obesity- and DM-related pancreatic carcinogenesis and dissects how metabolic disorders impair anticancer immunity and influence pathophysiological processes to favor cancer initiation.}, }
@article {pmid36963900, year = {2023}, author = {Elghannam, MT and Hassanien, MH and Ameen, YA and Turky, EA and Elattar, GM and ElRay, AA and Eltalkawy, MD}, title = {Oral microbiota and liver diseases.}, journal = {Clinical nutrition ESPEN}, volume = {54}, number = {}, pages = {68-72}, doi = {10.1016/j.clnesp.2022.12.030}, pmid = {36963900}, issn = {2405-4577}, abstract = {Gut microbiota plays a crucial role in our health and particularly liver diseases, including NAFLD, cirrhosis, and HCC. Oral microbiome and its role in health and disease represent an active field of research. Several lines of evidence have suggested that oral microbiota dysbiosis represents a major factor contributing to the occurrence and progression of many liver diseases. The human microbiome is valuable to the diagnosis of cancer and provides a novel strategy for targeted therapy of HCC. The most studied liver disease in relation to oral-gut-liver axis dysbiosis includes MAFLD; however, other diseases include Precancerous liver disease as viral liver diseases, liver cirrhosis, AIH and liver carcinoma (HCC). It seems that restoring populations of beneficial organisms and correcting dysbiosis appears to improve outcomes in liver disorders. We discuss the possible role of oral microbiota in these diseases.}, }
@article {pmid36963861, year = {2023}, author = {St-Amant, A and Bergdahl, A}, title = {A systematic review and meta-analysis of randomized controlled trials investigating the effects of probiotics on oxidative stress in healthy adults.}, journal = {Clinical nutrition ESPEN}, volume = {54}, number = {}, pages = {180-186}, doi = {10.1016/j.clnesp.2023.01.016}, pmid = {36963861}, issn = {2405-4577}, abstract = {BACKGROUND: The oxidative stress (OS) theory of disease stipulates that a chronic imbalance in the ratio of oxidants to antioxidants in the cellular environment leads to a variety of debilitating conditions, including type 2 diabetes, cardiovascular and liver diseases. Metabolites in the gut microbiome have been associated with increases in reactive oxygen species (ROS). Many randomized controlled trials (RCTs) have thus investigated the potential of probiotics as a nutraceutical intervention to improve parameters of OS.<br><br>AIM: The objective of this paper is to review relevant human RCTs exploring the potential of probiotic supplementation to prevent OS in metabolically healthy individuals.<br><br>METHODS: This systematic review and meta-analysis was registered on PROSPERO (CRD42021297210). The PubMed database was searched using keywords related to probiotics and OS. In total, out of the 652 studies were screened, 9 respected the inclusion criteria.<br><br>RESULTS: Total antioxidant capacity (TAC) (SMD: 0.83&#xa0;mmol/L, 95% CI: 0.25-1.40, p&#xa0;=&#xa0;0.005) and glutathione (GSH) (SMD: 0.45, 95% CI: 0.13-0.77, p&#xa0;=&#xa0;0.006) are improved with probiotic ingestion, although there are no alterations in superoxide dismutase (SOD) (SMD: 0.33, 95% CI:&#xa0;-0.27-0.93, p&#xa0;=&#xa0;0.28). Decreases in plasma concentrations of the OS biomarker malondialdehyde (MDA) (SMD:&#xa0;-0.55, 95% CI:&#xa0;-1.11-0.00, p&#xa0;=&#xa0;0.05) are also detected.<br><br>CONCLUSION: Probiotics improve AS and OS in metabolically healthy individuals. However, more studies are needed to address the moderate to high degree of heterogeneity in methodology.}, }
@article {pmid36963683, year = {2023}, author = {Perdomo-González, A and Pérez-Reverón, R and Goberna, M and León-Barrios, M and Fernández-López, M and Villadas, PJ and Reyes-Betancort, JA and Díaz-Peña, FJ}, title = {How harmful are exotic plantations for soils and its microbiome? A case study in an arid island.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163030}, doi = {10.1016/j.scitotenv.2023.163030}, pmid = {36963683}, issn = {1879-1026}, abstract = {The plantation of exotic species has been a common practice in (semi-) arid areas worldwide aiming to restore highly degraded habitats. The effects of these plantations on plant cover or soil erosion have been widely studied, while little attention has been paid to the consequences on soil quality and belowground biological communities. This study evaluates the long-term (>60 years) effects of the exotic species Acacia cyclops and Pinus halepensis revegetation on soil properties, including microbiome, in an arid island. Soils under exotic plantation were compared to both degraded soils with a very low cover of native species and soils with well-preserved native plant communities. Seven scenarios were selected in a small area (~25 ha) with similar soil type but differing in the plant cover. Topsoils (0-15 cm) were analyzed for physical, chemical and biochemical properties, and amplicon sequencing of bacterial and fungal communities. Microbial diversity was similar among soils with exotic plants and native vegetation (Shannon's index = 5.26 and 5.34, respectively), while the most eroded soils exhibited significantly lower diversity levels (Shannon's index = 4.72). Bacterial and fungal communities' composition in degraded soils greatly differed from those in vegetated soils (Canberra index = 0.85 and 0.92, respectively) likely due to high soil sodicity, fine textures and compaction. Microbial communities' composition also differed in soils covered with exotic and native species, to a greater extent for fungi than for bacteria (Canberra index = 0.94 and 0.89, respectively), due to higher levels of nutrients, microbial biomass and activity in soils with native species. Results suggest that reforestation succeeded in avoiding further soil degradation but still leading to relevant changes in soil microbial community that may have negative effects on ecosystem stability. Information gained in this research could be useful for environmental agencies and decision makers about the controversial replacement of exotic plants in insular territories.}, }
@article {pmid36963629, year = {2023}, author = {Lincke, JB and Christe, L and Unterlauft, JD and Zinkernagel, MS and Zysset-Burri, DC}, title = {Microbiome and retinal vascular diseases.}, journal = {The American journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajpath.2023.02.017}, pmid = {36963629}, issn = {1525-2191}, abstract = {The gut microbiome consists of more than thousand different microbes and their associated genes and microbial metabolites. It influences various host metabolic pathways and is therefore important for homeostasis. In recent years, its influence on health and disease was extensively researched. In case of a microbiome disequilibrium called dysbiosis, the gut microbiome is associated with several diseases. Consequent chronic inflammation may lead to or promote inflammatory bowel disease, obesity, diabetes mellitus, atherosclerosis, alcoholic and non-alcoholic liver disease, cirrhosis, hepatocellular carcinoma and other diseases. The pathogenesis of the three most common retinal vascular diseases, diabetic retinopathy, retinal vein and artery occlusion, may also be influenced by an altered microbiome and associated risk factors such as diabetes mellitus, atherosclerosis, hypertension and obesity. Direct cause-effect relationships remain less well understood. A potential prevention or treatment modality for these diseases could be targeting and modulating the individual's gut microbiome.}, }
@article {pmid36963568, year = {2023}, author = {Weil, PP and Reincke, S and Hirsch, CA and Giachero, F and Aydin, M and Scholz, J and Jönsson, F and Hagedorn, C and Nguyen, DN and Thymann, T and Pembaur, A and Orth, V and Wünsche, V and Jiang, PP and Wirth, S and Jenke, ACW and Sangild, PT and Kreppel, F and Postberg, J}, title = {Uncovering the gastrointestinal passage, intestinal epithelial cellular uptake and AGO2 loading of milk miRNAs in neonates using xenomiRs as tracers.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2023.03.016}, pmid = {36963568}, issn = {1938-3207}, abstract = {BACKGROUND: Human breast milk has a high microRNA (miRNA) content. It remains unknown whether and how milk miRNAs might affect intestinal gene regulation and homeostasis of the developing microbiome after initiation of enteral nutrition. However, this requires that relevant milk miRNA amounts survive gastrointestinal passage, are taken up by cells, and become available to the RNA interference (RNAi) machinery. It seems important to dissect the fate of these miRNAs after oral ingestion and gastrointestinal passage.<br><br>OBJECTIVE: Our goal was to analyze the potential transmissibility of milk miRNAs via the gastrointestinal system in neonate humans and a porcine model in vivo to contribute to the discussion whether milk miRNAs could influence gene regulation in neonates and thus might vertically transmit developmental relevant signals.<br><br>DESIGN: We performed cross-species profiling of miRNAs via deep-sequencing and utilized dietary xenobiotic taxon-specific milk miRNA (xenomiRs) as tracers in human and porcine neonates, followed by functional studies in primary human fetal intestinal epithelial cells (HIEC-6) using Ad5-mediated miRNA-gene transfer.<br><br>RESULTS: Mammals share many milk miRNAs yet exhibit taxon-specific miRNA fingerprints. We traced bovine-specific miRNAs from formula-nutrition in human preterm stool and 9 days after onset of enteral feeding in intestinal cells of preterm piglets. Thereafter, several xenomiRs accumulated in the intestinal cells. Moreover, few hours after introducing enteral feeding in preterm piglets with supplemented reporter miRNAs (cel-miR-39-5p/-3p), we observed their enrichment in blood serum and in AGO2-immunocomplexes from intestinal biopsies.<br><br>CONCLUSIONS: Milk-derived miRNAs survived gastrointestinal passage in human and porcine neonates. Bovine-specific miRNAs accumulated in intestinal cells of preterm piglets after enteral feeding with bovine colostrum/formula. In piglets, colostrum supplementation with cel-miR-39-5p/-3p resulted in increased blood levels of cel-miR-39-3p and argonaute RISC catalytic component 2 (AGO2) loading in intestinal cells. This suggests the possibility of vertical transmission of miRNA signaling from milk through the neonatal digestive tract.}, }
@article {pmid36970453, year = {2023}, author = {Panyod, S and Wu, WK and Chen, CC and Wu, MS and Ho, CT and Sheen, LY}, title = {Modulation of gut microbiota by foods and herbs to prevent cardiovascular diseases.}, journal = {Journal of traditional and complementary medicine}, volume = {13}, number = {2}, pages = {107-118}, pmid = {36970453}, issn = {2225-4110}, abstract = {UNLABELLED: Dietary nutrients are associated with the development of cardiovascular disease (CVD) both through traditional pathways (inducing hyperlipidemia and chronic inflammation) and through the emergence of a metaorganism-pathogenesis pathway (through the gut microbiota, its metabolites, and host). Several molecules from food play an important role as CVD risk-factor precursors either themselves or through the metabolism of the gut microbiome. Animal-based dietary proteins are the primary source of CVD risk-factor precursors; however, some plants also possess these precursors, though at relatively low levels compared with animal-source food products. Various medications have been developed to treat CVD through the gut-microbiota-circulation axis, and they exhibit potent effects in CVD treatment. Nevertheless, such medicines are still being improved, and there are many research gaps that need to be addressed. Furthermore, some medications have unpleasant or adverse effects. Numerous foods and herbs impart beneficial effects upon health and disease. In the past decade, many studies have focused on treating and preventing CVD by modulating the gut microbiota and their metabolites. This review provides an overview of the available information, summarizes current research related to the gut-microbiota-heart axis, enumerates the foods and herbs that are CVD-risk precursors, and illustrates how metabolites become CVD risk factors through the metabolism of gut microbiota. Moreover, we present perspectives on the application of foods and herbs-including prebiotics, probiotics, synbiotics, postbiotics, and antibiotic-like substances-as CVD prevention agents to modulate gut microbiota by inhibiting gut-derived CVD risk factors.<br><br>Cardiovascular disease, gut microbiota, herbal medicine, preventive medicine, dietary therapy, nutrition supplements.}, }
@article {pmid36963522, year = {2023}, author = {Pezzini, MF and Rampelotto, PH and Dall'Agnol, J and Guerreiro, GTS and Longo, L and Suarez Uribe, ND and Lange, EC and Álvares-da-Silva, MR and Joveleviths, D}, title = {Changes in the gut microbiota of rats after exposure to the fungicide Mancozeb.}, journal = {Toxicology and applied pharmacology}, volume = {}, number = {}, pages = {116480}, doi = {10.1016/j.taap.2023.116480}, pmid = {36963522}, issn = {1096-0333}, abstract = {Mancozeb is a fungicide commonly used in pest control programs, especially to protect vineyards. Its toxicity has already been evidenced in several studies. However, its influence on the composition and diversity of the gut microbiota remains unknown. In this work, the adverse impact of Mancozeb on the intestinal microbiota was investigated using a rodent model. Adult male Sprague Dawley rats were randomized into three groups: Control (standard diet), MZ1 (Mancozeb dose: 250 mg/kg bw/day), and MZ2 (Mancozeb dose: 500 mg/kg bw/day). After 12 weeks of experiment, animals were euthanized, and feces present in the intestine were collected. After fecal DNA extraction, the V4 region of the 16S rRNA gene was amplified followed by sequencing in an Ion S5™ System. Alpha and beta diversity analysis showed significant differences between Control and Mancozeb groups (MZ1 e MZ2), but no difference between MZ1 and MZ2 was observed. Seven genera significantly increased in abundance following Mancozeb exposure, while five genera decreased. Co-occurrence analyses revealed that the topological properties of the microbial networks, which can be used to infer co-occurrence interaction patterns among microorganisms, were significantly lower in both groups exposed to Mancozeb when compared to Control. In addition, 23 differentially abundant microbial metabolic pathways were identified in Mancozeb-treated groups mainly related to a change in energy metabolism, LPS biosynthesis, and nucleotide biosynthesis. In conclusion, the exposure to Mancozeb presented side effects by changing the composition of the microbiota in rats, increasing bacterial diversity regardless of the dose used, reducing the interaction patterns of the microbial communities, and changing microbial metabolic pathways.}, }
@article {pmid36963394, year = {2023}, author = {Chen, H and Tong, T and Lu, SY and Ji, L and Xuan, B and Zhao, G and Yan, Y and Song, L and Zhao, L and Xie, Y and Leng, X and Zhang, X and Cui, Y and Chen, X and Xiong, H and Yu, T and Li, X and Sun, T and Wang, Z and Chen, J and Chen, YX and Hong, J and Fang, JY}, title = {Urea cycle activation triggered by host-microbiota maladaptation driving colorectal tumorigenesis.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2023.03.003}, pmid = {36963394}, issn = {1932-7420}, abstract = {Maladaptation of host-microbiota metabolic interplay plays a critical role in colorectal cancer initiation. Here, through a combination of single-cell transcriptomics, microbiome profiling, metabonomics, and clinical analysis on colorectal adenoma and carcinoma tissues, we demonstrate that host's urea cycle metabolism is significantly activated during colorectal tumorigenesis, accompanied by the absence of beneficial bacteria with ureolytic capacity, such as Bifidobacterium, and the overabundance of pathogenic bacteria lacking ureolytic function. Urea could enter into macrophages, inhibit the binding efficiency of p-STAT1 to SAT1 promotor region, and further skew macrophages toward a pro-tumoral phenotype characterized by the accumulation of polyamines. Treating a murine model using urea cycle inhibitors or Bifidobacterium-based supplements could mitigate urea-mediated tumorigenesis. Collectively, this study highlights the utility of urea cycle inhibitors or therapeutically manipulating microbial composition using probiotics to prevent colorectal cancer.}, }
@article {pmid36963360, year = {2023}, author = {Zhang, X and Pan, Z and Wang, Y and Liu, P and Hu, K}, title = {Taraxacum officinale-derived exosome-like nanovesicles modulate gut metabolites to prevent intermittent hypoxia-induced hypertension.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {161}, number = {}, pages = {114572}, doi = {10.1016/j.biopha.2023.114572}, pmid = {36963360}, issn = {1950-6007}, abstract = {BACKGROUND: We aimed to investigate whether Taraxacum officinale (T. officinale)-derived exosome-like nanovesicles (ELNs) exerted hypotensive effects in intermittent hypoxia (IH)-induced hypertensive disorders and their potential mechanisms.<br><br>RESULTS: In this study, we developed T. officinale-derived natural nanoparticles with ideal size and stable negative surface charge, containing large amount of lipids and some functional proteins. We found that ELNs effectively reduced IH-induced hypertension, exhibited local anti-inflammatory effects on intestinal tissues in a rat model of IH-induced hypertension, and reduced intestinal tissue damage, including loss of goblet cells and barrier integrity damage, and ultimately inhibited the systemic inflammatory response. In addition, we evaluated intestinal microbial composition and SCFAs content and found significant changes in the structure and diversity of intestinal microbes, where butyrate was identified as the most important cause of the overall differences in the flora. Therefore, we further evaluated whether butyrate was a key target for ELNs to exert their effects in IH-induced hypertensive disease. We found that butyrate intervention further inhibited systemic inflammatory response and vascular wall remodeling by improving the intestinal microenvironment in IH rats, thereby attenuating IH-induced hypertension.<br><br>CONCLUSIONS: T. officinale-derived ELNs were effective in the treatment of IH-induced hypertensive disease, whereas butyrate played a major role in mediating the effects of ELNs in anti-IH-induced hypertensive disease.}, }
@article {pmid36963248, year = {2023}, author = {Descamps, A and Van der Borght, K and De Spiegeleer, A and Wynendaele, E and De Spiegeleer, B}, title = {Peptidomics: LC-MS operational parameters do matter.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {229}, number = {}, pages = {115348}, doi = {10.1016/j.jpba.2023.115348}, pmid = {36963248}, issn = {1873-264X}, abstract = {The sensitive and specific detection of peptides at low levels in biofluids is critical to increase the lab-to-human translation of peptidomic research. An interesting group of peptides with increasing evidence for involvement in human diseases are quorum sensing peptides. To obtain more reliable conclusions on peptide measurands in biofluids, a selection of often neglected parts of the analytical process using LC-MS were investigated, with novel approaches recommended for each part. Quorum sensing peptides were used as the main model-peptides. The peptidomic parts investigated and discussed here are: Our work addresses aQbD-approached solutions to these challenges, encompassing sample stabilization measures, a suitable peptide anti-adsorption tool, judicious choice of injection solvent versus gradient system and optimal duty cycle parameters. Our recommendations will improve the peptidomics bio-analytics of not only quorum sensing peptides, but can also be of value for other measurands at low concentrations.}, }
@article {pmid36963164, year = {2023}, author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M}, title = {Decipher enzymes from human microbiota for drug discovery and development.}, journal = {Current opinion in structural biology}, volume = {80}, number = {}, pages = {102567}, doi = {10.1016/j.sbi.2023.102567}, pmid = {36963164}, issn = {1879-033X}, abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.}, }
@article {pmid36961872, year = {2023}, author = {Janker, L and Schuster, D and Bortel, P and Hagn, G and Meier-Menches, SM and Mohr, T and Mader, JC and Slany, A and Bileck, A and Brunmair, J and Madl, C and Unger, L and Hennlich, B and Weitmayr, B and Del Favero, G and Pils, D and Pukrop, T and Pfisterer, N and Feichtenschlager, T and Gerner, C}, title = {Multi-omics empowered deep phenotyping of ulcerative colitis identifies biomarker signatures reporting functional remission states.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjad052}, pmid = {36961872}, issn = {1876-4479}, abstract = {INTRODUCTION: Ulcerative colitis (UC) is a chronic disease with rising incidence and unclear etiology. Deep molecular phenotyping by multi omics analyses may provide novel insights into disease processes and characteristic features of remission states.<br><br>METHODS: UC pathomechanisms were assessed by proteome profiling of human tissue specimen, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multi-omics analyses comprising proteins, metabolites and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission in comparison to healthy controls.<br><br>RESULTS: Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B- and T-cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general down-regulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. While pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission, several, but not all, molecular candidate biomarker levels recovered back to normal.<br><br>CONCLUSIONS: The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission but apparently persist as disease-associated molecular signature. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms potentially supporting the assessment of disease and remission states in UC patients.}, }
@article {pmid36961605, year = {2023}, author = {Basiru, S and Ait Si Mhand, K and Hijri, M}, title = {Disentangling arbuscular mycorrhizal fungi and bacteria at the soil-root interface.}, journal = {Mycorrhiza}, volume = {}, number = {}, pages = {}, pmid = {36961605}, issn = {1432-1890}, abstract = {Arbuscular mycorrhizal fungi (AMF) are essential components of the plant root mycobiome and are found in approximately 80% of land plants. As obligate plant symbionts, AMF harbor their own microbiota, both inside and outside the plant root system. AMF-associated bacteria (AAB) possess various functional traits, including nitrogen fixation, organic and inorganic phosphate mobilization, growth hormone production, biofilm production, enzymatic capabilities, and biocontrol against pathogen attacks, which not only contribute to the health of the arbuscular mycorrhizal symbiosis but also promote plant growth. Because of this, there is increasing interest in the diversity, functioning, and mechanisms that underlie the complex interactions between AMF, AAB, and plant hosts. This review critically examines AMF-associated bacteria, focusing on AAB diversity, the factors driving richness and community composition of these bacteria across various ecosystems, along with the physical, chemical, and biological connections that enable AMF to select and recruit beneficial bacterial symbionts on and within their structures and hyphospheres. Additionally, potential applications of these bacteria in agriculture are discussed, emphasizing the potential importance of AMF fungal highways in engineering plant rhizosphere and endophyte bacteria communities, and the importance of a functional core of AAB taxa as a promising tool to improve plant and soil productivity. Thus, AMF and their highly diverse bacterial taxa represent important tools that could be efficiently explored in sustainable agriculture, carbon sequestration, and reduction of greenhouse gas emissions related to nitrogen fertilizer applications. Nevertheless, future studies adopting integrated multidisciplinary approaches are crucial to better understand AAB functional diversity and the mechanisms that govern these tripartite relationships.}, }
@article {pmid36961604, year = {2023}, author = {Nöltner, C and Bulashevska, A and Hübscher, K and Haberstroh, H and Grimbacher, B and Proietti, M}, title = {Fecal Immunoglobulin Levels as a Modifier of the Gut Microbiome in Patients with Common Variable Immunodeficiency.}, journal = {Journal of clinical immunology}, volume = {}, number = {}, pages = {}, pmid = {36961604}, issn = {1573-2592}, abstract = {OBJECTIVE: Common variable immunodeficiency (CVID) is the most common clinically relevant entity of inborn errors of immunity. In these patients, an altered gut microbiome composition with reduced diversity has been described. We sought to investigate the fecal immunoglobulin levels and their impact on the gut microflora in patients with CVID.<br><br>METHODS: We analyzed the gut microbiome of 28 CVID patients and 42 healthy donors (HDs), including 21 healthy household controls, by sequencing the V3 and V4 regions of the bacterial 16S rRNA gene extracted from stool samples. The fecal levels of immunoglobulin A, M, and G of 27 CVID patients and 41 HDs were measured in the supernatant by ELISA and normalized for protein concentration.<br><br>RESULTS: We measured decreased IgA and increased IgG in stool samples from CVID patients compared to HDs. Decreased levels of fecal IgA and IgM were associated with reduced microbial diversity and increased dysbiosis. We identified a large number of significantly differentially abundant taxa, especially in patients with decreased IgA levels, but also in patients with decreased IgM levels compared to their counterparts.<br><br>CONCLUSIONS: CVID patients have an altered gut microbiota composition, which is most prevalent in patients with decreased fecal IgA and IgM levels. In this study, we identify fecal immunoglobulins as a potential modifier of the gut microbiome in CVID patients.}, }
@article {pmid36961409, year = {2023}, author = {Vishnoi, V and Morey, T and Hoedt, EC and Keely, S and Pockney, P and Smith, SR}, title = {A Systematic Review and Meta-Analysis of Intra-Operative Surgical Site Sampling: Culture versus Culture-Independent Techniques in Predicting Downstream Surgical Site Infection.}, journal = {Surgical infections}, volume = {}, number = {}, pages = {}, doi = {10.1089/sur.2023.012}, pmid = {36961409}, issn = {1557-8674}, abstract = {Background: Surgical site infection remains a significant cause of morbidity and mortality. Traditionally, the causation has been inferred from the organism(s) detected in the post-operative setting. However, the intra-operative surgical site and the bacteria it harbors have been scarcely studied. Compared with culture-dependent methods, the development of genomic technology provides a new sensitive tool that could aid in characterizing the bacteria within the surgical site. The purpose of this literature review is to establish if there is a predictive role of sampling the intra-operative surgical site. Methods: A systematic literature review was conducted identifying relevant literature reporting on studies that sampled the intra-operative surgical site of any specialty, using either traditional culture or a culture-independent genomic sequencing-based technique and correlation with infection was attempted. The review identified studies between 1959 and 2021 in MEDLINE, EMBASE and Cochrane. Results: The initial search identified 7,835 articles; 36 remained after screening. Thirty-one articles focused on culture-dependent techniques, five on culture-independent. Subgroup meta-analysis demonstrates that a positive intra-operative culture carries a risk of downstream infection with an odds ratio of 8.6, however limited by a high false-positive and inability to correlate the intra-operative culture with the post-operative infection. In contrast, culture-independent studies through genomic sequencing are not predictive but suggest that the surgical incision is a complex microbial community with a shift toward dysbiosis in certain patients. Conclusion: The intra-operative surgical site clearly harbors bacteria. Both techniques give rise to separate explanations underpinning the role of bacteria in surgical site infection. It is possible there is a more complex dynamic community within the incision that makes a patient susceptible to infection. Characterizing this microbial community in large scale studies, including patients with infections may enhance our ability to predict and prevent incisional surgical site infections in patients undergoing surgical procedures.}, }
@article {pmid36960914, year = {2023}, author = {Cable, J and Rathmell, JC and Pearce, EL and Ho, PC and Haigis, MC and Mamedov, MR and Wu, MJ and Kaech, SM and Lynch, L and Febbraio, MA and Bapat, SP and Hong, HS and Zou, W and Belkaid, Y and Sullivan, ZA and Keller, A and Wculek, SK and Green, DR and Postic, C and Amit, I and Benitah, SA and Jones, RG and Reina-Campos, M and Torres, SV and Beyaz, S and Brennan, D and O'Neill, LAJ and Perry, RJ and Brenner, D}, title = {Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report.}, journal = {Annals of the New York Academy of Sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/nyas.14976}, pmid = {36960914}, issn = {1749-6632}, support = {/NH/NIH HHS/United States ; }, abstract = {Immunometabolism considers the relationship between metabolism and immunity. Typically, researchers focus on either the metabolic pathways within immune cells that affect their function or the impact of immune cells on systemic metabolism. A more holistic approach that considers both these viewpoints is needed. On September 5-8, 2022, experts in the field of immunometabolism met for the Keystone symposium "Immunometabolism at the Crossroads of Obesity and Cancer" to present recent research across the field of immunometabolism, with the setting of obesity and cancer as an ideal example of the complex interplay between metabolism, immunity, and cancer. Speakers highlighted new insights on the metabolic links between tumor cells and immune cells, with a focus on leveraging unique metabolic vulnerabilities of different cell types in the tumor microenvironment as therapeutic targets and demonstrated the effects of diet, the microbiome, and obesity on immune system function and cancer pathogenesis and therapy. Finally, speakers presented new technologies to interrogate the immune system and uncover novel metabolic pathways important for immunity.}, }
@article {pmid36960491, year = {2023}, author = {Johnston, W and Rosier, BT and Carda-Diéguez, M and Paterson, M and Watson, P and Piela, K and Goulding, M and Ramage, G and Baranyia, D and Chen, T and Al-Hebshi, N and Mira, A and Culshaw, S}, title = {Longitudinal changes in subgingival biofilm composition following periodontal treatment.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JPER.22-0749}, pmid = {36960491}, issn = {1943-3670}, abstract = {BACKGROUND: Current periodontal treatment involves instrumentation using hand and/or ultrasonic instruments, which are used either alone or in combination based on patient and clinician preference, with comparable clinical outcomes. This study sought to investigate early and later changes in the subgingival biofilm following periodontal treatment; to identify whether these changes were associated with treatment outcomes; and to investigate whether the biofilm responded differently to hand compared with ultrasonic instruments.<br><br>METHODS: This was a secondary-outcome analysis of a randomised controlled trial. Thirty-eight periodontitis patients received full-mouth subgingival instrumentation using hand (n = 20) or ultrasonic instrumentation (n = 18). Subgingival plaque was sampled at baseline and 1, 7 and 90 days following treatment. Bacterial DNA was analysed using 16S rRNA sequencing. Periodontal clinical parameters were evaluated before and after treatment.<br><br>RESULTS: Biofilm composition was comparable in both (hand and ultrasonics) treatment groups at all timepoints (all genus and species; p[adjusted]>0.05). Large-scale changes were observed within-groups across timepoints. At days 1 and 7, taxonomic diversity and dysbiosis were reduced, with an increase in health-associated genera including Streptococcus and Rothia equating to 30-40% of the relative abundance. When reassessed at day 90 a subset of samples reformed a microbiome more comparable with baseline, which was independent of instrumentation choice and residual disease.<br><br>CONCLUSIONS: Hand and ultrasonic instruments induced comparable impacts on the subgingival plaque microbiome. There were marked early changes in the subgingival biofilm composition, although there was limited evidence that community shifts associated with treatment outcomes. This article is protected by copyright. All rights reserved.}, }
@article {pmid36960395, year = {2023}, author = {Uzuner, C and Mak, J and El-Assaad, F and Condous, G}, title = {The bidirectional relationship between endometriosis and microbiome.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1110824}, pmid = {36960395}, issn = {1664-2392}, abstract = {Endometriosis has been described by many different theories of pathogenesis over the years. It is now also appreciated to be a state of chronic inflammation, and the role of immune dysfunction in its development has been proven. There is increasing evidence to support the role of the microbiome in the formation and progression of endometriosis via inflammatory pathways. The dysbiosis seen in endometriosis is thought to be both causative and a consequence of the pathogenesis. Gut, peritoneal fluid and female reproductive tract microbiota has been studied to understand if there are any microbiome signatures specific to endometriosis. New research on how to manipulate the microbiome for better detection and treatment of endometriosis is emerging.}, }
@article {pmid36960288, year = {2023}, author = {Zeng, Q and Man, X and Huang, Z and Zhuang, L and Yang, H and Sha, Y}, title = {Effects of rice blast biocontrol strain Pseudomonas alcaliphila Ej2 on the endophytic microbiome and proteome of rice under salt stress.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1129614}, pmid = {36960288}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinity is a prevalent environmental stress in agricultural production. Microbial inoculants could effectively help plants to alleviate salt stress. However, there is little knowledge of the biocontrol strain Pseudomonas alcaliphila Ej2 mechanisms aiding rice plants to reduce the adverse effects caused by salt stress.<br><br>METHODS: We performed integrated field and greenhouse experiments, microbial community profiling, and rice proteomic analysis to systematically investigate the Ej2 mechanism of action.<br><br>RESULTS: The results displayed that biocontrol strain Ej2 increased shoot/root length and fresh/dry weight compared with control under salt stress. Meanwhile, strain Ej2 has the ability to control rice blast disease and promote rice growth. Furthermore, the microbial community analysis revealed that the alpha-diversity of Ej2-inoculated plants was higher than the control plants, expect the Shannon index of the bacterial microbiome and the Ej2-inoculated samples clustered and separated from the control samples based on beta-diversity analysis. Importantly, the enriched and specific OTUs after Ej2 inoculation at the genus level were Streptomyces, Pseudomonas, Flavobacterium, and Bacillus. Moreover, we observed that Ej2 inoculation influenced the rice proteomic profile, including metabolism, plant-pathogen interactions, and biosynthesis of unsaturated fatty acids. These results provide comprehensive evidence that Ej2 inoculation induced the rice endophytic microbiome and proteomic profiles to promote plant growth under salt stress.<br><br>DISCUSSION: Understanding the biocontrol strain effects on the endophytic microbiome and rice proteomics will help us better understand the complex interactions between plants and microorganisms under salt stress. Furthermore, unraveling the mechanisms underlying salt tolerance will help us more efficiently ameliorate saline soils.}, }
@article {pmid36960281, year = {2023}, author = {Kapinusova, G and Lopez Marin, MA and Uhlik, O}, title = {Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089630}, pmid = {36960281}, issn = {1664-302X}, abstract = {In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.}, }
@article {pmid36960045, year = {2023}, author = {Yang, Z and Cai, T and Li, Y and Jiang, D and Luo, J and Zhou, Z}, title = {Effects of topical fluoride application on oral microbiota in young children with severe dental caries.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1104343}, pmid = {36960045}, issn = {2235-2988}, abstract = {While the effect of fluoride on severe early childhood caries (S-ECC) is clear, knowledge of how it influences the oral microbiota and the consequential effects on oral health is limited. In this cohort study, we investigated the changes introduced in the oral ecosystem before and after using fluoride varnish in 54- to 66-month-old individuals (n=90: 18 children were sampled at 5 different time points). 16S rDNA was amplified from bacterial samples using polymerase chain reaction, and high-throughput sequencing was performed using Illumina MiSeq platforms. Many pronounced microbial changes were related to the effects of fluoride varnishing. The health-associated Bacteroides and Uncultured_bacterium_f_Enterobacteriaceae were enriched in the saliva microbiome following treatment with fluoride varnishing. Co-occurrence network analysis of the dominant genera showed that different groups clearly showed different bacterial correlations. The PICRUSt algorithm was used to predict the function of the microbial communities from saliva samples. The results showed that starch and sucrose metabolism was greater after fluoride use. BugBase was used to determine phenotypes present in microbial community samples. The results showed that Haemophilus and Neisseria (phylum Proteobacteria) was greater before fluoride use. We conclude that the changes in oral microbiology play a role in fluoride prevention of S-ECC.}, }
@article {pmid36960044, year = {2023}, author = {Zhao, H and Chen, Y and Zheng, Y and Xu, J and Zhang, C and Fu, M and Xiong, K}, title = {Conjunctival sac microbiome in anophthalmic patients: Flora diversity and the impact of ocular prosthesis materials.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1117673}, pmid = {36960044}, issn = {2235-2988}, abstract = {PURPOSE: To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.<br><br>METHODS: A cross-sectional clinical study was conducted, involving 19 OP patients and 23 healthy subjects. Samples were collected from the upper, lower palpebral, caruncle, and fornix conjunctiva. 16S rRNA sequencing was applied to identify the bacterial flora in the samples. The eye comfort of each OP patient was determined by a questionnaire. In addition, demographics information of each participant was also collected.<br><br>RESULTS: The diversity and richness of ocular flora in OP patients were significantly higher than that in healthy subjects. The results of flora species analysis also indicated that in OP patients, pathogenic microorganisms such as Escherichia Shigella and Fusobacterium increased significantly, while the resident flora of Lactobacillus and Lactococcus decreased significantly. Within the self-comparison of OP patients, compared with Polymethyl Methacrylate (PMMA), prosthetic material of glass will lead to the increased colonization of opportunistic pathogens such as Alcaligenes, Dermabacter and Spirochaetes, while gender and age have no significant impact on ocular flora.<br><br>CONCLUSIONS: The ocular flora of OP patients was significantly different from that of healthy people. Abundant colonization of pathogenic microorganisms may have an important potential relationship with eye discomfort and eye diseases of OP patients. PMMA, as an artificial eye material, demonstrated potential advantages in reducing the colonization of opportunistic pathogens.}, }
@article {pmid36960043, year = {2023}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1158392}, doi = {10.3389/fcimb.2023.1158392}, pmid = {36960043}, issn = {2235-2988}, }
@article {pmid36959989, year = {2022}, author = {Khanna, HN and Roy, S and Shaikh, A and Bandi, V}, title = {Emerging Role and Place of Probiotics in the Management of Pediatric Neurodevelopmental Disorders.}, journal = {Euroasian journal of hepato-gastroenterology}, volume = {12}, number = {2}, pages = {102-108}, pmid = {36959989}, issn = {2231-5047}, abstract = {UNLABELLED: The current decade has witnessed significant developments with the latest therapeutic agents for managing various infectious diseases to complex hemato-oncological conditions, leading to a decrease in morbidity and mortality, while improving the quality of life (QoL), and increasing the life span. Non-communicable diseases (NCDs), which are on the rise across all age-groups, are being driven by unhealthy lifestyles and improved mental health issues. The current therapeutic agents were found to offer only symptomatic relief of varying efficacy and significant adverse effects, leading clinicians to evaluate other options for the management of both neurodevelopmental and neurodegenerative disorders. The role of gut microbiota has emerged as a potential target for the treatment of both neurodegenerative diseases and neurodevelopmental disorders like attention-deficit hyperactivity disorder (ADHD)/autism spectrum disorders (ASD) as a result of the decoding of the human genome and advances in our understanding of the human gut microbiome, including its interactions with the human brain. This review has been undertaken to understand on date level of understanding of human microbiota and towards identifying probiotic strains with proven efficacy and safety. According to recent investigations, several lactobacillus strains, including L. Paracasei 37, L. Planetarium 128, L. reuteri DSM 17938, and Bifidobacterium longum, have been effective in treating children's neurodevelopmental disorders such as ASD and ADHD. Future clinical studies are nonetheless required to confirm the long-term safety and effectiveness of probiotic strains in managing the primary and comorbid symptoms, hence improving patient and family quality of life.<br><br>HOW TO CITE THIS ARTICLE: Khanna HN, Roy S, Shaikh A, et al. Emerging Role and Place of Probiotics in the Management of Pediatric Neurodevelopmental Disorders. Euroasian J Hepato-Gastroenterol 2022;12(2):102-108.}, }
@article {pmid36959951, year = {2023}, author = {Mundra, S and Shockey, J and Morsy, M}, title = {Editorial: Plant microbiome: Ecology, functions, and application trends.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1175556}, pmid = {36959951}, issn = {1664-462X}, }
@article {pmid36959686, year = {2023}, author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J}, title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {36959686}, issn = {2542-5641}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.<br><br>METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.<br><br>RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella, Hungatella, Peptostreptococcus, and Parvimonas, and decreased Butyricicoccus, Lactobacillus, and Paraprevotella. The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas, Desulfurispora, Sebaldella, and Veillonellales, among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium, Thermococci, and Cellulophaga.<br><br>CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.}, }
@article {pmid36959568, year = {2023}, author = {Ivashkin, V and Shifrin, O and Maslennikov, R and Poluektova, E and Korolev, A and Kudryavtseva, A and Krasnov, G and Benuni, N and Barbara, G}, title = {Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study.}, journal = {BMC gastroenterology}, volume = {23}, number = {1}, pages = {82}, pmid = {36959568}, issn = {1471-230X}, abstract = {BACKGROUND: Rifaximin effectively treats symptomatic uncomplicated diverticular disease (SUDD) and has shown eubiotic potential (i.e., an increase in resident microbial elements with potential beneficial effects) in other diseases. This study investigated changes in the fecal microbiome of patients with SUDD after repeated monthly treatment with rifaximin and the association of these changes with the severity of abdominal pain.<br><br>METHODS: This was a single-center, prospective, observational, uncontrolled cohort study. Patients received rifaximin 400&#xa0;mg twice a day for 7 days per month for 6 months. Abdominal pain (assessed on a 4-point scale from 0 [no pain] to 3 [severe pain]) and fecal microbiome (assessed using 16&#xa0;S rRNA gene sequencing) were assessed at inclusion (baseline) and 3 and 6 months. The Spearman's rank test analyzed the relationship between changes in the gut microbiome and the severity of abdominal pain. A p-value&#x2009;&#x2264;&#x2009;0.05 was considered statistically significant.<br><br>RESULTS: Of the 23 patients enrolled, 12 patients completed the study and were included in the analysis. Baseline abdominal pain levels decreased significantly after 3 (p&#x2009;=&#x2009;0.036) and 6 (p&#x2009;=&#x2009;0.008) months of treatment with rifaximin. The abundance of Akkermansia in the fecal microbiome was significantly higher at 3 (p&#x2009;=&#x2009;0.017) and 6 (p&#x2009;=&#x2009;0.015) months versus baseline. The abundance of Ruminococcaceae (p&#x2009;=&#x2009;0.034), Veillonellaceae (p&#x2009;=&#x2009;0.028), and Dialister (p&#x2009;=&#x2009;0.036) were significantly increased at 6 months versus baseline, whereas Anaerostipes (p&#x2009;=&#x2009;0.049) was significantly decreased. The severity of abdominal pain was negatively correlated with the abundance of Akkermansia (r=-0.482; p&#x2009;=&#x2009;0.003) and Ruminococcaceae (r=-0.371; p&#x2009;=&#x2009;0.026) but not with Veillonellaceae, Dialister, or Anaerostipes. After 3 months of rifaximin, abdominal pain was significantly less in patients with Akkermansia in their fecal microbiome than in patients without Akkermansia (p&#x2009;=&#x2009;0.022).<br><br>CONCLUSION: The eubiotic effect of rifaximin was associated with decreased abdominal pain in patients with SUDD.}, }
@article {pmid36959296, year = {2023}, author = {Bernard, NJ}, title = {Microbiome checkpoint.}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41590-023-01486-1}, pmid = {36959296}, issn = {1529-2916}, }
@article {pmid36959286, year = {2023}, author = {Ye, W and Xing, J and Yu, Z and Hu, X and Zhao, Y}, title = {Mechanism and treatments of antipsychotic-induced weight gain.}, journal = {International journal of obesity (2005)}, volume = {}, number = {}, pages = {}, pmid = {36959286}, issn = {1476-5497}, abstract = {The long-term use of antipsychotics (APs) may cause a variety of diseases, such as metabolic syndrome, antipsychotic-induced weight gain (AIWG), and even obesity. This paper reviews the various mechanisms of AIWG and obesity in detail, involving genetics, the central nervous system, the neuroendocrine system, and the gut microbiome. The common drug and non-drug therapies used in clinical practice are also introduced, providing the basis for research on the molecular mechanisms and the future selection of treatments.}, }
@article {pmid36959210, year = {2023}, author = {Wu, CM and Wheeler, KM and Cárcamo-Oyarce, G and Aoki, K and McShane, A and Datta, SS and Mark Welch, JL and Tiemeyer, M and Griffen, AL and Ribbeck, K}, title = {Mucin glycans drive oral microbial community composition and function.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {11}, pmid = {36959210}, issn = {2055-5008}, abstract = {Human microbiome composition is closely tied to health, but how the host manages its microbial inhabitants remains unclear. One important, but understudied, factor is the natural host environment: mucus, which contains gel-forming glycoproteins (mucins) that display hundreds of glycan structures with potential regulatory function. Leveraging a tractable culture-based system to study how mucins influence oral microbial communities, we found that mucin glycans enable the coexistence of diverse microbes, while resisting disease-associated compositional shifts. Mucins from tissues with unique glycosylation differentially tuned microbial composition, as did isolated mucin glycan libraries, uncovering the importance of specific glycan patterns in microbiome modulation. We found that mucins shape microbial communities in several ways: serving as nutrients to support metabolic diversity, organizing spatial structure through reduced aggregation, and possibly limiting antagonism between competing taxa. Overall, this work identifies mucin glycans as a natural host mechanism and potential therapeutic intervention to maintain healthy microbial communities.}, }
@article {pmid36959041, year = {2023}, author = {Ait-Zenati, F and Djoudi, F and Mehelleb, D and Madaoui, M}, title = {Involvement of the human microbiome in frequent cancers, current knowledge and carcinogenesis mechanisms.}, journal = {Bulletin du cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bulcan.2023.01.022}, pmid = {36959041}, issn = {1769-6917}, abstract = {The human body is home to a complex microbial community, living in symbiosis. However, when an imbalance occurs, known as dysbiosis, it can lead to organic diseases such as cancers. Helicobacter pylori is commonly recognized as the causative agent of gastric cancer. Numerous studies have explored the potential role of other microorganisms in cancers. For example, the role of intestinal microbiota in the hepatocellular carcinoma formation and progression, the microbiota in breast cancer and the interaction between the microbiome and TP53 in human lung carcinogenesis. In this review, we highlight the latest findings on the microbiome involved in the most common cancers and the suggested mechanisms of carcinogenesis.}, }
@article {pmid36958817, year = {2023}, author = {Vich Vila, A and Hu, S and Andreu-Sánchez, S and Collij, V and Jansen, BH and Augustijn, HE and Bolte, LA and Ruigrok, RAAA and Abu-Ali, G and Giallourakis, C and Schneider, J and Parkinson, J and Al-Garawi, A and Zhernakova, A and Gacesa, R and Fu, J and Weersma, RK}, title = {Faecal metabolome and its determinants in inflammatory bowel disease.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2022-328048}, pmid = {36958817}, issn = {1468-3288}, abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD.<br><br>DESIGN: We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels.<br><br>RESULTS: We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism.<br><br>CONCLUSION: In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.}, }
@article {pmid36958642, year = {2023}, author = {Detcharoen, M and Jiggins, FM and Schlick-Steiner, BC and Steiner, FM}, title = {Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa.}, journal = {Journal of invertebrate pathology}, volume = {198}, number = {}, pages = {107915}, doi = {10.1016/j.jip.2023.107915}, pmid = {36958642}, issn = {1096-0805}, abstract = {Wolbachia are known to cause reproductive manipulations and in some arthropod species, Wolbachia were reported to cause changes in gut microbiome. However, the effects of Wolbachia bacteria on the microbiomes of their hosts, including Drosophila flies, have not been fully accessed. Here, we checked the bacterial microbiome in guts of Wolbachia-uninfected and of Wolbachia-infected Drosophila nigrosparsa, both separated into a bleach-only (embryos bleached) and a gnotobiotic (embryos bleached and inoculated with bacteria) treatment. We observed a clear separation between the Wolbachia-infected and the Wolbachia-uninfected samples, and the infected samples had higher variation in alpha diversity than the uninfected ones. There were reductions in the abundances of Proteobacteria (Pseudomonadota), especially Acetobacter, in the infected samples of both treatments. These findings highlight that Wolbachia change the gut microbiome in D. nigrosparsa as well as that the interactions between Wolbachia and bacteria like Acetobacter need to be investigated.}, }
@article {pmid36958561, year = {2023}, author = {Mancuso, FP and Morrissey, KL and De Clerck, O and Airoldi, L}, title = {Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162919}, doi = {10.1016/j.scitotenv.2023.162919}, pmid = {36958561}, issn = {1879-1026}, abstract = {Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.}, }
@article {pmid36958158, year = {2023}, author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH}, title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131200}, doi = {10.1016/j.jhazmat.2023.131200}, pmid = {36958158}, issn = {1873-3336}, abstract = {The preeminence of sulfonamide drug resistance genes in food waste (FW) and the increased utilization of high-strength organic FW in anaerobic digestion (AD) to enhance methane production have raised severe public health concerns in wastewater treatment plants worldwide. In this regard, the dissemination patterns of different sulfonamide resistance genes (sul1 and sul2) and their impact on the digester core microbiota during AD of FW leachate (FWL) were evaluated. The presence of various sulfonamide antibiotics (SAs) in FWL digesters improved the final methane yield by 37 % during AD compared with FWL digesters without SAs. Microbial population shifts towards hydrolytic, acidogenic, and acetogenic bacteria in the phyla Actinobacteriota, Bacteroidota, Chloroflexi, Firmicutes, Proteobacteria, and Synergistota occurred due to SA induced substrate digestion and absorption through active transport; butanoate, propanoate, and pyruvate metabolism; glycolysis; gluconeogenesis; the citrate cycle; and pentose phosphate pathway. The initial dominance of Methanosaeta (89-96 %) declined to 47-53 % as AD progressed and shifted towards Methanosarcina (40 %) in digesters with the highest SA concentrations at the end of AD. Dissemination of sul1 depended on class 1 integron gene (intl1)-based horizontal gene transfer to pathogenic members of Chloroflexi, Firmicutes, and Patescibacteria, whereas sul2 was transmitted to Synergistota independent of intl1. Low susceptibility and ability to utilize SAs during methanogenesis shielded methanogenic archaea against selection pressure, thus preventing them from interacting with sul or intl1 genes, thereby minimizing the risk of antibiotic resistance development. The observed emergence of cationic antimicrobial peptide, vancomycin, and β-lactam resistance in the core microbiota during AD of FWL in the presence of SAs suggests that multidrug resistance caused by bacterial transformation could lead to an increase in the environmental resistome through wastewater sludge treatment.}, }
@article {pmid36870434, year = {2023}, author = {Maves, RC and Kalil, AC}, title = {Which trial do we need? Doxycycline in combination with ceftriaxone for the treatment of community-acquired pneumonia.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2023.02.020}, pmid = {36870434}, issn = {1469-0691}, }
@article {pmid36957979, year = {2023}, author = {Kato, I and Sun, J}, title = {Microbiome and Diet in Colon Cancer Development and Treatment.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {89-97}, pmid = {36957979}, issn = {1540-336X}, abstract = {Diet plays critical roles in defining our immune responses, microbiome, and progression of human diseases. With recent progress in sequencing and bioinformatic techniques, increasing evidence indicates the importance of diet-microbial interactions in cancer development and therapeutic outcome. Here, we focus on the epidemiological studies on diet-bacterial interactions in the colon cancer. We also review the progress of mechanistic studies using the experimental models. Finally, we discuss the limits and future directions in the research of microbiome and diet in cancer development and therapeutic outcome. Now, it is clear that microbes can influence the efficacy of cancer therapies. These research results open new possibilities for the diagnosis, prevention, and treatment of cancer. However, there are still big gaps to apply these new findings to the clinical practice.}, }
@article {pmid36957978, year = {2023}, author = {Amit, U and Facciabene, A and Ben-Josef, E}, title = {Radiation Therapy and the Microbiome; More Than a Gut Feeling.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {84-88}, doi = {10.1097/PPO.0000000000000650}, pmid = {36957978}, issn = {1540-336X}, abstract = {It is increasingly recognized that heterogeneities in tumor response and severity of adverse effects in irradiated patients can be attributed to the tumor microenvironment and host-related factors. Among the latter, a growing body of literature in recent years has demonstrated the role of the patient's microbiome in modulating both tumor and normal tissue response to radiotherapy (RT). Upon contact with the environment after birth, the infant's gastrointestinal tract is rapidly colonized by microbiota, which is low in diversity and predominantly characterized by 2 dominant species, Actinobacteria and Proteobacteria. With time, intestinal microbiota diversity increases, and colonization of Firmicutes and Bacteroidetes becomes dominant. By the time a child reaches 3 years, the gut microbiota composition has been reshaped and is relatively similar to that of an adult. The microbiome colonizing the different body organs comprises various species and abundances, which may impact human health. Although the adult microbiome composition is thought to remain stable in health, microbiome diversity and composition respond to different environmental and pathological conditions, including pharmaceutical interventions and RT. Our review focuses on how the gut microbiota modulates normal tissue toxicity and tumor control. Readers who want to learn more about how RT shapes gut microbiome diversity and composition are referred to several excellent recently published reviews.}, }
@article {pmid36957977, year = {2023}, author = {Malard, F and Jenq, RR}, title = {The Microbiome and Its Impact on Allogeneic Hematopoietic Cell Transplantation.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {75-83}, pmid = {36957977}, issn = {1540-336X}, abstract = {Allogeneic hematopoietic cell transplantation (alloHCT) is a standard curative therapy for a variety of benign and malignant hematological diseases. Previously, patients who underwent alloHCT were at high risk for complications with potentially life-threatening toxicities, including a variety of opportunistic infections as well as acute and chronic manifestations of graft-versus-host disease (GVHD), where the transplanted immune system can produce inflammatory damage to the patient. With recent advances, including newer conditioning regimens, advances in viral and fungal infection prophylaxis, and novel GVHD prophylactic and treatment strategies, improvements in clinical outcomes have steadily improved. One modality with great potential that has yet to be fully realized is targeting the microbiome to further improve clinical outcomes.In recent years, the intestinal microbiota, which includes bacteria, fungi, viruses, and other microbes that reside within the intestinal tract, has become established as a potent modulator of alloHCT outcomes. The composition of intestinal bacteria, in particular, has been found in large multicenter prospective studies to be strongly associated with GVHD, treatment-related mortality, and overall survival. Murine studies have demonstrated a causal relationship between intestinal microbiota injury and aggravated GVHD, and more recently, clinical interventional studies of repleting the intestinal microbiota with fecal microbiota transplantation have emerged as effective therapies for GVHD. How the composition of the intestinal bacterial microbiota, which is often highly variable in alloHCT patients, can modulate GVHD and other outcomes is not fully understood. Recent studies, however, have begun to make substantial headway, including identifying particular bacterial subsets and/or bacterial-derived metabolites that can mediate harm or benefit. Here, the authors review recent studies that have improved our mechanistic understanding of the relationship between the microbiota and alloHCT outcomes, as well as studies that are beginning to establish strategies to modulate the microbiota with the hope of optimizing clinical outcomes.}, }
@article {pmid36957976, year = {2023}, author = {Jiminez, V and Yusuf, N}, title = {Role of the Microbiome in Immunotherapy of Melanoma.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {70-74}, pmid = {36957976}, issn = {1540-336X}, abstract = {Novel immunotherapeutics for advanced melanoma have drastically changed survival rates and management strategies in recent years. Immune checkpoint inhibitors have emerged as efficacious agents for some patients but have not been proven to be as beneficial in other patient cohorts. Recent investigation into this observation has implicated the gut microbiome as a potential immunomodulator in regulating patient response to therapy. Numerous studies have provided evidence for this link. Bacterial colonization patterns have been associated with therapeutic outcomes, under the notion that favorable commensal organisms improve host immune response. This review aims to report the most recent and pertinent findings related to the relationship between gut microbial communities and melanoma therapy efficacy. This article also highlights the emerging frontier of artificial intelligence in its application regarding patient microbial composition evaluation, predictive models for therapy response, and recommendations for the future of probiotics and dietary interventions to optimize melanoma survival and outcomes.}, }
@article {pmid36957975, year = {2023}, author = {Kennedy, K and Khaddour, K and Ramnath, N and Weinberg, F}, title = {The Lung Microbiome in Carcinogenesis and Immunotherapy Treatment.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {61-69}, pmid = {36957975}, issn = {1540-336X}, abstract = {Lung cancer is the leading cause of cancer-related deaths. Over the past 10 years, significant advances in treatment modalities, including immune checkpoint inhibitor (ICI) blockade, have led to improved outcomes. Elucidating predicative biomarkers in responders and nonresponders to ICI will lead to development of therapeutic targets that could enhance ICI efficacy. Recently, the gut microbiome was identified as a predictive biomarker for ICI in patients with multiple cancer types. However, it is unclear how other host microbiomes influence tumorigenesis and response to ICI. Other groups have explored the lung microbiome as it relates to carcinogenesis and immunotherapy efficacy. In this review, we explore the role of the lung microbiome in health and disease. We also review the current state of lung microbiome research as it relates to tumorigenesis and treatments and provide potential insights into how the lung microbiome could improve outcomes in patients with cancer.}, }
@article {pmid36957974, year = {2023}, author = {Myojin, Y and Greten, TF}, title = {The Microbiome and Liver Cancer.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {57-60}, pmid = {36957974}, issn = {1540-336X}, abstract = {The gut microbiome and liver are anatomically and functionally connected. The impact of the gut microbiota or microbial metabolites on liver cancer progression via immune cells has been recently revealed across various preclinical models. Commensal gut microbes of liver cancer patients differ from control subjects, and their composition is affected by the etiology of the hepatocellular carcinoma. The gut microbiota represents a potential novel target for intervention as shown in patients with melanoma, but we still lack data in patients with hepatocellular carcinoma. Fecal microbiota transplantation and dietary approaches may improve immunotherapy efficacy, and a couple of clinical trials are ongoing. In liver cancer, the ongoing recognition of interactions between gut microbes and the tumor immune microenvironment provides an exciting therapeutic avenue to complement established immunotherapy.}, }
@article {pmid36957973, year = {2023}, author = {Attebury, H and Daley, D}, title = {The Gut Microbiome and Pancreatic Cancer Development and Treatment.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {49-56}, pmid = {36957973}, issn = {1540-336X}, abstract = {Changes in the gut microbiome have been increasingly shown to accompany oncogenesis across various tumors. Similarly, microbial dysbiosis was found to be associated with pancreatic cancer progression and survival outcomes, expanding the field of tumor microenvironment research in pancreatic cancer. Mechanistic studies in pancreatic cancer models implicate components of the gut and pancreatic cancer microbiome in regulating tumorigenesis by altering cancer cell signaling, modulating immune function, and influencing the efficacy of current therapies in pancreatic cancer. This review discusses the outcomes of microbial modulation across various preclinical and clinical studies and highlights ongoing trials targeting the microbiome for pancreatic cancer therapy.}, }
@article {pmid36957972, year = {2023}, author = {Chen, GY}, title = {The Human Microbiome and Cancer.}, journal = {Cancer journal (Sudbury, Mass.)}, volume = {29}, number = {2}, pages = {47-48}, doi = {10.1097/PPO.0000000000000653}, pmid = {36957972}, issn = {1540-336X}, }
@article {pmid36952261, year = {2023}, author = {Ryan, E and Joyce, SA and Clarke, DJ}, title = {Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {3}, pages = {}, doi = {10.1099/mic.0.001315}, pmid = {36952261}, issn = {1465-2080}, abstract = {Bacteria produce an array of diverse, dynamic and often complex lipid structures, some of which function beyond their typical role in membrane structure. The model organism, E. coli, has three major membrane lipids, which are glycerophosphoglycerol (phosphatidylglycerol), glycerophosphoethanolamine (phosphatidylethanolamine) and cardiolipin. However, it is now appreciated that some bacteria have the capacity to synthesize a range of lipids, including glycerophosphocholines, glycerophosphoinositols, 'phosphorous-free' N-acyl amines, sphingolipids and plasmalogens. In recent years, some of these bacterial lipids have emerged as influential contributors to the microbe-host molecular dialogue. This review outlines our current knowledge of bacterial lipid diversity, with a focus on the membrane lipids of microbiome-associated bacteria that have documented roles as signalling molecules.}, }
@article {pmid36951975, year = {2023}, author = {Long, X and Mu, S and Zhang, J and Xiang, H and Wei, W and Sun, J and Kuang, Z and Yang, Y and Chen, Y and Zhao, H and Dong, Y and Yin, J and Zheng, H and Song, Z}, title = {Global signatures of the microbiome and metabolome during hospitalization of septic patients.}, journal = {Shock (Augusta, Ga.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/SHK.0000000000002117}, pmid = {36951975}, issn = {1540-0514}, abstract = {BACKGROUND: The gut plays an important role in the development of sepsis and acts as one of the possible drivers of multiple organ dysfunction syndrome (MODS). This study aimed to explore the dynamic alterations in the gut microbiota and its metabolites in septic patients at different stages of ICU admission.<br><br>METHODS: In this prospective observational study, a total of 109 fecal samples from 23 septic patients, 16 non-septic ICU patients and 10 healthy controls were analyzed. 16S rRNA gene sequencing and UPLC-MS/MS targeted metabolomics were used for microbiota and metabolome analysis. A prediction model combining the SOFA score, Klebsiella , taurocholic acid, and butyric acid was used to predict the prognosis of sepsis.<br><br>RESULTS: The diversity and dominant species of the gut microbiota of septic patients were significantly disturbed. The proportions of normal gut microbiota, such as Firmicutes on the phylum level, as well as Faecalibacterium, Subdoligranulum , Ruminococcus , Agathobacter , and Blautia on the genus level, were decreased at different stages of ICU admission, while the proportions of potential pathogenic bacteria, such as Proteobacteria on the phylum level, and Enterococcus and Stenotrophomonas on the genus level were significantly increased. In addition, the amount of short-chain fatty acids and secondary bile acids decreased in septic patients, while that of the primary bile acids increased markedly. Bacterial richness and diversity were lower in the non-surviving patients than those in the surviving patients in the later stage of ICU admission. In the nomogram model, the higher abundance of Klebsiella , concentration of taurocholic acid and SOFA score, combined with a lower butyric acid concentration, could predict a higher probability of death from sepsis.<br><br>CONCLUSION: Our study indicated that the dynamical alterations of gut microbiota and its metabolites were associated with the prognosis of the sepsis. Based on these alterations and clinical indicators, a nomogram model to predict the prognosis of septic patients was performed.}, }
@article {pmid36951585, year = {2023}, author = {Singavarapu, B and Du, J and Beugnon, R and Cesarz, S and Eisenhauer, N and Xue, K and Wang, Y and Bruelheide, H and Wubet, T}, title = {Functional Potential of Soil Microbial Communities and Their Subcommunities Varies with Tree Mycorrhizal Type and Tree Diversity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0457822}, doi = {10.1128/spectrum.04578-22}, pmid = {36951585}, issn = {2165-0497}, abstract = {Soil microbial communities play crucial roles in the earth's biogeochemical cycles. Yet, their genomic potential for nutrient cycling in association with tree mycorrhizal type and tree-tree interactions remained unclear, especially in diverse tree communities. Here, we studied the genomic potential of soil fungi and bacteria with arbuscular (AM) and ectomycorrhizal (EcM) conspecific tree species pairs (TSPs) at three tree diversity levels in a subtropical tree diversity experiment (BEF-China). The soil fungi and bacteria of the TSPs' interaction zone were characterized by amplicon sequencing, and their subcommunities were determined using a microbial interkingdom co-occurrence network approach. Their potential genomic functions were predicted with regard to the three major nutrients carbon (C), nitrogen (N), and phosphorus (P) and their combinations. We found the microbial subcommunities that were significantly responding to different soil characteristics. The tree mycorrhizal type significantly influenced the functional composition of these co-occurring subcommunities in monospecific stands mixtures and two-tree-species mixtures but not in mixtures with more than three tree species (here multi-tree-species mixtures). Differentiation of subcommunities was driven by differentially abundant taxa producing different sets of nutrient cycling enzymes across the tree diversity levels, predominantly enzymes of the P (n = 11 and 16) cycles, followed by the N (n = 9) and C (n = 9) cycles, in monospecific stands and two-tree-species mixtures, respectively. Fungi of the Agaricomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes and bacteria of the Verrucomicrobia, Acidobacteria, Alphaproteobacteria, and Actinobacteria were the major differential contributors (48% to 62%) to the nutrient cycling functional abundances of soil microbial communities across tree diversity levels. Our study demonstrated the versatility and significance of microbial subcommunities in different soil nutrient cycling processes of forest ecosystems. IMPORTANCE Loss of multifunctional microbial communities can negatively affect ecosystem services, especially forest soil nutrient cycling. Therefore, exploration of the genomic potential of soil microbial communities, particularly their constituting subcommunities and taxa for nutrient cycling, is vital to get an in-depth mechanistic understanding for better management of forest soil ecosystems. This study revealed soil microbes with rich nutrient cycling potential, organized in subcommunities that are functionally resilient and abundant. Such microbial communities mainly found in multi-tree-species mixtures associated with different mycorrhizal partners can foster soil microbiome stability. A stable and functionally rich soil microbiome is involved in the cycling of nutrients, such as carbon, nitrogen, and phosphorus, and their combinations could have positive effects on ecosystem functioning, including increased forest productivity. The new findings could be highly relevant for afforestation and reforestation regimes, notably in the face of growing deforestation and global warming scenarios.}, }
@article {pmid36951567, year = {2023}, author = {Goswami, A and Adkins-Jablonsky, SJ and Barreto Filho, MM and Shilling, MD and Dawson, A and Heiser, S and O'Connor, A and Walker, M and Roberts, Q and Morris, JJ}, title = {Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0242622}, doi = {10.1128/spectrum.02426-22}, pmid = {36951567}, issn = {2165-0497}, abstract = {Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.}, }
@article {pmid36951555, year = {2023}, author = {Chu, Y and Meng, Q and Yu, J and Zhang, J and Chen, J and Kang, Y}, title = {Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0455122}, doi = {10.1128/spectrum.04551-22}, pmid = {36951555}, issn = {2165-0497}, abstract = {The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.}, }
@article {pmid36951547, year = {2023}, author = {Yang, Q and Wang, B and Zheng, Q and Li, H and Meng, X and Zhou, F and Zhang, L}, title = {A Review of Gut Microbiota-Derived Metabolites in Tumor Progression and Cancer Therapy.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2207366}, doi = {10.1002/advs.202207366}, pmid = {36951547}, issn = {2198-3844}, abstract = {Gut microbiota-derived metabolites are key hubs connecting the gut microbiome and cancer progression, primarily by remodeling the tumor microenvironment and regulating key signaling pathways in cancer cells and multiple immune cells. The use of microbial metabolites in radiotherapy and chemotherapy mitigates the severe side effects from treatment and improves the efficacy of treatment. Immunotherapy combined with microbial metabolites effectively activates the immune system to kill tumors and overcomes drug resistance. Consequently, various novel strategies have been developed to modulate microbial metabolites. Manipulation of genes involved in microbial metabolism using synthetic biology approaches directly affects levels of microbial metabolites, while fecal microbial transplantation and phage strategies affect levels of microbial metabolites by altering the composition of the microbiome. However, some microbial metabolites harbor paradoxical functions depending on the context (e.g., type of cancer). Furthermore, the metabolic effects of microorganisms on certain anticancer drugs such as irinotecan and gemcitabine, render the drugs ineffective or exacerbate their adverse effects. Therefore, a personalized and comprehensive consideration of the patient's condition is required when employing microbial metabolites to treat cancer. The purpose of this review is to summarize the correlation between gut microbiota-derived metabolites and cancer, and to provide fresh ideas for future scientific research.}, }
@article {pmid36951501, year = {2023}, author = {Latour, YL and Allaman, MM and Barry, DP and Smith, TM and Williams, KJ and McNamara, KM and Jacobse, J and Goettel, JA and Delgado, AG and Piazuelo, MB and Zhao, S and Gobert, AP and Wilson, KT}, title = {Epithelial talin-1 protects mice from citrobacter rodentium-induced colitis by restricting bacterial crypt intrusion and enhancing t cell immunity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192623}, doi = {10.1080/19490976.2023.2192623}, pmid = {36951501}, issn = {1949-0984}, abstract = {Pathogenic enteric Escherichia coli present a significant burden to global health. Food-borne enteropathogenic E. coli (EPEC) and Shiga toxin-producing E. coli (STEC) utilize attaching and effacing (A/E) lesions and actin-dense pedestal formation to colonize the gastrointestinal tract. Talin-1 is a large structural protein that links the actin cytoskeleton to the extracellular matrix though direct influence on integrins. Here we show that mice lacking talin-1 in intestinal epithelial cells (Tln1[Δepi]) have heightened susceptibility to colonic disease caused by the A/E murine pathogen Citrobacter rodentium. Tln1[Δepi] mice exhibit decreased survival, and increased colonization, colon weight, and histologic colitis compared to littermate Tln1[fl/fl] controls. These findings were associated with decreased actin polymerization and increased infiltration of innate myeloperoxidase-expressing immune cells, confirmed as neutrophils by flow cytometry, but more bacterial dissemination deep into colonic crypts. Further evaluation of the immune population recruited to the mucosa in response to C. rodentium revealed that loss of Tln1 in colonic epithelial cells (CECs) results in impaired recruitment and activation of T cells. C. rodentium infection-induced colonic mucosal hyperplasia was exacerbated in Tln1[Δepi] mice compared to littermate controls. We demonstrate that this is associated with decreased CEC apoptosis and crowding of proliferating cells in the base of the glands. Taken together, talin-1 expression by CECs is important in the regulation of both epithelial renewal and the inflammatory T cell response in the setting of colitis caused by C. rodentium, suggesting that this protein functions in CECs to limit, rather than contribute to the pathogenesis of this enteric infection.}, }
@article {pmid36951379, year = {2023}, author = {Rak, MB and Moyers, TD and Price, JM and Whittemore, JC}, title = {Clinicopathologic and gastrointestinal effects of administration of prednisone, prednisone with omeprazole, or prednisone with probiotics to dogs: A double-blind randomized trial.}, journal = {Journal of veterinary internal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/jvim.16672}, pmid = {36951379}, issn = {1939-1676}, abstract = {BACKGROUND: The efffect of administering of probiotics or twice-daily omeprazole on glucocorticoid-induced gastric bleeding in dogs is unknown.<br><br>HYPOTHESIS: Compare gastrointestinal bleeding among dogs administered placebo, prednisone (2&#xa0;mg/kg q24h), prednisone with omeprazole (1&#xa0;mg/kg q12h), or prednisone with probiotics (Visbiome, 11.2-22.5 billion CFU/kg q24h) for 28&#x2009;days.<br><br>ANIMALS: Twenty-four healthy research dogs.<br><br>METHODS: Double-blinded, placebo-controlled randomized trial. Clinical signs and endoscopic gastrointestinal mucosal lesion scores at baseline (t1), day 14 (t2), and day 28 (t3) were compared using split-plot repeated-measures mixed-model ANOVAs.<br><br>RESULTS: Fecal score differed by treatment-by-time (F[6,40] =&#x2009;2.65, P&#x2009;<&#x2009;.03), with higher scores in groups receiving prednisone at t3 than t1 . Nineteen of thirty-three episodes of diarrhea occurred in the prednisone with omeprazole group. Gastric mucosal lesion scores differed by treatment-by-time (F[6,60] =&#x2009;2.86, P&#xa0;=&#xa0;.05), among treatment groups (F[3,60] =&#x2009;4.9, P&#xa0;=&#xa0;.004), and over time (F[2,60] =&#x2009;16.5, P&#x2009;<&#x2009;.001). Post hoc analysis revealed lesion scores increased over time for all groups receiving prednisone. At t3 , scores for the prednisone (8.7&#x2009;&#xb1;&#x2009;4.9) and prednisone with probiotics (8.7&#x2009;&#xb1;&#x2009;4.9) groups differed significantly from placebo (1.8&#x2009;&#xb1;&#x2009;1.8; P&#x2009;&#x2264;&#x2009;.04), whereas scores for the prednisone with omeprazole (6.5&#x2009;&#xb1;&#x2009;5.5) group did not differ from placebo (P&#xa0;=&#xa0;.7). Ulcers occurred only in dogs receiving prednisone.<br><br>Prednisone-induced gastric bleeding. Co-administration of omeprazole partially mitigated bleeding, but a similar protective benefit was not demonstrated by co-administration of the evaluated probiotic.}, }
@article {pmid36951365, year = {2023}, author = {Ricci, F and Tandon, K and Moßhammer, M and Cho, EH and Blackall, LL and Kühl, M and Verbruggen, H}, title = {Fine-scale mapping of physicochemical and microbial landscapes of the coral skeleton.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16369}, pmid = {36951365}, issn = {1462-2920}, abstract = {The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 and pH gradients, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. In this study, we employed chemical imaging of O2 and pH, hyperspectral reflectance imaging and spatially resolved taxonomic and inferred functional microbiome characterisation to explore links between the skeleton microenvironment and microbiome in the reef-building corals Porites lutea and Paragoniastrea benhami. The physicochemical environment was more stable in the deep skeleton and the diversity and evenness of the bacterial community increased with skeletal depth, suggesting that the microbiome was stratified along the physicochemical gradients. The bulk of the coral skeleton was a low O2 habitat, whereas pH varied from pH 6 to 9 with depth. Physicochemical gradients of O2 and pH of the coral skeleton explained the β-diversity of the bacterial communities, and skeletal layers that showed O2 peaks had a higher relative abundance of endolithic algae, reflecting a link between the abiotic environment and the microbiome composition. Our study links the physicochemical, microbial and functional landscapes of the coral skeleton and provides new insights into the involvement of skeletal microbes in coral holobiont metabolism. This article is protected by copyright. All rights reserved.}, }
@article {pmid36951135, year = {2023}, author = {Zhou, M and Yue, Y and Wang, Y and Yan, S}, title = {Polysaccharides from Chinese herbs as natural weapons against colorectal cancer.}, journal = {Bioscience reports}, volume = {}, number = {}, pages = {}, doi = {10.1042/BSR20230041}, pmid = {36951135}, issn = {1573-4935}, abstract = {Colorectal cancer (CRC) ranks third and second among the most widespread cancers worldwide and the most common causes of human death due to cancer, respectively. Further, for unknown reasons, numbers of young patients diagnosed with colon cancer has increased. Polysaccharides are important functional phytochemicals reported to have anti-CRC effects. Moreover, CRC development and progression is closely related to the gut microbiome. Although approaches for treating CRC have been the subject of some review papers, research into traditional Chinese medicine (TCM) treatments for CRC and the underlying mechanisms involving polysaccharides have not been reviewed. Here, we reviewed the mechanisms underlying treatment of CRC using TCM polysaccharides, based on the etiology of CRC, and common treatment methods applied. The relationship between intestinal microbes and CRC, the mechanism by which TCM polysaccharides induce CRC cell apoptosis, and how TCM polysaccharides promote immune responses are discussed, as well as TCM polysaccharide use in combination with chemotherapy. TCM polysaccharides provide options for CRC treatment, due to their advantages of having multiple targets, eliciting modest adverse reactions, and wide range of available sources.}, }
@article {pmid36950983, year = {2023}, author = {Wang, J and Yan, Y and Si, H and Li, J and Zhao, Y and Gao, T and Pi, J and Zhang, R and Chen, R and Chen, W and Zheng, Y and Jiang, M}, title = {The effect of real-ambient PM2.5 exposure on the lung and gut microbiomes and the regulation of Nrf2.}, journal = {Ecotoxicology and environmental safety}, volume = {254}, number = {}, pages = {114702}, doi = {10.1016/j.ecoenv.2023.114702}, pmid = {36950983}, issn = {1090-2414}, mesh = {Mice ; Humans ; Animals ; *Air Pollutants/toxicity/analysis ; *Gastrointestinal Microbiome ; NF-E2-Related Factor 2/genetics ; Particulate Matter/toxicity ; Lung/chemistry ; }, abstract = {The influence of air pollution on human health has sparked widespread concerns across the world. Previously, we found that exposure to ambient fine particulate matter (PM2.5) in our "real-ambient exposure" system can result in reduced lung function. However, the mechanism of organ-specific toxicity is still not fully elucidated. The balance of the microbiome contributes to maintaining lung and gut health, but the changes in the microbiome under PM2.5 exposure are not fully understood. Recently, crosstalk between nuclear factor E2-related factor 2 (Nrf2) and the microbiome was reported. However, it is unclear whether Nrf2 affects the lung and gut microbiomes under PM2.5 exposure. In this study, wild-type (WT) and Nrf2[-/-] (KO) mice were exposed to filtered air (FA) and real ambient PM2.5 (PM) in the " real-ambient exposure" system to examine changes in the lung and gut microbiomes. Here, our data suggested microbiome dysbiosis in lung and gut of KO mice under PM2.5 exposure, and Nrf2 ameliorated the microbiome disorder. Our study demonstrated the detrimental impacts of PM2.5 on the lung and gut microbiome by inhaled exposure to air pollution and supported the protective role of Nrf2 in maintaining microbiome homeostasis under PM2.5 exposure.}, }
@article {pmid36950861, year = {2023}, author = {Nierengarten, MB}, title = {Gut microbiome contributes to neutropenic fever.}, journal = {Cancer}, volume = {129}, number = {8}, pages = {1142}, doi = {10.1002/cncr.34739}, pmid = {36950861}, issn = {1097-0142}, }
@article {pmid36950169, year = {2023}, author = {Hofmann, B and Dreyling, L and Dal Grande, F and Otte, J and Schmitt, I}, title = {Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1067906}, pmid = {36950169}, issn = {1664-302X}, abstract = {INTRODUCTION: Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests.<br><br>METHODS: Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany.<br><br>RESULTS: ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks.<br><br>DISCUSSION: Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.}, }
@article {pmid36950158, year = {2023}, author = {Wang, Z and Li, Q and Lan, X and Shen, W and Wan, F and He, J and Tang, S and Tan, Z}, title = {Evaluation of stirring time through a rumen simulation technique: Influences on rumen fermentation and bacterial community.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1103222}, pmid = {36950158}, issn = {1664-302X}, abstract = {INTRODUCTION: Rumen motility is a key element that influences ruminant nutrition, whereas little is known about the effects of rumen contraction duration on rumen fermentation and ruminal microbiome. We previously reported that proper rotation speed of a rumen simulation technique (RUSITEC) system enhanced rumen fermentation and microbial protein (MCP) production. In the present study, different contraction durations and intervals were simulated by setting different stirring times and intervals of the stirrers in a RUSITEC system. The objective of this trial was to evaluate the influences of stirring time on rumen fermentation characteristics, nutrient degradation, and ruminal bacterial microbiota in vitro.<br><br>METHODS: This experiment was performed in a 3&#x2009;&#xd7;&#x2009;3 Latin square design, with each experimental period comprising 4 d for adjustment and 3 d for sample collection. Three stirring time treatments were set: the constant stir (CS), the intermittent stir 1 (each stir for 5&#x2009;min with an interval of 2&#x2009;min, IS1), and the intermittent stir 2 (each stir for 4&#x2009;min with an interval of 3&#x2009;min, IS2).<br><br>RESULTS: The total volatile fatty acid (TVFA) concentration, valerate molar proportion, ammonia nitrogen level, MCP density, protozoa count, disappearance rates of dry matter, organic matter, crude protein, neutral detergent fiber, and acid detergent fiber, emissions of total gas and methane, and the richness index Chao 1 for the bacterial community were higher (p&#x2009;<&#x2009;0.05) in the IS1 when compared to those in the CS. The greatest TVFA, MCP, protozoa count, nutrient disappearance rates, gas productions, and bacterial richness indices of Ace and Chao 1 amongst all treatments were observed in the IS2. The relative abundance of the genus Treponema was enriched (p&#x2009;<&#x2009;0.05) in CS, while the enrichment (p&#x2009;<&#x2009;0.05) of Agathobacter ruminis and another two less known bacterial genera were identified in IS2.<br><br>DISCUSSION: It could be concluded that the proper reduction in the stirring time might help to enhance the feed fermentation, MCP synthesis, gas production, and the relative abundances of specific bacterial taxa.}, }
@article {pmid36950061, year = {2023}, author = {Awan, I and Schultz, E and Sterrett, JD and Dawud, LM and Kessler, LR and Schoch, D and Lowry, CA and Feldman-Winter, L and Phadtare, S}, title = {A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life.}, journal = {Pediatric gastroenterology, hepatology &amp; nutrition}, volume = {26}, number = {2}, pages = {99-115}, pmid = {36950061}, issn = {2234-8646}, abstract = {PURPOSE: Exclusive breastfeeding promotes gut microbial compositions associated with lower rates of metabolic and autoimmune diseases. Its cessation is implicated in increased microbiome-metabolome discordance, suggesting a vulnerability to dietary changes. Formula supplementation is common within our low-income, ethnic-minority community. We studied exclusively breastfed (EBF) neonates' early microbiome-metabolome coupling in efforts to build foundational knowledge needed to target this inequality.<br><br>METHODS: Maternal surveys and stool samples from seven EBF neonates at first transitional stool (0-24 hours), discharge (30-48 hours), and at first appointment (days 3-5) were collected. Survey included demographics, feeding method, medications, medical history and tobacco and alcohol use. Stool samples were processed for 16S rRNA gene sequencing and lipid analysis by gas chromatography-mass spectrometry. Alpha and beta diversity analyses and Procrustes randomization for associations were carried out.<br><br>RESULTS: Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the most abundant taxa. Variation in microbiome composition was greater between individuals than within (p=0.001). Palmitic, oleic, stearic, and linoleic acids were the most abundant lipids. Variation in lipid composition was greater between individuals than within (p=0.040). Multivariate composition of the metabolome, but not microbiome, correlated with time (p=0.030). Total lipids, saturated lipids, and unsaturated lipids concentrations increased over time (p=0.012, p=0.008, p=0.023). Alpha diversity did not correlate with time (p=0.403). Microbiome composition was not associated with each samples' metabolome (p=0.450).<br><br>CONCLUSION: Neonate gut microbiomes were unique to each neonate; respective metabolome profiles demonstrated generalizable temporal developments. The overall variability suggests potential interplay between influences including maternal breastmilk composition, amount consumed and living environment.}, }
@article {pmid36949872, year = {2023}, author = {Babu, TM and Srinivasan, S and Magaret, A and Proll, S and Karita, HS and Wallis, JM and Selke, S and Varon, D and Pholsena, T and Fredricks, D and Marrazzo, J and Wald, A and Johnston, C}, title = {Genital Herpes Simplex Virus Type 2 Suppression With Valacyclovir Is Not Associated With Changes in Nugent Score or Absolute Abundance of Key Vaginal Bacteria.}, journal = {Open forum infectious diseases}, volume = {10}, number = {3}, pages = {ofad099}, pmid = {36949872}, issn = {2328-8957}, abstract = {BACKGROUND: In women, genital herpes simplex virus type 2 (HSV-2) infection is associated with increased risk for recurrent bacterial vaginosis (BV), but causal relationships are unclear.<br><br>METHODS: Women with a self-reported history of BV and HSV-2 seropositivity self-collected vaginal and anogenital swabs for 2 nonconsecutive 28-day periods, in the absence or presence of valacyclovir suppressive therapy (500&#x2005;mg daily). HSV polymerase chain reaction was performed on anogenital swabs; vaginal swabs were used for assessment of BV by Nugent score and quantification of vaginal microbiota. Days with BV, defined by Nugent score &#x2265;7, were compared during the observational period and valacyclovir treatment.<br><br>RESULTS: Forty-one women collected swabs for a median of 28&#x2005;days (range, 20-32 days) each study period. The HSV-2 shedding rate decreased from 109 of 1126&#x2005;days (9.7%) presuppression to 6 of 1125&#x2005;days (0.05%) during valacyclovir (rate ratio [RR], 0.06 [95% confidence interval {CI}, .02-.13]). BV occurred on 343 of 1103&#x2005;days (31.1%) during observation and 302 of 1091&#x2005;days (27.7%) during valacyclovir (RR, 0.90 [95% CI, .68-1.20]). The median per-person Nugent score was 3.8 during observation and 4.0 during valacyclovir. Average log10 concentrations of vaginal bacterial species did not change significantly during valacyclovir treatment.<br><br>CONCLUSIONS: Short-term HSV-2 suppression with valacyclovir did not significantly affect the Nugent score or the vaginal microbiome despite potent suppression of HSV-2 shedding.}, }
@article {pmid36949813, year = {2023}, author = {Rego, ROM and Lopez, JE and Cabesas-Cruz, A}, title = {Editorial: Biological drivers of vector-pathogen interactions - vol II.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1170834}, doi = {10.3389/fcimb.2023.1170834}, pmid = {36949813}, issn = {2235-2988}, }
@article {pmid36949549, year = {2023}, author = {Liukkonen, M and Hukkanen, M and Cossin-Sevrin, N and Stier, A and Vesterinen, E and Grond, K and Ruuskanen, S}, title = {No evidence for associations between brood size, gut microbiome diversity and survival in great tit (Parus major) nestlings.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {19}, pmid = {36949549}, issn = {2524-4671}, abstract = {BACKGROUND: The gut microbiome forms at an early stage, yet data on the environmental factors influencing the development of wild avian microbiomes is limited. As the gut microbiome is a vital part of organismal health, it is important to understand how it may connect to host performance. The early studies with wild gut microbiome have shown that the rearing environment may be of importance in gut microbiome formation, yet the results vary across taxa, and the effects of specific environmental factors have not been characterized. Here, wild great tit (Parus major) broods were manipulated to either reduce or enlarge the original brood soon after hatching. We investigated if brood size was associated with nestling bacterial gut microbiome, and whether gut microbiome diversity predicted survival. Fecal samples were collected at mid-nestling stage and sequenced with the 16S rRNA gene amplicon sequencing, and nestling growth and survival were measured.<br><br>RESULTS: Gut microbiome diversity showed high variation between individuals, but this variation was not significantly explained by brood size or body mass. Additionally, we did not find a significant effect of brood size on body mass or gut microbiome composition. We also demonstrated that early handling had no impact on nestling performance or gut microbiome. Furthermore, we found no significant association between gut microbiome diversity and short-term (survival to fledging) or mid-term (apparent juvenile) survival.<br><br>CONCLUSIONS: We found no clear association between early-life environment, offspring condition and gut microbiome. This suggests that brood size is not a significantly contributing factor to great tit nestling condition, and that other environmental and genetic factors may be more strongly linked to offspring condition and gut microbiome. Future studies should expand into other early-life environmental factors e.g., diet composition and quality, and parental influences.}, }
@article {pmid36949545, year = {2023}, author = {Graham, EH and Tom, WA and Neujahr, AC and Adamowicz, MS and Clarke, JL and Herr, JR and Fernando, SC}, title = {The persistence and stabilization of auxiliary genes in the human skin virome.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {49}, pmid = {36949545}, issn = {1743-422X}, abstract = {BACKGROUND: The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.<br><br>RESULTS: Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions.<br><br>CONCLUSIONS: This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.}, }
@article {pmid36949474, year = {2023}, author = {Regueira-Iglesias, A and Vázquez-González, L and Balsa-Castro, C and Vila-Blanco, N and Blanco-Pintos, T and Tamames, J and Carreira, MJ and Tomás, I}, title = {In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {58}, pmid = {36949474}, issn = {2049-2618}, abstract = {BACKGROUND: Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.<br><br>RESULTS: A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) &#x2265;75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.<br><br>CONCLUSIONS: Given the three amplicon length categories (100-300, 301-600, and >600 base&#xa0;pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.}, }
@article {pmid36949471, year = {2023}, author = {Volmer, JG and Soo, RM and Evans, PN and Hoedt, EC and Astorga Alsina, AL and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Morrison, M}, title = {Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {59}, pmid = {36949471}, issn = {1741-7007}, abstract = {BACKGROUND: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.<br><br>RESULTS: Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).<br><br>CONCLUSIONS: Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.}, }
@article {pmid36949458, year = {2023}, author = {Huang, X and Huang, X and Huang, Y and Zheng, J and Lu, Y and Mai, Z and Zhao, X and Cui, L and Huang, S}, title = {The oral microbiome in autoimmune diseases: friend or foe?.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {211}, pmid = {36949458}, issn = {1479-5876}, abstract = {The human body is colonized by abundant and diverse microorganisms, collectively known as the microbiome. The oral cavity has more than 700 species of bacteria and consists of unique microbiome niches on mucosal surfaces, on tooth hard tissue, and in saliva. The homeostatic balance between the oral microbiota and the immune system plays an indispensable role in maintaining the well-being and health status of the human host. Growing evidence has demonstrated that oral microbiota dysbiosis is actively involved in regulating the initiation and progression of an array of autoimmune diseases.Oral microbiota dysbiosis is driven by multiple factors, such as host genetic factors, dietary habits, stress, smoking, administration of antibiotics, tissue injury and infection. The dysregulation in the oral microbiome plays a crucial role in triggering and promoting autoimmune diseases via several mechanisms, including microbial translocation, molecular mimicry, autoantigen overproduction, and amplification of autoimmune responses by cytokines. Good oral hygiene behaviors, low carbohydrate diets, healthy lifestyles, usage of prebiotics, probiotics or synbiotics, oral microbiota transplantation and nanomedicine-based therapeutics are promising avenues for maintaining a balanced oral microbiome and treating oral microbiota-mediated autoimmune diseases. Thus, a comprehensive understanding of the relationship between oral microbiota dysbiosis and autoimmune diseases is critical for providing novel insights into the development of oral microbiota-based therapeutic approaches for combating these refractory diseases.}, }
@article {pmid36949312, year = {2023}, author = {Kim, IB and Park, SC and Kim, YK}, title = {Microbiota-Gut-Brain Axis in Major Depression: A New Therapeutic Approach.}, journal = {Advances in experimental medicine and biology}, volume = {1411}, number = {}, pages = {209-224}, pmid = {36949312}, issn = {0065-2598}, abstract = {Major depression is impacted by the disruption of gut microbiota. Defects in gut microbiota can lead to microbiota-gut-brain axis dysfunction and increased vulnerability to major depression. While traditional chemotherapeutic approaches, such as antidepressant use, produce an overall partial therapeutic effect on depression, the gut microbiome has emerged as an effective target for better therapeutic outcomes. Recent representative studies on the microbiota hypothesis to explore the association between gut pathophysiology and major depression have indicated that restoring gut microbiota and microbiota-gut-brain axis could alleviate depression. We reviewed studies that supported the gut microbiota hypothesis to better understand the pathophysiology of depression; we also explored reports suggesting that gut microbiota restoration is an effective approach for improving depression. These findings indicate that gut microbiota and microbiota-gut-brain axis are appropriate new therapeutic targets for major depression.}, }
@article {pmid36949306, year = {2023}, author = {Evrensel, A}, title = {Microbiome-Induced Autoimmunity and Novel Therapeutic Intervention.}, journal = {Advances in experimental medicine and biology}, volume = {1411}, number = {}, pages = {71-90}, pmid = {36949306}, issn = {0065-2598}, abstract = {Microorganisms' flora, which colonize in many parts of our body, stand out as one of the most important components for a healthy life. This microbial organization called microbiome lives in integration with the body as a single and whole organ/system. Perhaps, the human first encounters the microbial activity it carries through the immune system. This encounter and interaction are vital for the development of immune system cells that protect the body against pathogenic organisms and infections throughout life. In recent years, it has been determined that some disruptions in the host-microbiome interaction play an important role in the physiopathology of autoimmune diseases. Although the details of this interaction have not been clarified yet, the focus is on leaky gut syndrome, dysbiosis, toll-like receptor ligands, and B cell dysfunction. Nutritional regulations, prebiotics, probiotics, fecal microbiota transplantation, bacterial engineering, and vaccination are being investigated as new therapeutic approaches in the treatment of problems in these areas. This article reviews recent research in this area.}, }
@article {pmid36948991, year = {2023}, author = {Le Sayec, M and Lecomte, M and Fança-Berthon, P and Rodriguez-Mateos, A}, title = {Reply letter to editor - The effects of aronia berry (poly)phenol supplementation on arterial function and the gut microbiome in middle aged men and women.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnu.2023.03.002}, pmid = {36948991}, issn = {1532-1983}, }
@article {pmid36948151, year = {2023}, author = {Toh, E and Xing, Y and Gao, X and Jordan, SJ and Batteiger, TA and Batteiger, BE and Van Der Pol, B and Muzny, CA and Gebregziabher, N and Williams, JA and Fortenberry, LJ and Fortenberry, JD and Dong, Q and Nelson, DE}, title = {Sexual behavior shapes male genitourinary microbiome composition.}, journal = {Cell reports. Medicine}, volume = {4}, number = {3}, pages = {100981}, doi = {10.1016/j.xcrm.2023.100981}, pmid = {36948151}, issn = {2666-3791}, abstract = {The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.}, }
@article {pmid36948121, year = {2023}, author = {Wang, K and Cai, M and Sun, J and Chen, H and Lin, Z and Wang, Z and Niu, Q and Ji, T}, title = {Atrazine exposure can dysregulate the immune system and increase the susceptibility against pathogens in honeybees in a dose-dependent manner.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131179}, doi = {10.1016/j.jhazmat.2023.131179}, pmid = {36948121}, issn = {1873-3336}, abstract = {Recently, concerns regarding the impact of agrochemical pesticides on non-target organisms have increased. The effect of atrazine, the second-most widely used herbicide in commercial farming globally, on honeybees remains poorly understood. Here, we evaluated how atrazine impacts the survival of honeybees and pollen and sucrose consumption, investigating the morphology and mRNA expression levels of midgut tissue, along with bacterial composition (relative abundance) and load (absolute abundance) in the whole gut. Atrazine did not affect mortality, but high exposure (37.3 mg/L) reduced pollen and sucrose consumption, resulting in peritrophic membrane dysplasia. Sodium channels and chitin synthesis were considered potential atrazine targets, with the expression of various genes related to lipid metabolism, detoxification, immunity, and chemosensory activity being inhibited after atrazine exposure. Importantly, 37.3 mg/L atrazine exposure substantially altered the composition and size of the gut microbial community, clearly reducing both the absolute and relative abundance of three core gram-positive taxa, Lactobacillus Firm-5, Lactobacillus Firm-4, and Bifidobacterium asteroides. With altered microbiome composition and a weakened immune system following atrazine exposure, honeybees became more susceptible to infection by the opportunistic pathogen Serratia marcescens. Thus, considering its scale of use, atrazine could negatively impact honeybee populations worldwide, which may adversely affect global food security.}, }
@article {pmid36948003, year = {2023}, author = {Hua, H and Huang, L and Yang, B and Jiang, S and Zhang, Y and Liu, J and Yan, C and Xu, J}, title = {The mediating role of gut microbiota in the associations of prenatal maternal combined exposure to lead and stress with neurodevelopmental deficits in young rats.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114798}, doi = {10.1016/j.ecoenv.2023.114798}, pmid = {36948003}, issn = {1090-2414}, abstract = {Prenatal single and combined exposure to lead (Pb) and stress (Ps) impairs neurodevelopment. Prenatal single exposure to Pb or Ps affects the composition of intestinal microbiota, and bidirectional communication between gut microbiota and central nervous system has been well recognized. However, whether gut microbiota mediated the effects of prenatal Pb+Ps co-exposure on neurodevelopmental deficits remains unclear. This study established rat models with prenatal single and combined exposure to Ps and Pb. We investigated the effects of such prenatal single and combined exposure on hippocampal structures using morphological analyses, on learning/memory using the Morris-water-maze test, and on fecal microbiota using 16S rRNA sequencing. The mediating roles of gut microbiota were analyzed using the bootstrap method. The study found both single and combined exposure affected hippocampal ultra-structures and spatial learning/memory, and the most significant impairments were observed in the Pb+Ps group. Prenatal Pb+Ps co-exposure decreased fecal microbial alpha/beta-diversity. Significantly lower levels of B/F-ratio, class-Bacteroidia, order-Bacteroidales, and family-S24-7, and significantly higher levels of class-Bacilli, order-Lactobacillales, family-Lactobacillaceae, and genus-Lactobacillus were observed in the co-exposure group, compared with the controls. Increased relative abundances of genus-Helicobacter mediated the detrimental effect of prenatal Ps+Pb co-exposure on learning/memory [β (95%CI) for the total and indirect effects: - 10.70 (-19.19, -2.21) and - 4.65(-11.07, -1.85)], accounting for 43.47% of the total effect. As a result, increased relative abundances of genus-Lactobacillus alleviated the adverse effects of the co-exposure on learning/memory, and the alleviation effect accounted for 44.55% of the direct effect [β (95%CI) for the direct and indirect effects: - 0.28(-0.48, -0.08) and 0.13(0.01, 0.41)]. This study suggested that prenatal combined exposure to Pb and Ps induced more impairments in offspring gut microbiota and neurodevelopment than single exposure, and alterations in fecal microbiome may mediate the developmental neurotoxicity induced by such prenatal co-exposure.}, }
@article {pmid36947551, year = {2023}, author = {Bourne, ME and Gloder, G and Weldegergis, BT and Slingerland, M and Ceribelli, A and Crauwels, S and Lievens, B and Jacquemyn, H and Dicke, M and Poelman, EH}, title = {Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1011262}, doi = {10.1371/journal.ppat.1011262}, pmid = {36947551}, issn = {1553-7374}, abstract = {Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.}, }
@article {pmid36947239, year = {2023}, author = {Pielhop, TP and Popp, C and Fricke, S and Knierim, D and Margaria, P and Maiß, E}, title = {Molecular characterization of two new alternaviruses identified in members of the fungal family Nectriaceae.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {129}, pmid = {36947239}, issn = {1432-072X}, abstract = {Since the first report in 2009, at least ten additional viruses have been identified and assigned to the proposed virus family Alternaviridae. Here we report two new mycoviruses tentatively assigned to this family, both identified as members of the fungal family Nectriaceae, which were isolated from surface-disinfected apple roots (Malus x domestica, Borkh.) affected by apple replant disease (ARD). ARD is a highly complex, worldwide-occurring disease resulting from plant reactions to a disturbed (micro)-biome and leads to high economic losses every year. The first alternavirus characterized in this study was identified in a Dactylonectria torresensis isolate. The virus was tentatively named dactylonectria torresensis alternavirus 1 (DtAV1) as the first member of the proposed new species Alternavirus dactylonectriae. The second virus was identified in an isolate of Ilyonectria robusta and was tentatively named ilyonectria robusta alternavirus 1 (IrAV1) as the first member of the proposed new species Alternavirus ilyonectriae. Full genomic sequences of the viruses were determined and are presented. Further, we found hints for putative components of a methyl transferase machinery using in silico approaches. This putative protein domain is encoded by segment 2. However, this result only establishes the basis for subsequent studies in which the function must be confirmed experimentally in vitro. Thus, this is the first study where a function is predicted to all three genomic segments within the group of the alternaviruses. These findings provide further insights into the virome of ARD-associated fungi and are therefore another brick in the wall of understanding the complexity of the disease.}, }
@article {pmid36947108, year = {2023}, author = {Sherif, ZA and Gomez, CR and Connors, TJ and Henrich, TJ and Reeves, WB and , }, title = {Pathogenic mechanisms of post-acute sequelae of SARS-CoV-2 infection (PASC).}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36947108}, issn = {2050-084X}, support = {OT2HL161847-01/NH/NIH HHS/United States ; }, abstract = {COVID-19, with persistent and new onset of symptoms such as fatigue, post-exertional malaise, and cognitive dysfunction that last for months and impact everyday functioning, is referred to as Long COVID under the general category of post-acute sequelae of SARS-CoV-2 infection (PASC). PASC is highly heterogenous and may be associated with multisystem tissue damage/dysfunction including acute encephalitis, cardiopulmonary syndromes, fibrosis, hepatobiliary damages, gastrointestinal dysregulation, myocardial infarction, neuromuscular syndromes, neuropsychiatric disorders, pulmonary damage, renal failure, stroke, and vascular endothelial dysregulation. A better understanding of the pathophysiologic mechanisms underlying PASC is essential to guide prevention and treatment. This review addresses potential mechanisms and hypotheses that connect SARS-CoV-2 infection to long-term health consequences. Comparisons between PASC and other virus-initiated chronic syndromes such as myalgic encephalomyelitis/chronic fatigue syndrome and postural orthostatic tachycardia syndrome will be addressed. Aligning symptoms with other chronic syndromes and identifying potentially regulated common underlining pathways may be necessary for understanding the true nature of PASC. The discussed contributors to PASC symptoms include sequelae from acute SARS-CoV-2 injury to one or more organs, persistent reservoirs of the replicating virus or its remnants in several tissues, re-activation of latent pathogens such as Epstein-Barr and herpes viruses in COVID-19 immune-dysregulated tissue environment, SARS-CoV-2 interactions with host microbiome/virome communities, clotting/coagulation dysregulation, dysfunctional brainstem/vagus nerve signaling, dysautonomia or autonomic dysfunction, ongoing activity of primed immune cells, and autoimmunity due to molecular mimicry between pathogen and host proteins. The individualized nature of PASC symptoms suggests that different therapeutic approaches may be required to best manage specific patients.}, }
@article {pmid36946910, year = {2023}, author = {Richardson, BN and Noh, HI and Webster, CI and Zhang, W and Kim, S and Yang, I and Bai, J}, title = {Oral Microbiome, Mental Health, and Sleep Outcomes During the COVID-19 Pandemic: An Observational Study in Chinese and Korean American Immigrants.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/omi.2022.0182}, pmid = {36946910}, issn = {1557-8100}, abstract = {COVID-19 is a systemic disease whose effects are not limited to the respiratory system. The oral microbiome (OM)-brain axis is of growing interest in understanding the broader, neuropsychiatric, impacts of the COVID-19 pandemic through a systems biology lens. In this context, mental health and sleep disturbance are often reported by Asian Americans. In a cross-sectional observational study design, we examined the associations of the oral microbiome with mental health among Asian Americans during the COVID-19 pandemic (between November 2020 and April 2021). Participants (n = 20) were adult Chinese and Korean American immigrants in Atlanta, Georgia, and primarily born outside the United States (60%) with a mean age of 34.8 years ±14 (standard deviation). Participants reported depressive symptoms, anxiety, and sleep disturbance, as measured by standard questionnaires. The OM was characterized by 16S rRNA V3-V4 gene using saliva. Depressive symptoms and anxiety were reported by 60% (n = 12) of participants, whereas 35% (n = 7) reported sleep disturbance. The α-diversity was significantly associated with depressive symptoms, and marginally with anxiety. Participants with depressive symptoms and anxiety had enriched Rothia and Scardovia, respectively, whereas those without symptoms had enriched Fusobacterium. Individuals with sleep disturbance had enriched Kingella. In conclusion, this study suggests significant associations of the OM diversity with certain mental health dimensions such as depressive symptoms and anxiety. Specific taxa were associated with these symptoms. The present observations in a modest sample size suggest the possible relevance of the OM-brain axis in studies of mental health during COVID-19.}, }
@article {pmid36946724, year = {2023}, author = {Wang, Z and Hu, X and Solanki, MK and Pang, F}, title = {A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c08017}, pmid = {36946724}, issn = {1520-5118}, abstract = {Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.}, }
@article {pmid36946722, year = {2023}, author = {Chung, T and Yan, R and Weller, DL and Kovac, J}, title = {Conditional Forest Models Built Using Metagenomic Data Accurately Predicted Salmonella Contamination in Northeastern Streams.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0038123}, doi = {10.1128/spectrum.00381-23}, pmid = {36946722}, issn = {2165-0497}, abstract = {The use of water contaminated with Salmonella for produce production contributes to foodborne disease burden. To reduce human health risks, there is a need for novel, targeted approaches for assessing the pathogen status of agricultural water. We investigated the utility of water microbiome data for predicting Salmonella contamination of streams used to source water for produce production. Grab samples were collected from 60 New York streams in 2018 and tested for Salmonella. Separately, DNA was extracted from the samples and used for Illumina shotgun metagenomic sequencing. Reads were trimmed and used to assign taxonomy with Kraken2. Conditional forest (CF), regularized random forest (RRF), and support vector machine (SVM) models were implemented to predict Salmonella contamination. Model performance was assessed using 10-fold cross-validation repeated 10 times to quantify area under the curve (AUC) and Kappa score. CF models outperformed the other two algorithms based on AUC (0.86, CF; 0.81, RRF; 0.65, SVM) and Kappa score (0.53, CF; 0.41, RRF; 0.12, SVM). The taxa that were most informative for accurately predicting Salmonella contamination based on CF were compared to taxa identified by ALDEx2 as being differentially abundant between Salmonella-positive and -negative samples. CF and differential abundance tests both identified Aeromonas salmonicida (variable importance [VI] = 0.012) and Aeromonas sp. strain CA23 (VI = 0.025) as the two most informative taxa for predicting Salmonella contamination. Our findings suggest that microbiome-based models may provide an alternative to or complement existing water monitoring strategies. Similarly, the informative taxa identified in this study warrant further investigation as potential indicators of Salmonella contamination of agricultural water. IMPORTANCE Understanding the associations between surface water microbiome composition and the presence of foodborne pathogens, such as Salmonella, can facilitate the identification of novel indicators of Salmonella contamination. This study assessed the utility of microbiome data and three machine learning algorithms for predicting Salmonella contamination of Northeastern streams. The research reported here both expanded the knowledge on the microbiome composition of surface waters and identified putative novel indicators (i.e., Aeromonas species) for Salmonella in Northeastern streams. These putative indicators warrant further research to assess whether they are consistent indicators of Salmonella contamination across regions, waterways, and years not represented in the data set used in this study. Validated indicators identified using microbiome data may be used as targets in the development of rapid (e.g., PCR-based) detection assays for the assessment of microbial safety of agricultural surface waters.}, }
@article {pmid36946508, year = {2023}, author = {Mannan, A and Hoque, MN and Noyon, SH and Hamidullah Mehedi, HM and Foisal, J and Salauddin, A and Rafiqul Islam, SM and Sharmen, F and Tanni, AA and Siddiki, AZ and Tay, A and Siddique, M and Shaminur Rahman, M and Galib, SM and Akter, F}, title = {SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.28691}, pmid = {36946508}, issn = {1096-9071}, abstract = {Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19 positive participants with or without T2DM compared with healthy control subjects. Microbiome data of thirty participants with T2DM were compared with twenty-two age-, sex-, and BMI-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which nine genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25.0%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients. This article is protected by copyright. All rights reserved.}, }
@article {pmid36946486, year = {2023}, author = {Cullen, AE and Labad, J and Oliver, D and Al-Diwani, A and Minichino, A and Fusar-Poli, P}, title = {The Translational Future of Stress Neurobiology and Psychosis Vulnerability: A Review of the Evidence.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/1570159X21666230322145049}, pmid = {36946486}, issn = {1875-6190}, abstract = {Psychosocial stress is a well-established risk factor for psychosis, yet the neurobiological mechanisms underlying this relationship have yet to be fully elucidated. Much of the research in this field has investigated hypothalamic-pituitary-adrenal (HPA) axis function and immuno-inflammatory processes among individuals with established psychotic disorders. However, as such studies are limited in their ability to provide knowledge that can be used to develop preventative interventions, it is important to shift the focus to individuals with increased vulnerability for psychosis (i.e., high-risk groups). In the present article, we provide an overview of the current methods for identifying individuals at high-risk for psychosis and review the psychosocial stressors that have been most consistently associated with psychosis risk. We then describe a network of interacting physiological systems that are hypothesised to mediate the relationship between psychosocial stress and the manifestation of psychotic illness and critically review evidence that abnormalities within these systems characterise high risk populations. We found that studies of high-risk groups have yielded highly variable findings, likely due to (i) the heterogeneity both within and across high-risk samples, (ii) the diversity of psychosocial stressors implicated in psychosis, and (iii) that most studies examine single markers of isolated neurobiological systems. We propose that to move the field forward, we require well-designed, large- scale translational studies that integrate multi-domain, putative stress-related biomarkers to determine their prognostic value in high-risk samples. We advocate that such investigations are highly warranted, given that psychosocial stress is undoubtedly a relevant risk factor for psychotic disorders.}, }
@article {pmid36946468, year = {2023}, author = {Zhang, X and Zhu, K and Zeng, S and Zheng, Y and Cao, J and Li, C}, title = {Microbiome-Metabolomics Analysis Reveals the Mechanism of Holothuria leucospilota Polysaccharides (HLP) in Ulcerative Colitis.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2200633}, doi = {10.1002/mnfr.202200633}, pmid = {36946468}, issn = {1613-4133}, abstract = {SCOPE: Holothuria leucospilota polysaccharides (HLP) are bioactive polysaccharides with immunomodulatory effects. This study aimed to investigate the impact of HLP on dextran sodium sulfate (DSS)-induced colitis in rats and further investigate the complex interactions between changes in intestinal microbiota, co-metabolites, and intestinal inflammation under HLP intervention.<br><br>METHODS AND RESULTS: The ulcerative colitis (UC) model of Sprague Dawley (SD) rats was established by a normal diet with 3%DSS. The effects of HLP on UC were studied by gavage of different doses of HLP for two weeks. The results showed that HLP alleviated the inflammation of UC and reduced histological damage and secretion of TNF-&#x3b1;, IL-6, IL-1&#x3b2;, and IL-10. After HLP treatment, the intestinal flora of UC rats was regulated, and the flora diversity was restored. Fecal metabolomics analysis revealed the modulatory effects of HLP on amino acid metabolism, antimicrobial peptide anabolism and energy metabolism in rats with colitis. Correlation analysis of microbial and intestinal metabolites revealed the potential mechanism of HLP affecting colitis.<br><br>CONCLUSION: HLP repaired the intestinal compartment's metabolic disorder by regulating intestinal flora's structure and alleviating colonic mucosal injury and inflammation in colitis rats. This article is protected by copyright. All rights reserved.}, }
@article {pmid36946295, year = {2023}, author = {Zhang, M and Zhang, W and Chen, Y and Zhao, J and Wu, S and Su, X}, title = {Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad148}, pmid = {36946295}, issn = {1367-4811}, abstract = {MOTIVATION: Beta-diversity quantitatively measures the difference among microbial communities, thus enlightening the association between microbiome composition and environment properties or host phenotypes. The beta-diversity analysis mainly relies on distances among microbiomes that are calculated by all microbial features. However, in some cases, only a small fraction of members in a community plays crucial roles. Such tiny proportion is insufficient to alter the overall distance, which is always missed by end-to-end comparison. On the other hand, beta-diversity pattern can also be interfered due to the data sparsity when only focusing on non-abundant microbes.<br><br>RESULTS: Here we develop Flex Meta-Storms (FMS) distance algorithm that implements the "local alignment" of microbiomes for the first time. Using a flexible extraction that considers the weighted phylogenetic and functional relations of microbes, FMS produces a normalized phylogenetic distance among members of interest for microbiome pairs. We demonstrated the advantage of FMS in detecting the subtle variations of microbiomes among different states using artificial and real datasets, which were neglected by regular distance metrics. Therefore, FMS effectively discriminates microbiomes with higher sensitivity and flexibility, thus contributing to in-depth comprehension of microbe-host interactions, as well as promoting the utilization of microbiome data such as disease screening and prediction.<br><br>AVAILABILITY: FMS is implemented in C&#x2009;++ and the source code is released at https://github.com/qdu-bioinfo/flex-meta-storms.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36946260, year = {2023}, author = {Wang, Y and Duan, S and Xu, J and Long, Y and Zhang, S and Li, S and Wu, L and Zhang, Y}, title = {Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14248}, pmid = {36946260}, issn = {1751-7915}, abstract = {The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.}, }
@article {pmid36946107, year = {2023}, author = {Jones, KR and Hughey, MC and Belden, LK}, title = {Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1995}, pages = {20230308}, pmid = {36946107}, issn = {1471-2954}, mesh = {Animals ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anura/genetics ; Biota ; Bacteria ; }, abstract = {Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.}, }
@article {pmid36946080, year = {2023}, author = {Meng, J and Liu, S and Wu, X}, title = {Engineered probiotics as live biotherapeutics for diagnosis and treatment of human diseases.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/1040841X.2023.2190392}, pmid = {36946080}, issn = {1549-7828}, abstract = {The use of probiotics to regulate the intestinal microbiota to prevent and treat a large number of disorders and diseases has been an international research hotspot. Although conventional probiotics have a certain regulatory role in nutrient metabolism, inhibiting pathogens, inducing immune regulation, and maintaining intestinal epithelial barrier function, they are unable to treat certain diseases. In recent years, aided by the continuous development of synthetic biology, engineering probiotics with desired characteristics and functionalities to benefit human health has made significant progress. In this article, we summarise the mechanism of action of conventional probiotics and their limitations and highlight the latest developments in the design and construction of probiotics as living diagnostics and therapeutics for the detection and treatment of a series of diseases, including pathogen infections, cancer, intestinal inflammation, metabolic disorders, vaccine delivery, cognitive health, and fatty liver. Besides we discuss the concerns regarding engineered probiotics and corresponding countermeasures and outline the desired features in the future development of engineered live biotherapeutics.}, }
@article {pmid36945966, year = {2023}, author = {Kasperek, MC and Mailing, L and Piccolo, BD and Moody, B and Lan, R and Gao, X and Hernandez-Saavedra, D and Woods, JA and Adams, SH and Allen, JM}, title = {Exercise training modifies xenometabolites in gut and circulation of lean and obese adults.}, journal = {Physiological reports}, volume = {11}, number = {6}, pages = {e15638}, pmid = {36945966}, issn = {2051-817X}, mesh = {Adult ; Humans ; *Insulin Resistance ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Obesity/metabolism ; Exercise/physiology ; }, abstract = {Regular, moderate exercise modifies the gut microbiome and contributes to human metabolic and immune health. The microbiome may exert influence on host physiology through the microbial production and modification of metabolites (xenometabolites); however, this has not been extensively explored. We hypothesized that 6 weeks of supervised, aerobic exercise 3×/week (60%-75% heart rate reserve [HRR], 30-60 min) in previously sedentary, lean (n = 14) and obese (n = 10) adults would modify both the fecal and serum xenometabolome. Serum and fecal samples were collected pre- and post-6 week intervention and analyzed by liquid chromatography/tandem mass spectrometry (LC-MS/MS). Linear mixed models (LMMs) identified multiple fecal and serum xenometabolites responsive to exercise training. Further cluster and pathway analysis revealed that the most prominent xenometabolic shifts occurred within aromatic amino acid (ArAA) metabolic pathways. Fecal and serum ArAA derivatives correlated with body composition (lean mass), markers of insulin sensitivity (insulin, HOMA-IR) and cardiorespiratory fitness (V ̇ O 2 max $$ \dot{\mathrm{V}}{\mathrm{O}}_{2\max } $$), both at baseline and in response to exercise training. Two serum aromatic microbial-derived amino acid metabolites that were upregulated following the exercise intervention, indole-3-lactic acid (ILA: fold change: 1.2, FDR p < 0.05) and 4-hydroxyphenyllactic acid (4-HPLA: fold change: 1.3, FDR p < 0.05), share metabolic pathways within the microbiota and were associated with body composition and markers of insulin sensitivity at baseline and in response to training. These data provide evidence of physiologically relevant shifts in microbial metabolism that occur in response to exercise training, and reinforce the view that host metabolic health influences gut microbiota population and function. Future studies should consider the microbiome and xenometabolome when investigating the health benefits of exercise.}, }
@article {pmid36945965, year = {2023}, author = {Konak, HE and Erden, A and Armağan, B and Güven, SC and Apaydın, H and Dağlı, PA and Uzun, Y and Kaygısız, M and Küçükşahin, O and Omma, A}, title = {Effects of breast milk on Behçet's disease clinical features.}, journal = {Turkish journal of medical sciences}, volume = {53}, number = {1}, pages = {121-129}, pmid = {36945965}, issn = {1303-6165}, mesh = {Infant, Newborn ; Female ; Humans ; Infant ; *Behcet Syndrome/epidemiology/diagnosis ; Milk, Human ; *Sacroiliitis ; Cross-Sectional Studies ; *Low Back Pain ; }, abstract = {BACKGROUND: The etiology of Behçet's disease (BD) is not clearly known, however, abnormal activity in T helper (Th) 1, Th 17, and regulatory T cells (Treg) has critical importance in pathogenesis. It has been shown that the intestinal microbiome can be effective in the modulation of these immune abnormalities in BD patients. Breastfeeding increases the maturation of the infant's intestinal permeability by affecting the newborn's immature intestinal microbiome and metagenome. We aimed to examine the effects of breastfeeding on disease related symptoms, organ involvements and course of the disease in BD patients.<br><br>METHODS: This study was designed as a cross-sectional study in Ankara City Hospital rheumatology clinic between December 2021 and March 2022. Patients who were diagnosed with BD by meeting the criteria of the 'International Study Group' and whose information we could access by agreeing to participate in the study were enrolled. The mothers of the patients were also contacted and asked whether these patients were breastfed, the duration of breastfeeding, and the mode of birth. Demographic and clinical data of the patients, comorbid diseases, and drugs used for BD were collected from the records in the hospital database. The presence of sacroiliitis in patients was evaluated with sacroiliac X-ray and/or magnetic resonance imaging (MRI), which was requested because of low back pain symptoms and only patients with previous sacroiliac imaging for low back pain were included in the study. BD-related organ damage was measured by the Vasculitis Damage Index (VDI) and Beh&#xe7;et's syndrome Overall Damage Index (BODI) scores.<br><br>RESULTS: : A total of 304 patients were included in the study. The percentage of patients who were reported to have ever breastfed (median duration (IQR): 12(12) months, 33.5% < 6 months, 66.4% &#x2265; 6 months, and 59.6% &#x2265; 12 months) is 92%. When the breastfed and nonbreastfed patients were compared, 6.8% of the breastfed patients needed TNF-i against 18.2% of the nonbreastfed patients (p = 0.052). While the rate of having at least one comorbidity was 26.4% for those who were breastfed, this rate was 50% for those who had never been breastfed. When the organ and system involvements of the patients were compared, the incidence of sacroiliitis was statistically significantly higher in the nonbreastfed group (p = 0.025). Patients who were breastfed for less than 6 months were diagnosed with BD at an earlier age than those who were breastfed for more than 6 months, and those who were breastfed for less than 12 months compared to those who were breastfed for more than 12 months (respectively, p = 0.039, p = 0.035).<br><br>DISCUSSION: Our results imply that history of breastfeeding may have some positive effects on the course of the disease in BD patients.}, }
@article {pmid36945880, year = {2023}, author = {Yin, L and Wang, X and Li, Y and Liu, Z and Mei, Q and Chen, Z}, title = {Uptake of the Plant Agriculture-Used Antibiotics Oxytetracycline and Streptomycin by Cherry Radish─Effect on Plant Microbiome and the Potential Health Risk.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {11}, pages = {4561-4570}, doi = {10.1021/acs.jafc.3c01052}, pmid = {36945880}, issn = {1520-5118}, mesh = {Humans ; Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Oxytetracycline/pharmacology ; Streptomycin/pharmacology ; Agriculture ; Plants ; *Microbiota ; Bacteria/genetics ; Soil ; }, abstract = {Antibiotics are used to control certain bacterial diseases in plant agriculture. Understanding antibiotic uptake by edible vegetables after application and associated risks on plant microbiome and human health is critical. In this study, oxytetracycline and streptomycin, the two most commonly used antibiotics in plant agriculture, were applied to cherry radish via continuous soil drenching to study their translocations into plant tissues, influence on radish microbiome, and the potential health risk to mice. The results demonstrated that oxytetracycline induced hormesis in radish plants and both antibiotics were translocated into the leaves, fruits, and roots of radishes from the soil, with significantly higher plant uptake of streptomycin than oxytetracycline. Interestingly, the proportion of culturable oxytetracycline or streptomycin-resistant bacteria in the antibiotic-accumulated radish tissues was significantly higher than that in the antibiotic-free radish tissues, although both bacterial and fungal communities in different radish tissues were not affected by the accumulated antibiotics, demonstrating that antibiotic application could enrich antibiotic resistance in the plant microbiome. Feeding mice with antibiotics-accumulated radish tissues did not show significant effects on the weight and blood glucose levels of mice. Overall, this study provides important insights into the risk of using antibiotics in plant agriculture.}, }
@article {pmid36945505, year = {2023}, author = {Golob, JL and Oskotsky, TT and Tang, AS and Roldan, A and Chung, V and Ha, CWY and Wong, RJ and Flynn, KJ and Parraga-Leo, A and Wibrand, C and Minot, SS and Andreoletti, G and Kosti, I and Bletz, J and Nelson, A and Gao, J and Wei, Z and Chen, G and Tang, ZZ and Novielli, P and Romano, D and Pantaleo, E and Amoroso, N and Monaco, A and Vacca, M and Angelis, M and Bellotti, R and Tangaro, S and Kuntzleman, A and Bigcraft, I and Techtmann, S and Bae, D and Kim, E and Jeon, J and Joe, S and ,  and Theis, KR and Ng, S and Lee Li, YS and Bennett, PR and MacIntyre, DA and Stolovitzky, G and Lynch, SV and Albrecht, J and Gomez-Lopez, N and Romero, R and Stevenson, DK and Aghaeepour, N and Tarca, AL and Costello, JC and Sirota, M}, title = {Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.07.23286920}, pmid = {36945505}, abstract = {Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We present a crowdsourcing approach to predict: (a) preterm or (b) early preterm birth from 9 publicly available vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from raw sequences via an open-source tool, MaLiAmPi. We validated the crowdsourced models on novel datasets representing 331 samples from 148 pregnant individuals. From 318 DREAM challenge participants we received 148 and 121 submissions for our two separate prediction sub-challenges with top-ranking submissions achieving bootstrapped AUROC scores of 0.69 and 0.87, respectively. Alpha diversity, VALENCIA community state types, and composition (via phylotype relative abundance) were important features in the top performing models, most of which were tree based methods. This work serves as the foundation for subsequent efforts to translate predictive tests into clinical practice, and to better understand and prevent preterm birth.}, }
@article {pmid36945445, year = {2023}, author = {Johnson, JP and Diener, C and Levine, AE and Wilmanski, T and Suskind, DL and Ralevski, A and Hadlock, J and Magis, AT and Hood, L and Rappaport, N and Gibbons, SM}, title = {Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.04.531100}, pmid = {36945445}, abstract = {OBIECTIVE: Bowel movement frequency (BMF) variation has been linked to changes in the composition of the human gut microbiome and to many chronic conditions, like metabolic disorders, neurodegenerative diseases, chronic kidney disease (CKD), and other intestinal pathologies like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Slow intestinal transit times (constipation) are thought to lead to compromised intestinal barrier integrity and a switch from saccharolytic to proteolytic fermentation within the microbiota, giving rise to microbially-derived toxins that may make their way into circulation and cause damage to organ systems. However, these phenomena have not been characterized in generally-healthy populations, and the connections between microbial metabolism and the early-stage development and progression of chronic disease remain underexplored.<br><br>DESIGN: Here, we examine the phenotypic impact of BMF variation across a cohort of over 2,000 generally-healthy, community dwelling adults with detailed clinical, lifestyle, and multi-omic data.<br><br>RESULTS: We show significant differences in key blood plasma metabolites, proteins, chemistries, gut bacterial genera, and lifestyle factors across BMF groups that have been linked, in particular, to inflammation and CKD severity and progression.<br><br>DISCUSSION: In addition to dissecting BMF-related heterogeneity in blood metabolites, proteins, and the gut microbiome, we identify self-reported diet, lifestyle, and psychological factors associated with BMF variation, which suggest several potential strategies for mitigating constipation and diarrhea. Overall, this work highlights the potential for managing BMF to prevent disease.<br><br>Constipation and diarrhea are linked to several chronic diseases, like IBD, CKD, and neurodegenerative disorders. Chronic constipation, in particular, is associated with the increased production of microbially-derived uremic toxins in the gut due to an ecosystem-wide switch from fiber fermentation to protein fermentation. A build-up of these gut-derived toxins in blood, like p-cresol, has been associated with CKD disease progression and severity.<br><br>WHAT THIS STUDY ADDS: While prior work has demonstrated associations between microbially-derived uremic toxins, constipation, and CKD severity/progression, here we show similar signatures in a generally-healthy cohort. Overall, we map out the molecular phenotypic effects of aberrant BMFs across individuals without any apparent disease, and show how these effects precede, and may contribute to, the development of chronic disease. We find that certain lifestyle and dietary patterns, like higher levels of exercise, reduced anxiety levels, a more plant-based diet, and drinking more water, are associated with a more optimal BMF range.<br><br>Overall, we suggest that even mild levels of chronic constipation may cause damage to organ systems over time and ultimately give rise to chronic diseases, like CKD or neurodegeneration. These findings pave the way for future research into early interventions for individuals at risk of developing chronic diseases related to BMF abnormalities. Managing BMF abnormalities prior to disease development may be an important disease prevention strategy, but this will require further evidence through longitudinal human intervention trials.}, }
@article {pmid36945059, year = {2023}, author = {Ikeuchi, K and Tsutsumi, T and Ishizaka, A and Mizutani, T and Sedohara, A and Koga, M and Tamaoki, S and Yotsuyanagi, H}, title = {Modulation of duodenal and jejunal microbiota by rifaximin in mice with CCl4-induced liver fibrosis.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {14}, pmid = {36945059}, issn = {1757-4749}, abstract = {BACKGROUND: Rifaximin is a poorly absorbed broad-spectrum antibiotic used for hepatic encephalopathy. Although increased Lactobacillaceae and decreased Bacteroidetes abundance are characteristic of hepatic encephalopathy, rifaximin does not dramatically alter the stool microbiota. As the antimicrobial effect of rifaximin increases by micellization with bile acids, we hypothesized that rifaximin alters the microbiota in the duodenum and jejunum, where the levels of bile acids are abundant.<br><br>METHODS AND RESULTS: Eight-week-old BALB/c mice were injected with carbon tetrachloride (CCl4) intraperitoneally for 12&#xa0;weeks to induce liver fibrosis. The mice were grouped into the control (n&#x2009;=&#x2009;9), CCl4 (n&#x2009;=&#x2009;13), and rifaximin group in which mice were treated with rifaximin for two weeks after CCl4 administration (n&#x2009;=&#x2009;13). We analyzed the microbiota of the duodenum, jejunum, ileum, cecum, and stool using 16S ribosomal RNA gene analysis. The content of Lactobacillaceae, the most abundant bacterial family in the duodenum and small intestine, increased in the CCl4 group, especially in the jejunum (median 67.0% vs 87.8%, p&#x2009;=&#x2009;0.03). Rifaximin significantly decreased Lactobacillaceae content in the duodenum (median 79.4% vs 19.0%, p&#x2009;=&#x2009;0.006) and jejunum (median 87.8% vs 61.3%, p&#x2009;=&#x2009;0.03), but not in the ileum, cecum, and stool. Bacteroidetes abundance tended to decrease on CCl4 administration and increased following rifaximin treatment in the duodenum and jejunum. S24_7, the most abundant family in Bacteroidetes, demonstrated a significant inverse correlation with Lactobacillaceae (duodenum, r&#x2009;=&#x2009;-&#xa0;0.61, p&#x2009;<&#x2009;0.001; jejunum, r&#x2009;=&#x2009;-&#xa0;0.72, p&#x2009;<&#x2009;0.001). In the ileum, cecum, and stool, the effect of rifaximin on the microbiota was minimal, with changes within the same phylum. The percentage of bacterial families, such as Lactobacillaceae and S24_7 in the duodenum and small intestine, did not correlate with that in the stool.<br><br>CONCLUSIONS: The abundance of Lactobacillaceae increased in the jejunum of mice with CCl4-induced liver fibrosis, while rifaximin significantly reduced it in the duodenum and jejunum. Thus, rifaximin possibly exerts its effect by altering the duodenal and jejunal microbiota. Furthermore, changes in the duodenal and small intestinal microbiota were not associated with that of stool, suggesting that the analysis of stool microbiota is insufficient to evaluate upper intestinal microbiota.}, }
@article {pmid36945049, year = {2023}, author = {Nieto-Ruiz, A and Cerdó, T and Jordano, B and Torres-Espínola, FJ and Escudero-Marín, M and García-Ricobaraza, M and Bermúdez, MG and García-Santos, JA and Suárez, A and Campoy, C}, title = {Maternal weight, gut microbiota, and the association with early childhood behavior: the PREOBE follow-up study.}, journal = {Child and adolescent psychiatry and mental health}, volume = {17}, number = {1}, pages = {41}, pmid = {36945049}, issn = {1753-2000}, abstract = {BACKGROUND AND AIM: Maternal overweight and breastfeeding seem to have a significant impact on the gut microbiota colonization process, which co-occurs simultaneously with brain development and the establishment of the "microbiota-gut-brain axis", which potentially may affect behavior later in life. This study aimed to examine the influence of maternal overweight, obesity and/or gestational diabetes on the offspring behavior at 3.5 years of age and its association with the gut microbiota already established at 18 months of life.<br><br>METHODS: 156 children born to overweight (OV, n&#x2009;=&#x2009;45), obese (OB, n&#x2009;=&#x2009;40) and normoweight (NW, n&#x2009;=&#x2009;71) pregnant women participating in the PREOBE study were included in the current analysis. Stool samples were collected at 18&#xa0;months of life and gut microbiome was obtained by 16S rRNA gene sequencing. Behavioral problems were evaluated at 3.5&#xa0;years by using the Child Behavior Checklist (CBCL). ANOVA, Chi-Square Test, ANCOVA, Spearman's correlation, logistic regression model and generalized linear model (GLM) were performed.<br><br>RESULTS: At 3.5&#xa0;years of age, Children born to OV/OB mothers showed higher scores in behavioral problems than those born to NW mothers. Additionally, offspring born to OB mothers who developed gestational diabetes mellitus (GDM) presented higher scores in attention/deficit hyperactivity and externalizing problems than those born to GDM OV/NW mothers. Fusicatenibacter abundance found at 18&#xa0;months of age was associated to lower scores in total, internalizing and pervasive developmental problems, while an unidentified genus within Clostridiales and Flavonifractor families abundance showed a positive correlation with anxiety/depression and somatic complaints, respectively. On the other hand, children born to mothers with higher BMI who were breastfed presented elevated anxiety, internalizing problems, externalizing problems and total problems scores; likewise, their gut microbiota composition at 18&#xa0;months of age showed positive correlation with behavioral problems at 3.5&#xa0;years: Actinobacteria abundance and somatic complaints and between Fusobacteria abundance and withdrawn behavior and pervasive developmental problems.<br><br>CONCLUSIONS: Our findings suggests that OV/OB and/or GDM during pregnancy is associated with higher behavioral problems scores in children at 3.5&#xa0;years old. Additionally, associations between early life gut microbiota composition and later mental health in children was also found.}, }
@article {pmid36928862, year = {2023}, author = {Bulanda, E and Wypych, TP}, title = {Microbes, antibodies, and breastfeeding as the trans-generational axis of microbiota maturation.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.15713}, pmid = {36928862}, issn = {1398-9995}, }
@article {pmid36945040, year = {2023}, author = {Broderick, D and Marsh, R and Waite, D and Pillarisetti, N and Chang, AB and Taylor, MW}, title = {Realising respiratory microbiomic meta-analyses: time for a standardised framework.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {57}, pmid = {36945040}, issn = {2049-2618}, abstract = {In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those of the gut and sinuses. Meta-analyses also represent a powerful and efficient approach to leverage existing scientific data to both reaffirm existing findings and generate new hypotheses within the field. However, there are currently limited data in other fields, such as the paediatric respiratory tract, where extension of original data becomes even more critical due to samples often being difficult to obtain and process for a range of both technical and ethical reasons. Performing such analyses in an evolving field comes with challenges related to data accessibility and heterogeneity. This is particularly the case in paediatric respiratory microbiomics - a field in which best microbiome-related practices are not yet firmly established, clinical heterogeneity abounds and ethical challenges can complicate sharing of patient data. Having recently conducted a large-scale, individual participant data meta-analysis of the paediatric respiratory microbiota (n = 2624 children from 20 studies), we discuss here some of the unique barriers facing these studies and open and invite a dialogue towards future opportunities. Video Abstract.}, }
@article {pmid36945017, year = {2023}, author = {Hussein, MA and Khattak, F and Vervelde, L and Athanasiadou, S and Houdijk, JGM}, title = {Growth performance, caecal microbiome profile, short-chain fatty acids, and litter characteristics in response to placement on reused litter and combined threonine, arginine and glutamine supplementation to juvenile male broiler chickens.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {18}, pmid = {36945017}, issn = {2524-4671}, abstract = {BACKGROUND: Exposure of broilers to litter microbiome may increase specific amino acid (AA) requirements towards activated immune responses. This may challenge the generality of the ideal protein (IP) concept, in which dietary essential AA to lysine ratios aimed to mimic presumably constant AA to lysine ratios in whole bird requirements. Therefore, we tested the effect of threonine, arginine and glutamine (TAG) supplementation to IP-based control diets (C) on performance, caecal microbiome composition, short-chain fatty acids and litter characteristics of broiler chickens placed on reused litter.<br><br>RESULTS: Thirty-two pens with ten male broiler chickens each were used in a 2&#x2009;&#xd7;&#x2009;2 factorial arrangement of two diet treatments (with or without TAG supplementation) and two litter treatments (placement on clean or reused litter) for 21&#xa0;days (n&#x2009;=&#x2009;8). Caecal contents were analysed for microbiome profile using percent guanine&#x2009;+&#x2009;cytosine (%G&#x2009;+&#x2009;C profile) method and short chain fatty acids. TAG-supplemented birds underperformed compared to C birds (P&#x2009;=&#x2009;0.002), whereas birds placed on reused litter outperformed those on clean litter (P&#x2009;=&#x2009;0.047). Diet, reused litter and their interaction impacted the %G&#x2009;+&#x2009;C profile at different ranges. Whilst TAG supplementation reduced bacterial abundance at %G&#x2009;+&#x2009;C 51-56 (P&#x2009;<&#x2009;0.05), reused litter placement tended to reduce %G&#x2009;+&#x2009;C 23-31 and increase %G&#x2009;+&#x2009;C 56-59 (P&#x2009;<&#x2009;0.10). However, TAG supplementation reduced bacterial abundance at %G&#x2009;+&#x2009;C 47-51 (P&#x2009;<&#x2009;0.05) and increased caecal branched chain fatty acids on clean litter only (P&#x2009;=&#x2009;0.025). Greater levels of propionic acid were observed for C birds placed on reused litter only (P&#x2009;=&#x2009;0.008). Litter pH was greater for reused litter pens than clean litter pens at day 21 (P&#x2009;<&#x2009;0.001). In addition, litter moisture content was less for TAG birds and reused litter pens compared to C birds (P&#x2009;=&#x2009;0.041) and clean litter pens (P&#x2009;<&#x2009;0.001), respectively.<br><br>CONCLUSIONS: These data support the view that irrespective of performance benefits arising from bird placement on reused litter, TAG supplementation to IP-formulated baseline rations impaired growth, supported by the lowered abundance of caecal bacteria known to dominate in well-performing birds and greater levels of caecal branched chain fatty acids.}, }
@article {pmid36944780, year = {2023}, author = {Oh, M and Zhang, L}, title = {DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4599}, pmid = {36944780}, issn = {2045-2322}, abstract = {Recent studies revealed that gut microbiota modulates the response to cancer immunotherapy and fecal microbiota transplantation has clinical benefits in melanoma patients during treatment. Understanding how microbiota affects individual responses is crucial for precision oncology. However, it is challenging to identify key microbial taxa with limited data as statistical and machine learning models often lose their generalizability. In this study, DeepGeni, a deep generalized interpretable autoencoder, is proposed to improve the generalizability and interpretability of microbiome profiles by augmenting data and by introducing interpretable links in the autoencoder. DeepGeni-based machine learning classifier outperforms state-of-the-art classifier in the microbiome-driven prediction of responsiveness of melanoma patients treated with immune checkpoint inhibitors. Moreover, the interpretable links of DeepGeni elucidate the most informative microbiota associated with cancer immunotherapy response. DeepGeni not only improves microbiome-driven prediction of immune checkpoint inhibitor responsiveness but also suggests potential microbial targets for fecal microbiota transplant or probiotics improving the outcome of cancer immunotherapy.}, }
@article {pmid36944767, year = {2023}, author = {Park, JY and Yun, H and Lee, SB and Kim, HJ and Jung, YH and Choi, CW and Shin, JY and Park, JS and Seo, JS}, title = {Comprehensive characterization of maternal, fetal, and neonatal microbiomes supports prenatal colonization of the gastrointestinal tract.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4652}, pmid = {36944767}, issn = {2045-2322}, abstract = {In this study, we aimed to comprehensively characterize the microbiomes of various samples from pregnant women and their neonates, and to explore the similarities and associations between mother-neonate pairs, sample collection sites, and obstetrical factors. We collected samples from vaginal discharge and amniotic fluid in pregnant women and umbilical cord blood, gastric liquid, and meconium from neonates. We identified 19,597,239 bacterial sequences from 641 samples of 141 pregnant women and 178 neonates. By applying rigorous filtering criteria to remove contaminants, we found evidence of microbial colonization in traditionally considered sterile intrauterine environments and the fetal gastrointestinal track. The microbiome distribution was strongly grouped by sample collection site, rather than the mother-neonate pairs. The distinct bacterial composition in meconium, the first stool passed by newborns, supports that microbial colonization occurs during normal pregnancy. The microbiome in neonatal gastric liquid was similar, but not identical, to that in maternal amnionic fluid, as expected since fetuses swallow amnionic fluid in utero and their urine returns to the fluid under normal physiological conditions. Establishing a microbiome library from various samples formed only during pregnancy is crucial for understanding human development and identifying microbiome modifications in obstetrical complications.}, }
@article {pmid36944617, year = {2023}, author = {Dodge, R and Jones, EW and Zhu, H and Obadia, B and Martinez, DJ and Wang, C and Aranda-Díaz, A and Aumiller, K and Liu, Z and Voltolini, M and Brodie, EL and Huang, KC and Carlson, JM and Sivak, DA and Spradling, AC and Ludington, WB}, title = {A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1557}, pmid = {36944617}, issn = {2041-1723}, abstract = {The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.}, }
@article {pmid36943918, year = {2023}, author = {Kharofa, J and Haslam, D and Wilkinson, R and Weiss, A and Patel, S and Wang, K and Esslinger, H and Olowokure, O and Sohal, D and Wilson, G and Ahmad, S and Apewokin, S}, title = {Analysis of the fecal metagenome in long-term survivors of pancreas cancer.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.34748}, pmid = {36943918}, issn = {1097-0142}, support = {5K08CA237735/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The 5-year overall survival of pancreas adenocarcinoma (PCa) remains less than 10%. Clinical and tumor genomic characteristics have not differentiated PCa long-term survivors (LTSs) from unselected patients. Preclinical studies using fecal transplant experiments from LTSs of PCa have revealed delayed tumor growth through unknown mechanisms involving the fecal microbiota. However, features of the fecal microbiome in patients with long-term survival are not well described.<br><br>METHODS: In this cross-sectional study, comprehensive shotgun metagenomics was performed on stool from PCa patients with long-term survival (n&#xa0;=&#xa0;16). LTS was defined as >4&#xa0;years from pancreatectomy and all therapy without recurrence. LTSs were compared to control patients with PCa who completed pancreatectomy and chemotherapy (n&#xa0;=&#xa0;8). Stool was sequenced using an Illumina NextSeq500. Statistical analyses were performed in R with MicrobiomeSeq and Phyloseq for comparison of LTSs and controls.<br><br>RESULTS: All patients underwent pancreatectomy and chemotherapy before sample donation. The median time from pancreatectomy of 6&#xa0;years (4-14&#xa0;years) for LTSs without evidence of disease compared to a median disease-free survival of 1.8&#xa0;years from pancreatectomy in the control group. No differences were observed in overall microbial diversity for LTSs and controls using Shannon/Simpson indexes. Significant enrichment of species relative abundance was observed in LTSs for the Ruminococacceae family specifically Faecalibacterium prausnitzii species as well as Akkermansia mucinophilia species.<br><br>CONCLUSIONS: Stool from patients cured from PCa has more relative abundance of Faecalibacterium prausnitzii and Akkermansia mucinophilia. Additional studies are needed to explore potential mechanisms by which the fecal microbiota may influence survival in PCa.<br><br>PLAIN LANGUAGE SUMMARY: Although pancreatic cancer treatments have improved, the number of long-term survivors has remained stagnant with a 5-year overall survival estimate of 9%. Emerging evidence suggests that microbes within the gastrointestinal tract can influence cancer response through activation of the immune system. In this study, we profiled the stool microbiome in long-term survivors of pancreas cancer and controls. Several enriched species previously associated with enhanced tumor immune response were observed including Faecalibacterium prausnitzii and Akkermansia mucinophilia. These findings warrant additional study assessing mechanisms by which the fecal microbiota may enhance pancreatic cancer immune response.}, }
@article {pmid36943505, year = {2023}, author = {Smolensky, IV and Zajac-Bakri, K and Gass, P and Inta, D}, title = {Ketogenic diet for mood disorders from animal models to clinical application.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {}, number = {}, pages = {}, pmid = {36943505}, issn = {1435-1463}, abstract = {Mood disorders such as major depressive disorder (MDD) and bipolar disorder (BD) are often resistant to current pharmacological treatment. Therefore, various alternative therapeutic approaches including diets are, therefore, under investigation. Ketogenic diet (KD) is effective for treatment-resistant epilepsy and metabolic diseases, however, only a few clinical studies suggest its beneficial effect also for mental disorders. Animal models are a useful tool to uncover the underlying mechanisms of therapeutic effects. Women have a twice-higher prevalence of mood disorders but very little is known about sex differences in nutritional psychiatry. In this review, we aim to summarize current knowledge of the sex-specific effects of KD in mood disorders. Ketone bodies improve mitochondrial functions and suppress oxidative stress, inducing neuroprotective and anti-inflammatory effects which are both beneficial for mental health. Limited data also suggest KD-induced improvement of monoaminergic circuits and hypothalamus-pituitary-adrenal axis-the key pathophysiological pathways of mood disorders. Gut microbiome is an important mediator of the beneficial and detrimental effects of diet on brain functioning and mental health. Gut microbiota composition is affected in mood disorders but its role in the therapeutic effects of different diets, including KD, remains poorly understood. Still little is known about sex differences in the effects of KD on mental health as well as on metabolism and body weight. Some animal studies used both sexes but did not find differences in behavior, body weight loss or gut microbiota composition. More studies, both on a preclinical and clinical level, are needed to better understand sex-specific effects of KD on mental health.}, }
@article {pmid36943402, year = {2023}, author = {Shah, S and Mu, C and Moossavi, S and Shen-Tu, G and Schlicht, K and Rohmann, N and Geisler, C and Laudes, M and Franke, A and Züllig, T and Köfeler, H and Shearer, J}, title = {Physical activity-induced alterations of the gut microbiota are BMI dependent.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {37}, number = {4}, pages = {e22882}, doi = {10.1096/fj.202201571R}, pmid = {36943402}, issn = {1530-6860}, abstract = {Physical inactivity is one of the leading causes of chronic metabolic disease including obesity. Increasing physical activity (PA) has been shown to improve cardiometabolic and musculoskeletal health and to be associated with a distinct gut microbiota composition in trained athletes. However, the impact of PA on the gut microbiota is inconclusive for individuals performing PA in their day-to-day life. This study examined the role of PA and hand-grip strength on gut microbiome composition in middle-aged adults (40-65 years, n = 350) with normal (18.5-24.9 kg/m[2]) and overweight (25-29.9 kg/m[2]) body mass index (BMI). PA was recorded using the International Physical Activity Questionnaire, and hand-grip strength was measured using a dynamometer. Serum samples were assessed for lipidomics while DNA was extracted from fecal samples for microbiome analysis. Overweight participants showed a higher concentration of triacylglycerols, and lower concentrations of cholesteryl esters, sphingomyelin, and lyso-phosphotidylcholine lipids (p < .05) compared with those with normal BMI. Additionally, overweight participants had a lower abundance of the Oscillibacter genus (p < .05). The impact of PA duration on the gut microbiome was BMI dependent. In normal but not overweight participants, high PA duration showed greater relative abundance of commensal taxa such as Actinobacteria and Proteobacteria phyla, as well as Collinsella and Prevotella genera (p < .05). Furthermore, in males with normal BMI, a stronger grip strength was associated with a higher relative abundance of Faecalibacterium and F. prausnitzii (p < .05) compared with lower grip strength. Taken together, data suggest that BMI plays a significant role in modeling PA-induced changes in gut microbiota.}, }
@article {pmid36943155, year = {2023}, author = {Shaikh, SR and Bazinet, RP}, title = {Heterogeneity in the response to n-3 polyunsaturated fatty acids.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCO.0000000000000930}, pmid = {36943155}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: A central goal in the study of long chain n-3 polyunsaturated fatty acids (PUFA) is to translate findings from the basic sciences to the population level to improve human health and prevent chronic diseases. A tenet of this vision is to think in terms of precision medicine and nutrition, that is, stratification of individuals into differing groups that will have different needs across the lifespan for n-3 PUFAs. Therefore, there is a critical need to identify the sources of heterogeneity in the human population in the dietary response to n-3 PUFA intervention.<br><br>RECENT FINDINGS: We briefly review key sources of heterogeneity in the response to intake of long chain n-3 PUFAs. These include background diet, host genome, composition of the gut microbiome, and sex. We also discuss the need to integrate data from newer rodent models (e.g. population-based approaches), multi -omics, and analyses of big data using machine learning and data-driven cluster analyses.<br><br>SUMMARY: Accounting for vast heterogeneity in the human population, particularly with the use of big data integrated with preclinical evidence, will drive the next generation of precision nutrition studies and randomized clinical trials with long-chain n-3 PUFAs.}, }
@article {pmid36943087, year = {2023}, author = {Mosby, CA and Edelmann, MJ and Jones, MK}, title = {Murine Norovirus Interaction with Enterobacter cloacae Leads to Changes in Membrane Stability and Packaging of Lipid and Metabolite Vesicle Content.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0469122}, doi = {10.1128/spectrum.04691-22}, pmid = {36943087}, issn = {2165-0497}, abstract = {Outer membrane vesicles (OMVs) are a primary means of communication for Gram-negative bacteria. The specific role of vesicle components in cellular communication and how components are packaged are still under investigation, but a correlation exists between OMV biogenesis and content. The two primary mechanisms of OMV biogenesis are membrane blebbing and explosive cell lysis, and vesicle content is based on the biogenesis mechanism. Hypervesiculation, which can be induced by stress conditions, also influences OMV content. Norovirus interaction with Enterobacter cloacae induces stress responses leading to increased OMV production and changes in DNA content, protein content, and vesicle size. The presence of genomic DNA and cytoplasmic proteins in these OMVs suggests some of the vesicles are formed by explosive cell lysis, so reduction or loss of these components indicates a shift away from this mechanism of biogenesis. Based on this, further investigation into bacterial stability and OMV content was conducted. Results showed that norovirus induced a dramatic shift in OMV lipid content. Specifically, the increased accumulation of phospholipids is associated with increased blebbing, thereby supporting previous observations that noroviruses shift the mechanism of OMV biogenesis. Slight differences in OMV metabolite content were also observed. While norovirus induced changes in OMV content, it did not change the lipid content of the bacterial outer membrane or the metabolite content of the bacterial cell. Overall, these results indicate that norovirus induces significant changes to OMV lipid architecture and cargo, which may be linked to a change in the mechanism of vesicle biogenesis. IMPORTANCE Extracellular vesicles from commensal bacteria are recognized for their importance in modulating host immune responses, and vesicle content is related to their impact on the host. Therefore, understanding how vesicles are formed and how their content shifts in response to stress conditions is necessary for elucidating their downstream functions. Our recent work has demonstrated that interactions between noroviruses and Enterobacter cloacae induce bacterial stress responses leading to hypervesiculation. In this article, we characterize and compare the lipid and metabolomic cargo of E. cloacae vesicles generated in the presence and absence of norovirus and show that viral interactions induce significant changes in vesicle content. Furthermore, we probe how these changes and changes to the bacterial cell may be indicative of a shift in the mechanism of vesicle biogenesis. Importantly, we find that noroviruses induce significant changes in vesicle lipid architecture and cargo that may be responsible for the immunogenic activity of these vesicles.}, }
@article {pmid36943054, year = {2023}, author = {Zhou, C and Wang, Y and Li, C and Xie, Z and Dai, L}, title = {Amelioration of Colitis by a Gut Bacterial Consortium Producing Anti-Inflammatory Secondary Bile Acids.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0333022}, doi = {10.1128/spectrum.03330-22}, pmid = {36943054}, issn = {2165-0497}, abstract = {The Integrative Human Microbiome Project and other cohort studies have indicated that inflammatory bowel disease is accompanied by dysbiosis of gut microbiota, decreased production of secondary bile acids, and increased levels of primary bile acids. Secondary bile acids, such as ursodeoxycholic acid (UDCA) and lithocholic acid (LCA), have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. In this study, we screened human gut bacterial strains for bile acid metabolism and designed a consortium of three species, including Clostridium AP sp000509125, Bacteroides ovatus, and Eubacterium limosum, and named it BAC (bile acid consortium). We showed that the three-strain gut bacterial consortium BAC is capable of converting conjugated primary bile acids taurochenodeoxycholic acid and glycochenodeoxycholic acid to secondary bile acids UDCA and LCA in vitro. Oral gavage treatment with BAC in mice resulted in protective effects against dextran sulfate sodium (DSS)-induced colitis, including reduced weight loss and increased colon length. Furthermore, BAC treatment increased the fecal level of bile acids, including UDCA and LCA. BAC treatment enhanced intestinal barrier function, which may be attributed to the increased activation of the bile acid receptor TGR5 by secondary bile acids. Finally, we examined the remodeling of gut microbiota by BAC treatment. Taken together, the three-strain gut bacterial consortium BAC restored the dysregulated bile acid metabolism and alleviated DSS-induced colitis. Our study provides a proof-of-concept demonstration that a rationally designed bacterial consortium can reshape the metabolism of the gut microbiome to treat diseases. IMPORTANCE Secondary bile acids have been reported to be anti-inflammatory, yet it remains to be studied whether introducing selected bacteria strains to restore bile acid metabolism of the gut microbiome can alleviate intestinal inflammation. To address this gap, we designed a consortium of human gut bacterial strains based on their metabolic capacity to produce secondary bile acids UDCA and LCA, and we evaluated the efficacy of single bacterial strains and the bacterial consortium in treating the murine colitis model. We found that oral gavage of the bacterial consortium to mice restored secondary bile acid metabolism to increase levels of UDCA and LCA, which induced the activation of TGR5 to improve gut-barrier integrity and reduced the inflammation in murine colitis. Overall, our study demonstrates that rationally designed bacterial consortia can reshape the metabolism of the gut microbiome and provides novel insights into the application of live biotherapeutics for treating IBD.}, }
@article {pmid36943043, year = {2023}, author = {Moore, ER and Carter, KR and Heneghan, JP and Steadman, CR and Nachtsheim, AC and Anderson-Cook, C and Dickman, LT and Newman, BD and Dunbar, J and Sevanto, S and Albright, MBN}, title = {Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0147622}, doi = {10.1128/spectrum.01476-22}, pmid = {36943043}, issn = {2165-0497}, abstract = {The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment. IMPORTANCE Globally, drought is an increasingly common and severe stress that causes significant damage to agricultural and wild plants, thereby threatening food security. Despite growing evidence of the potential benefits of soil microorganisms on plant performance under stress, decoupling the effects of the microbiome composition versus the water availability on plant growth and performance remains a challenge. We used a highly controlled and replicated greenhouse experiment to understand the impacts of microbial community composition and water limitation on corn growth and drought-relevant functions. We found that both factors affected corn growth, and, interestingly, that individual microbial relationships with corn growth and leaf function were unique to specific watering/microbiome treatment combinations. This finding may help explain the inconsistent success of previously identified microbial inocula in improving plant performance in the face of drought, outside controlled environments.}, }
@article {pmid36942920, year = {2023}, author = {D'Amico, F and Barone, M and Brigidi, P and Turroni, S}, title = {Gut microbiota in relation to frailty and clinical outcomes.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, pmid = {36942920}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: The gut microbiota is involved in several aspects of host health and disease, but its role is far from fully understood. This review aims to unveil the role of our microbial community in relation to frailty and clinical outcomes.<br><br>RECENT FINDINGS: Ageing, that is the continuous process of physiological changes that begin in early adulthood, is mainly driven by interactions between biotic and environmental factors, also involving the gut microbiota. Indeed, our gut microbial counterpart undergoes considerable compositional and functional changes across the lifespan, and ageing-related processes may be responsible for - and due to - its alterations during elderhood. In particular, a dysbiotic gut microbiota in the elderly population has been associated with the development and progression of several age-related disorders.<br><br>SUMMARY: Here, we first provide an overview of the lifespan trajectory of the gut microbiota in both health and disease. Then, we specifically focus on the relationship between gut microbiota and frailty syndrome, that is one of the major age-related burdens. Finally, examples of microbiome-based precision interventions, mainly dietary, prebiotic and probiotic ones, are discussed as tools to ameliorate the symptoms of frailty and its overlapping conditions (e.g. sarcopenia), with the ultimate goal of actually contributing to healthy ageing and hopefully promoting longevity.}, }
@article {pmid36942898, year = {2023}, author = {MacLaren, R}, title = {Considerations when administering medications enterally in the critically ill.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCO.0000000000000921}, pmid = {36942898}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: Enteral administration of medications to critically ill patients may be advantageous to other routes of administration. This review summarizes key considerations for the bedside clinician when medications are administered through enteral access devices (EADs).<br><br>RECENT FINDINGS: Critical illness is associated with gastrointestinal dysfunction that inconsistently affects drug dispersion and absorption and may enhance or reduce bioavailability. Other factors such as the first-pass metabolism, microbiome alterations and the concomitant use of other medications (vasopressors, acid suppressants) may influence drug absorption. Concurrent administration of medications with enteral nutrition is fraught with potential errors. Drug-nutrient and drug-drug interactions may lead to tube occlusion. Although liquid formulations of medications are preferred over solid dosage forms for EAD administration, they may be hyperosmotic or contain sorbitol to cause gastrointestinal disturbances. The size and placement of the EAD tube may influence drug dispersion and absorption to affect the pharmacokinetic profile and efficacy of a particular drug.<br><br>SUMMARY: The therapeutic effect may be diminished, or toxicity enhanced when medications are administered through EADs in the critically ill. The bedside clinician must be aware of factors impacting the bioavailability of enterally administered medications and be cognizant that the effect will differ by medication.}, }
@article {pmid36942883, year = {2023}, author = {Roager, HM and Stanton, C and Hall, LJ}, title = {Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192151}, doi = {10.1080/19490976.2023.2192151}, pmid = {36942883}, issn = {1949-0984}, mesh = {Humans ; Infant ; *Host Microbial Interactions ; *Gastrointestinal Microbiome ; }, abstract = {The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions. Here, we review the current knowledge on development of the infant gut microbiota and metabolism within the first year of life, and discuss how these microbial metabolites are key for enhancing our basic understanding of interactions during the early life developmental window.}, }
@article {pmid36942838, year = {2023}, author = {Neugent, ML and Hulyalkar, NV and Kumar, A and Xing, C and Zimmern, PE and Shulaev, V and De Nisco, NJ}, title = {Urinary Glycosaminoglycans Are Associated with Recurrent UTI and Urobiome Ecology in Postmenopausal Women.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.3c00027}, pmid = {36942838}, issn = {2373-8227}, abstract = {Glycosaminoglycans (GAGs) are linear, negatively charged polysaccharides composed of repeating disaccharide units of uronic acid and amino sugars. The luminal surface of the bladder epithelium is coated with a GAG layer. These urothelial GAGs are thought to provide a protective barrier and serve as a potential interaction site with the urinary microbiome (urobiome). Previous studies have profiled urinary GAG composition in mixed cohorts, but the urinary GAG composition in postmenopausal women remains undefined. To investigate the relationship between GAGs and recurrent urinary tract infection (rUTI), we profiled urinary GAGs in a controlled cohort of postmenopausal women. We found that chondroitin sulfate (CS) is the major urinary GAG in postmenopausal women and that urinary CS was elevated in women with active rUTI. We also associated urinary GAGs with urobiome composition and identified bacterial species that significantly associated with urinary GAG concentration. Corynebacterium amycolatum, Porphyromonas somerae, and Staphylococcus pasteuri were positively associated with heparin sulfate or hyaluronic acid, and bacterial species associated with vaginal dysbiosis were negatively correlated with urinary CS. Altogether, this work defines changes in urinary GAG composition associated with rUTI and identifies new associations between urinary GAGs and the urobiome that may play a role in rUTI pathobiology.}, }
@article {pmid36942804, year = {2022}, author = {Priadko, K and Romano, L and Olivieri, S and Romeo, M and Barone, B and Sciorio, C and Spirito, L and Morelli, M and Crocetto, F and Arcaniolo, D and Mirone, V and Romano, M and Napolitano, L}, title = {Intestinal microbiota, intestinal permeability and the urogenital tract: is there a pathophysiological link?.}, journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society}, volume = {73}, number = {5}, pages = {}, doi = {10.26402/jpp.2022.5.01}, pmid = {36942804}, issn = {1899-1505}, mesh = {Male ; Humans ; *Gastrointestinal Microbiome/physiology ; *Prostatic Hyperplasia ; *Microbiota ; Permeability ; }, abstract = {Human gut microbiome is related to different clinical conditions and diseases. Recently several hypotheses have been theorized about a link between gut microbiota and genitourinary disease including urinary tract infections, and benign prostatic hyperplasia. Despite several data, underlying mechanisms still remain unclear. The aim of this review is to report the current state of knowledge in relation to urinary tract infections, benign prostatic hyperplasia and intestinal microbiota with a focus on its role in the development of disease and the underlying pathophysiologic mechanisms.}, }
@article {pmid36942524, year = {2023}, author = {Ke, S and Guimond, AJ and Tworoger, SS and Huang, T and Chan, AT and Liu, YY and Kubzansky, LD}, title = {Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women.}, journal = {Psychological medicine}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S0033291723000612}, pmid = {36942524}, issn = {1469-8978}, abstract = {BACKGROUND: Accumulating evidence suggests that positive and negative emotions, as well as emotion regulation, play key roles in human health and disease. Recent work has shown the gut microbiome is important in modulating mental and physical health through the gut-brain axis. Yet, its association with emotions and emotion regulation are understudied. Here we examined whether positive and negative emotions, as well as two emotion regulation strategies (i.e. cognitive reappraisal and suppression), were associated with the gut microbiome composition and functional pathways in healthy women.<br><br>METHODS: Participants were from the Mind-Body Study (N = 206, mean age = 61), a sub-study of the Nurses' Health Study II cohort. In 2013, participants completed measures of emotion-related factors. Two pairs of stool samples were collected, 6 months apart, 3 months after emotion-related factors measures were completed. Analyses examined associations of emotion-related factors with gut microbial diversity, overall microbiome structure, and specific species/pathways and adjusted for relevant covariates.<br><br>RESULTS: Alpha diversity was negatively associated with suppression. In multivariate analysis, positive emotions were inversely associated with the relative abundance of Firmicutes bacterium CAG 94 and Ruminococcaceae bacterium D16, while negative emotions were directly correlated with the relative abundance of these same species. At the metabolic pathway level, negative emotions were inversely related to the biosynthesis of pantothenate, coenzyme A, and adenosine.<br><br>CONCLUSIONS: These findings offer human evidence supporting linkages of emotions and related regulatory processes with the gut microbiome and highlight the importance of incorporating the gut microbiome in our understanding of emotion-related factors and their associations with physical health.}, }
@article {pmid36941875, year = {2023}, author = {Mandour, MO and Al-Musawi, S and Idowu, E and Long, PF and Rashidghamat, E and Oben, JA}, title = {Metabolic endoscopy and a simplified low-carbohydrate-high-dietary fiber template as novel treatments for hidradenitis suppurativa - A case series.}, journal = {JAAD case reports}, volume = {34}, number = {}, pages = {23-26}, pmid = {36941875}, issn = {2352-5126}, }
@article {pmid36941627, year = {2023}, author = {Yajima, D and Fujita, H and Hayashi, I and Shima, G and Suzuki, K and Toju, H}, title = {Core species and interactions prominent in fish-associated microbiome dynamics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {53}, pmid = {36941627}, issn = {2049-2618}, mesh = {Animals ; *Microbiota/genetics ; Bacteria ; Archaea/genetics ; Fishes ; Aquaculture ; }, abstract = {BACKGROUND: In aquatic ecosystems, the health and performance of fish depend greatly on the dynamics of microbial community structure in the background environment. Nonetheless, finding microbes with profound impacts on fish's performance out of thousands of candidate species remains a major challenge.<br><br>METHODS: We examined whether time-series analyses of microbial population dynamics could illuminate core components and structure of fish-associated microbiomes in the background (environmental) water. By targeting eel-aquaculture-tank microbiomes as model systems, we reconstructed the population dynamics of the 9605 bacterial and 303 archaeal species/strains across 128 days.<br><br>RESULTS: Due to the remarkable increase/decrease of constituent microbial population densities, the taxonomic compositions of the microbiome changed drastically through time. We then found that some specific microbial taxa showed a positive relationship with eels' activity levels even after excluding confounding effects of environmental parameters (pH and dissolved oxygen level) on population dynamics. In particular, a vitamin-B12-producing bacteria, Cetobacterium somerae, consistently showed strong positive associations with eels' activity levels across the replicate time series of the five aquaculture tanks analyzed. Network theoretical and metabolic modeling analyses further suggested that the highlighted bacterium and some other closely-associated bacteria formed "core microbiomes" with potentially positive impacts on eels.<br><br>CONCLUSIONS: Overall, these results suggest that the integration of microbiology, ecological theory, and network science allows us to explore core species and interactions embedded within complex dynamics of fish-associated microbiomes.&#xa0; Video Abstract.}, }
@article {pmid36941563, year = {2023}, author = {Guo, M and Liu, H and Yu, Y and Zhu, X and Xie, H and Wei, C and Mei, C and Shi, Y and Zhou, N and Qin, K and Li, W}, title = {Lactobacillus rhamnosus GG ameliorates osteoporosis in ovariectomized rats by regulating the Th17/Treg balance and gut microbiota structure.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2190304}, doi = {10.1080/19490976.2023.2190304}, pmid = {36941563}, issn = {1949-0984}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; T-Lymphocytes, Regulatory ; Th17 Cells ; RNA, Ribosomal, 16S ; *Osteoporosis/therapy ; Estrogens ; Inflammation ; *Probiotics ; }, abstract = {BACKGROUND: With increasing knowledge about the gut - bone axis, more studies for treatments based on the regulation of postmenopausal osteoporosis by gut microbes are being conducted. Based on our previous work, this study was conducted to further investigate the therapeutic effects of Lactobacillus rhamnosus GG (LGG) on ovariectomized (OVX) model rats and the immunological and microecological mechanisms involved.<br><br>RESULTS: We found a protective effect of LGG treatment in OVX rats through changes in bone microarchitecture, bone biomechanics, and CTX-I, PINP, Ca, and RANKL expression levels. LGG was more advantageous in promoting osteogenesis, which may be responsible for the alleviation of osteoporosis. Th17 cells were imbalanced with Treg cells in mediastinal lymph nodes and bone marrow, with ROR&#x3b3;t and FOXP3 expression following a similar trend. TNF-&#x3b1; and IL-17 expression in colon and bone marrow increased, while TGF-&#x3b2; and IL-10 expression decreased; however, LGG treatment modulated these changes and improved the Th17/Treg balance significantly. Regarding the intestinal barrier, we found that LGG treatment ameliorated estrogen deficiency-induced inflammation and mucosal damage and increased the expression of GLP-2&#x2009;R and tight junction proteins. Importantly, 16S rRNA sequencing showed a significant increase in the Firmicutes/Bacteroidetes ratio during estrogen deficiency. Dominant intestinal flora showed significant differences in composition; LGG treatment regulated the various genera that were imbalanced in OVX, along with modifying those that did not change significantly in other groups with respect to the intestinal barrier, inflammation development, and bile acid metabolism.<br><br>CONCLUSIONS: Overall, LGG ameliorated estrogen deficiency-induced osteoporosis by regulating the gut microbiome and intestinal barrier and stimulating Th17/Treg balance in gut and bone.}, }
@article {pmid36941408, year = {2023}, author = {Baldrian, P and López-Mondéjar, R and Kohout, P}, title = {Forest microbiome and global change.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {36941408}, issn = {1740-1534}, abstract = {Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.}, }
@article {pmid36941399, year = {2023}, author = {Zheng, D and Mohapatra, G and Kern, L and He, Y and Shmueli, MD and Valdés-Mas, R and Kolodziejczyk, AA and Próchnicki, T and Vasconcelos, MB and Schorr, L and Hertel, F and Lee, YS and Rufino, MC and Ceddaha, E and Shimshy, S and Hodgetts, RJ and Dori-Bachash, M and Kleimeyer, C and Goldenberg, K and Heinemann, M and Stettner, N and Harmelin, A and Shapiro, H and Puschhof, J and Chen, M and Flavell, RA and Latz, E and Merbl, Y and Abdeen, SK and Elinav, E}, title = {Epithelial Nlrp10 inflammasome mediates protection against intestinal autoinflammation.}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, pmid = {36941399}, issn = {1529-2916}, abstract = {Unlike other nucleotide oligomerization domain-like receptors, Nlrp10 lacks a canonical leucine-rich repeat domain, suggesting that it is incapable of signal sensing and inflammasome formation. Here we show that mouse Nlrp10 is expressed in distal colonic intestinal epithelial cells (IECs) and modulated by the intestinal microbiome. In vitro, Nlrp10 forms an Apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC)-dependent, m-3M3FBS-activated, polyinosinic:polycytidylic acid-modulated inflammasome driving interleukin-1β and interleukin-18 secretion. In vivo, Nlrp10 signaling is dispensable during steady state but becomes functional during autoinflammation in antagonizing mucosal damage. Importantly, whole-body or conditional IEC Nlrp10 depletion leads to reduced IEC caspase-1 activation, coupled with enhanced susceptibility to dextran sodium sulfate-induced colitis, mediated by altered inflammatory and healing programs. Collectively, understanding Nlrp10 inflammasome-dependent and independent activity, regulation and possible human relevance might facilitate the development of new innate immune anti-inflammatory interventions.}, }
@article {pmid36941398, year = {2023}, author = {Zhu, X and Sakamoto, S and Ishii, C and Smith, MD and Ito, K and Obayashi, M and Unger, L and Hasegawa, Y and Kurokawa, S and Kishimoto, T and Li, H and Hatano, S and Wang, TH and Yoshikai, Y and Kano, SI and Fukuda, S and Sanada, K and Calabresi, PA and Kamiya, A}, title = {Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses.}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, pmid = {36941398}, issn = {1529-2916}, abstract = {The intestinal immune system interacts with commensal microbiota to maintain gut homeostasis. Furthermore, stress alters the microbiome composition, leading to impaired brain function; yet how the intestinal immune system mediates these effects remains elusive. Here we report that colonic γδ T cells modulate behavioral vulnerability to chronic social stress via dectin-1 signaling. We show that reduction in specific Lactobacillus species, which are involved in T cell differentiation to protect the host immune system, contributes to stress-induced social-avoidance behavior, consistent with our observations in patients with depression. Stress-susceptible behaviors derive from increased differentiation in colonic interleukin (IL)-17-producing γδ T cells (γδ17 T cells) and their meningeal accumulation. These stress-susceptible cellular and behavioral phenotypes are causally mediated by dectin-1, an innate immune receptor expressed in γδ T cells. Our results highlight the previously unrecognized role of intestinal γδ17 T cells in the modulation of psychological stress responses and the importance of dectin-1 as a potential therapeutic target for the treatment of stress-induced behaviors.}, }
@article {pmid36941332, year = {2023}, author = {Watanabe, K and Wilmanski, T and Diener, C and Earls, JC and Zimmer, A and Lincoln, B and Hadlock, JJ and Lovejoy, JC and Gibbons, SM and Magis, AT and Hood, L and Price, ND and Rappaport, N}, title = {Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {36941332}, issn = {1546-170X}, abstract = {Multiomic profiling can reveal population heterogeneity for both health and disease states. Obesity drives a myriad of metabolic perturbations and is a risk factor for multiple chronic diseases. Here we report an atlas of cross-sectional and longitudinal changes in 1,111 blood analytes associated with variation in body mass index (BMI), as well as multiomic associations with host polygenic risk scores and gut microbiome composition, from a cohort of 1,277 individuals enrolled in a wellness program (Arivale). Machine learning model predictions of BMI from blood multiomics captured heterogeneous phenotypic states of host metabolism and gut microbiome composition better than BMI, which was also validated in an external cohort (TwinsUK). Moreover, longitudinal analyses identified variable BMI trajectories for different omics measures in response to a healthy lifestyle intervention; metabolomics-inferred BMI decreased to a greater extent than actual BMI, whereas proteomics-inferred BMI exhibited greater resistance to change. Our analyses further identified blood analyte-analyte associations that were modified by metabolomics-inferred BMI and partially reversed in individuals with metabolic obesity during the intervention. Taken together, our findings provide a blood atlas of the molecular perturbations associated with changes in obesity status, serving as a resource to quantify metabolic health for predictive and preventive medicine.}, }
@article {pmid36941248, year = {2023}, author = {Butler, MI and Bastiaanssen, TFS and Long-Smith, C and Morkl, S and Berding, K and Ritz, NL and Strain, C and Patangia, D and Patel, S and Stanton, C and O'Mahony, SM and Cryan, JF and Clarke, G and Dinan, TG}, title = {The gut microbiome in social anxiety disorder: evidence of altered composition and function.}, journal = {Translational psychiatry}, volume = {13}, number = {1}, pages = {95}, pmid = {36941248}, issn = {2158-3188}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Autism Spectrum Disorder ; *Phobia, Social ; *Microbiota ; *Schizophrenia ; }, abstract = {The microbiome-gut-brain axis plays a role in anxiety, the stress response and social development, and is of growing interest in neuropsychiatric conditions. The gut microbiota shows compositional alterations in a variety of psychiatric disorders including depression, generalised anxiety disorder (GAD), autism spectrum disorder (ASD) and schizophrenia but studies investigating the gut microbiome in social anxiety disorder (SAD) are very limited. Using whole-genome shotgun analysis of 49 faecal samples (31 cases and 18 sex- and age-matched controls), we analysed compositional and functional differences in the gut microbiome of patients with SAD in comparison to healthy controls. Overall microbiota composition, as measured by beta-diversity, was found to be different between the SAD and control groups and several taxonomic differences were seen at a genus- and species-level. The relative abundance of the genera Anaeromassillibacillus and Gordonibacter were elevated in SAD, while Parasuterella was enriched in healthy controls. At a species-level, Anaeromassilibacillus sp An250 was found to be more abundant in SAD patients while Parasutterella excrementihominis was higher in controls. No differences were seen in alpha diversity. In relation to functional differences, the gut metabolic module 'aspartate degradation I' was elevated in SAD patients. In conclusion, the gut microbiome of patients with SAD differs in composition and function to that of healthy controls. Larger, longitudinal studies are warranted to validate these preliminary results and explore the clinical implications of these microbiome changes.}, }
@article {pmid36940878, year = {2023}, author = {Serna-García, R and Tsapekos, P and Treu, L and Bouzas, A and Seco, A and Campanaro, S and Angelidaki, I}, title = {Unraveling prevalence of homoacetogenesis and methanogenesis pathways due to inhibitors addition.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128922}, doi = {10.1016/j.biortech.2023.128922}, pmid = {36940878}, issn = {1873-2976}, abstract = {Three inhibitors targeting different microorganisms, both from Archaea and Bacteria domains, were evaluated for their effect on CO2 biomethanation: sodium ionophore III (ETH2120), carbon monoxide (CO), and sodium 2-bromoethanesulfonate (BES). This study examines how these compounds affect the anaerobic digestion microbiome in a biogas upgrading process. While archaea were observed in all experiments, methane was produced only when adding ETH2120 or CO, not when adding BES, suggesting archaea were in an inactivated state. Methane was produced mainly via methylotrophic methanogenesis from methylamines. Acetate was produced at all conditions, but a slight reduction on acetate production (along with an enhancement on CH4 production) was observed when applying 20 kPa of CO. Effects on CO2 biomethanation were difficult to observe since the inoculum used was from a real biogas upgrading reactor, being this a complex environmental sample. Nevertheless, it must be mentioned that all compounds had effects on the microbial community composition.}, }
@article {pmid36940867, year = {2023}, author = {English, J and Patrick, S and Stewart, LD}, title = {The potential role of molecular mimicry by the anaerobic microbiome in the aetiology of autoimmune disease.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102721}, doi = {10.1016/j.anaerobe.2023.102721}, pmid = {36940867}, issn = {1095-8274}, abstract = {Autoimmune diseases are thought to develop as a consequence of various environmental and genetic factors, each of which contributes to dysfunctional immune responses and/or a breakdown in immunological tolerance towards native structures. Molecular mimicry by microbial components is among the environmental factors thought to promote a breakdown in immune tolerance, particularly through the presence of cross-reactive epitopes shared with the human host. While resident members of the microbiome are essential promoters of human health through immunomodulation, defence against pathogenic colonisation and conversion of dietary fibre into nutritional resources for host tissues, there may be an underappreciated role of these microbes in the aetiology and/or progression of autoimmune disease. An increasing number of molecular mimics are being identified amongst the anaerobic microbiota which structurally resemble endogenous components and, in some cases, for example the human ubiquitin mimic of Bacteroides fragilis and DNA methyltransferase of Roseburia intestinalis, have been associated with promoting antibody profiles characteristic of autoimmune diseases. The persistent exposure of molecular mimics from the microbiota to the human immune system is likely to be involved in autoantibody production that contributes to the pathologies associated with immune-mediated inflammatory disorders. Here-in, examples of molecular mimics that have been identified among resident members of the human microbiome and their ability to induce autoimmune disease through cross-reactive autoantibody production are discussed. Improved awareness of the molecular mimics that exist among human colonisers will help elucidate the mechanisms involved in the breakdown of immune tolerance that ultimately lead to chronic inflammation and downstream disease.}, }
@article {pmid36940753, year = {2023}, author = {Stiernborg, M and Debelius, JW and Yang, LL and Skott, E and Millischer, V and Giacobini, M and Melas, PA and Boulund, F and Lavebratt, C}, title = {Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2023.03.012}, pmid = {36940753}, issn = {1090-2139}, abstract = {Recent evidence suggests that there is a link between neurodevelopmental disorders, such as attention deficit hyperactivity disorder (ADHD), and the gut microbiome. However, most studies to date have had low sample sizes, have not investigated the impact of psychostimulant medication, and have not adjusted for potential confounders, including body mass index, stool consistency and diet. To this end, we conducted the largest, to our knowledge, fecal shotgun metagenomic sequencing study in ADHD, with 147 well-characterized adult and child patients. For a subset of individuals, plasma levels of inflammatory markers and short-chain fatty acids were also measured. In adult ADHD patients (n=84), compared to controls (n=52), we found a significant difference in beta diversity both regarding bacterial strains (taxonomic) and bacterial genes (functional). In children with ADHD (n=63), we found that those on psychostimulant medication (n=33 on medication vs. n=30 not on medication) had (i) significantly different taxonomic beta diversity, (ii) lower functional and taxonomic evenness, (iii) lower abundance of the strain Bacteroides stercoris CL09T03C01 and bacterial genes encoding an enzyme in vitamin B12 synthesis, and (iv) higher plasma levels of vascular inflammatory markers sICAM-1 and sVCAM-1. Our study continues to support a role for the gut microbiome in neurodevelopmental disorders and provides additional insights into the effects of psychostimulant medication. However, additional studies are needed to replicate these findings and examine causal relationships with the disorder.}, }
@article {pmid36940655, year = {2023}, author = {Xi, Y and Li, Y and Ying, S and Yan, J and Shi, Z}, title = {Bacterial lipopolysaccharide with different administration routes affects intestinal mucosal morphological, immunological, and microbial barrier functions in goslings.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102599}, doi = {10.1016/j.psj.2023.102599}, pmid = {36940655}, issn = {1525-3171}, abstract = {The current study was conducted to evaluate the effects of different administration routes of bacterial lipopolysaccharide (LPS) on intestinal mucosal morphological, immunological, and microbial barrier functions in goslings. First, we compared intestinal villi morphology of goslings under intraperitoneal or oral LPS treatment through hematoxylin and eosin staining. Then, we determined the signatures of the microbiome in the ileum mucosa of goslings subjected to oral LPS treatment at 0, 2, 4, and 8 mg/kg BW by 16S sequencing, and analyzed the changes in intestinal barrier functions and permeability, levels of LPS in the ileum mucosa, plasma, and liver tissue, and the induced inflammatory response of Toll-like receptor 4 (TLR4). As a result, intraperitoneal LPS injection resulted in a thicker intestinal wall in the ileum within a short time, whereas villus height was less affected; in contrast, oral LPS treatment exerted a stronger influence on villus height but not on intestinal wall thickness. We also found that oral LPS treatment affected the structure of the intestinal microbiome, reflected by changes in the clustering of intestinal microbiota. The average abundance of Muribaculaceae showed an increasing trend with increasing LPS levels, and that of the genus Bacteroides decreased, compared with the control group. In addition, oral LPS treatment with 8 mg/kg BW affected the intestinal epithelial morphology, damage the mucosal immune barrier, downregulated the expression of tight junction proteins, increased circulating D-lactate levels, and stimulated the secretion of various inflammatory mediators and activation of the TLR4/MyD88/NFκB pathway. This study presented the injuries of intestinal mucosal barrier function induced by LPS challenges in goslings and provided a scientific model for searching the novel strategies to attenuate the immunological stress and gut injury caused by LPS.}, }
@article {pmid36940526, year = {2023}, author = {Wilms, W and Woźniak-Karczewska, M and Niemczak, M and Parus, A and Frankowski, R and Wolko, &#x141; and Czarny, J and Piotrowska-Cyplik, A and Zgoła-Grześkowiak, A and Heipieper, HJ and Chrzanowski, &#x141;}, title = {2,4-D versus 2,4-D based ionic liquids: Effect of cation on herbicide biodegradation, tfdA genes abundance and microbiome changes during soil bioaugmentation.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131209}, doi = {10.1016/j.jhazmat.2023.131209}, pmid = {36940526}, issn = {1873-3336}, abstract = {The commercial formulations of herbicides rely on surfactants which increase the efficiency of active substance. Herbicidal ionic liquids (ILs), in which cationic surfactants are combined with herbicidal anions, allow for additives' reduction and ensure very good herbicide performance with lower doses. We aimed to test the impact of synthetic and natural cations on biological degradation of 2,4-dichlorophenoxyacetic acid (2,4-D). Although primary biodegradation was high, the mineralization in agricultural soil indicated incomplete conversion of ILs to CO2. Even the introduction of naturally-derived cations resulted in an increase in the herbicide's half-lives - from 32 days for [Na][2,4-D] to 120 days for [Chol][2,4-D] and 300 days for the synthetic tetramethylammonium derivative [TMA][2,4-D]. Bioaugmentation with 2,4-D-degrading strains improves the herbicides' degradation, which was reflected by higher abundance of tfdA genes. Microbial community analysis confirmed that hydrophobic cationic surfactants, even those based on natural compounds, played a negative role on microbial biodiversity. Our study provides a valuable indication for further research related to the production of a new generation of environmentally friendly compounds. Moreover, the results shed a new light on the ionic liquids as independent mixtures of ions in the environment, as opposed to treating them as new type of environmental pollutants.}, }
@article {pmid36940301, year = {2023}, author = {Vernaci, G and Savarino, EV and Patuzzi, I and Facchin, S and Zingone, F and Massa, D and Faggioni, G and Giarratano, T and Miglietta, F and Griguolo, G and Fassan, M and Lo Mele, M and Gasparini, E and Bisagni, G and Guarneri, V and Dieci, MV}, title = {Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy.}, journal = {The oncologist}, volume = {}, number = {}, pages = {}, doi = {10.1093/oncolo/oyad060}, pmid = {36940301}, issn = {1549-490X}, abstract = {INTRODUCTION: Patients with triple-negative breast cancer (TNBC) achieving a pathological complete response (pCR) after neoadjuvant chemotherapy have a better event-free survival. The role of gut microbiome in early TNBC is underexplored.<br><br>METHODS: Microbiome was analyzed by 16SrRNA sequencing.<br><br>RESULTS: Twenty-five patients with TNBC treated with neoadjuvant anthracycline/taxane-based chemotherapy were included. Fifty-six percent achieved a pCR. Fecal samples were collected before (t0), at 1 (t1), and 8 weeks (t2) from chemotherapy. Overall, 68/75 samples (90.7%) were suitable for microbiome analysis. At t0, pCR group showed a significantly higher &#x3b1;-diversity as compared with no-pCR, (P = .049). The PERMANOVA test on &#x3b2;-diversity highlighted a significant difference in terms of BMI (P = 0.039). Among patients with available matched samples at t0 and t1, no significant variation in microbiome composition was reported over time.<br><br>CONCLUSIONS: Fecal microbiome analysis in early TNBC is feasible and deserves further investigation in order to unravel its complex correlation with immunity and cancer.}, }
@article {pmid36940225, year = {2023}, author = {Rashid, S and Noor, TA and Saeed, H and Ali, AS and Meheshwari, G and Mehmood, A and Fatima, L and Zaidi, SMJ and Malik, J and Mehmoodi, A and Hayat, A}, title = {Association of gut microbiome dysbiosis with the progression of atrial fibrillation: A systematic review.}, journal = {Annals of noninvasive electrocardiology : the official journal of the International Society for Holter and Noninvasive Electrocardiology, Inc}, volume = {}, number = {}, pages = {e13059}, doi = {10.1111/anec.13059}, pmid = {36940225}, issn = {1542-474X}, abstract = {OBJECTIVE: Many clinical and preclinical studies have implicated an association between atrial fibrillation (AF) and its progression to imbalances in the gut microbiome composition. The gut microbiome is a diverse and complex ecosystem containing billions of microorganisms that produce biologically active metabolites influencing the host disease development.<br><br>METHODS: For this review, a literature search was conducted using digital databases to systematically identify the studies reporting the association of gut microbiota with AF progression.<br><br>RESULTS: In a total of 14 studies, 2479 patients were recruited for the final analysis. More than half (n&#xa0;=&#x2009;8) of the studies reported alterations in alpha diversity in atrial fibrillation. As for the beta diversity, 10 studies showed significant alterations. Almost all studies that assessed gut microbiota alterations reported major taxa associated with atrial fibrillation. Most studies focused on short-chain fatty acids (SCFAs), whereas three studies evaluated TMAO levels in the blood, which is the breakdown product of dietary l-carnitine, choline, and lecithin. Moreover, an independent cohort study assessed the relationship between phenylacetylglutamine (PAGIn) and AF.<br><br>CONCLUSION: Intestinal dysbiosis is a modifiable risk factor that might provide newer treatment strategies for AF prevention. Well-designed research and prospective randomized interventional studies are required to target the gut dysbiotic mechanisms and determine the gut dysbiotic-AF relationship.}, }
@article {pmid36940072, year = {2023}, author = {Ren, QL and Wang, Q and Zhang, XQ and Wang, M and Hu, H and Tang, JJ and Yang, XT and Ran, YH and Liu, HH and Song, ZX and Liu, JG and Li, XL}, title = {Anticancer Activity of Diosgenin and Its Molecular Mechanism.}, journal = {Chinese journal of integrative medicine}, volume = {}, number = {}, pages = {}, pmid = {36940072}, issn = {1672-0415}, abstract = {Diosgenin, a steroidal sapogenin, obtained from Trigonella foenum-graecum, Dioscorea, and Rhizoma polgonati, has shown high potential and interest in the treatment of various cancers such as oral squamous cell carcinoma, laryngeal cancer, esophageal cancer, liver cancer, gastric cancer, lung cancer, cervical cancer, prostate cancer, glioma, and leukemia. This article aims to provide an overview of the in vivo, in vitro, and clinical studies reporting the diosgenin's anticancer effects. Preclinical studies have shown promising effects of diosgenin on inhibiting tumor cell proliferation and growth, promoting apoptosis, inducing differentiation and autophagy, inhibiting tumor cell metastasis and invasion, blocking cell cycle, regulating immunity and improving gut microbiome. Clinical investigations have revealed clinical dosage and safety property of diosgenin. Furthermore, in order to improve the biological activity and bioavailability of diosgenin, this review focuses on the development of diosgenin nano drug carriers, combined drugs and the diosgenin derivatives. However, further designed trials are needed to unravel the diosgenin's deficiencies in clinical application.}, }
@article {pmid36939800, year = {2022}, author = {Chen, H and Zhao, Q and Zhong, Q and Duan, C and Krutmann, J and Wang, J and Xia, J}, title = {Skin Microbiome, Metabolome and Skin Phenome, from the Perspectives of Skin as an Ecosystem.}, journal = {Phenomics (Cham, Switzerland)}, volume = {2}, number = {6}, pages = {363-382}, pmid = {36939800}, issn = {2730-5848}, abstract = {Skin is a complex ecosystem colonized by millions of microorganisms, including bacteria, fungi, and viruses. Skin microbiota is believed to exert critical functions in maintaining host skin health. Profiling the structure of skin microbial community is the first step to overview the ecosystem. However, the community composition is highly individualized and extremely complex. To explore the fundamental factors driving the complexity of the ecosystem, namely the selection pressures, we review the present studies on skin microbiome from the perspectives of ecology. This review summarizes the following: (1) the composition of substances/nutrients in the cutaneous ecological environment that are derived from the host and the environment, highlighting their proposed function on skin microbiota; (2) the features of dominant skin commensals to occupy ecological niches, through self-adaptation and microbe-microbe interactions; (3) how skin microbes, by their structures or bioactive molecules, reshape host skin phenotypes, including skin immunity, maintenance of skin physiology such as pH and hydration, ultraviolet (UV) protection, odor production, and wound healing. This review aims to re-examine the host-microbe interactions from the ecological perspectives and hopefully to give new inspiration to this field.}, }
@article {pmid36939622, year = {2023}, author = {Peterson, SR and Ali, S and Shrode, RL and Mangalam, AK}, title = {Effect of a Fructose-Rich Diet on Gut Microbiota and Immunomodulation: Potential Factors for Multiple Sclerosis.}, journal = {ImmunoHorizons}, volume = {7}, number = {3}, pages = {213-227}, doi = {10.4049/immunohorizons.2300008}, pmid = {36939622}, issn = {2573-7732}, abstract = {Multiple sclerosis (MS) is an autoimmune demyelinating disease of the CNS that is linked with both genetic and environmental factors. A Western-style diet rich in fat and simple sugars is hypothesized as a potential factor contributing to the increased incidence of inflammatory autoimmune diseases, such as MS, in developed countries. Although the adverse effects of a high-fat diet in MS have been studied extensively, the effect of a fructose-rich diet (FRD) on MS etiology is unknown. We hypothesized that an FRD will alter the gut microbiome, influence immune populations, and negatively impact disease in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. To test this, we fed C57BL/6 mice either an FRD or normal feed for 4 or 12 wk and analyzed the effect of an FRD on gut microbiota, immune populations, and EAE. An FRD significantly influenced the gut microbiota, with reduced abundance of beneficial bacteria and enrichment of potentially proinflammatory bacteria. We also observed immune modulation in the gut and periphery. Of particular interest was a population of Helios-RORγt+Foxp3+CD4+ T cells that was enriched in the small intestine lamina propria of FRD-fed mice. However, despite gut microbiota and immune modulations, we observed only a subtle effect of an FRD on EAE severity. Overall, our data suggest that in C57Bl6/J mice, an FRD modulates the gut microbiota and immune system without significantly impacting myelin oligodendrocyte glycoprotein 35-55/CFA-induced EAE.}, }
@article {pmid36939352, year = {2023}, author = {Nguyen, NH}, title = {Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0470822}, doi = {10.1128/spectrum.04708-22}, pmid = {36939352}, issn = {2165-0497}, abstract = {Mat-forming fungi are common in forest and grassland soils across the world, where their activity contributes to important soil ecological processes. These fungi maintain dominance through aggressive and abundant hyphae that modify their internal physical and chemical environments and through these modifications select for what appears to be a suite of mycophilic bacteria. Here, the bacteria associated with the fungal mats of Leucopaxillus gentianeus and Leucopaxillus albissimus from western North America are compared to adjacent nonmat substrates. Within the mats, the bacterial richness and diversity were significantly reduced, and the community composition was significantly different. The bacterial community structure between the two fungal hosts was marginally significant and indicated a shared set of bacterial associates. The genera Burkholderia, Streptomyces, Bacillus, Paenibacillus, and Mycobacterium were significantly abundant within the fungal mats and represent core members of these hypha-rich environments. Comparison with the literature from fungal mat studies worldwide showed that these genera are common and often significantly found within fungal mats, further reinforcing the concept of a mycophilic bacterial guild. These genera are incorporated into a synthesis discussion in the context of our current understanding of the nature of fungal-bacterial interactions and the potential outcomes of these interactions in soil nutrient cycling, plant productivity, and human health. IMPORTANCE Fungi and bacteria are the most abundant and diverse organisms in soils (perhaps more so than any other habitat on earth), and together these microorganisms contribute to broad soil ecosystem processes. There is a suite of bacteria that appears consistently within the physical space called the hyphosphere, the area of influence surrounding fungal hyphae. How these bacteria are selected for, how they are maintained, and what broader ecological functions they perform are subjects of interest in this relatively new field-the cross-kingdom interactions between fungi and bacteria. Understanding their cooccurrence and their interactions can open new realms of understanding in soil ecological processes with global consequences.}, }
@article {pmid36939337, year = {2023}, author = {Serebrinsky-Duek, K and Barra, M and Danino, T and Garrido, D}, title = {Engineered Bacteria for Short-Chain-Fatty-Acid-Repressed Expression of Biotherapeutic Molecules.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0004923}, doi = {10.1128/spectrum.00049-23}, pmid = {36939337}, issn = {2165-0497}, abstract = {Short-chain fatty acids (SCFA) such as propionate and butyrate are critical metabolites produced by the gut microbiota. Microbiome dysbiosis resulting in altered SCFA profiles is associated with certain diseases, including inflammatory bowel diseases (IBD), characterized by a reduction in butyrate concentration and active intestinal inflammation. There is an increasing interest in the use of engineered bacteria as diagnostic and therapeutic tools for gut diseases. In this study, we developed genetic circuits capable of sensing SCFA concentrations to build biosensors that express a response protein (superfolder green fluorescent protein [sfGFP]) in amounts inversely proportional to the SCFA concentration. We also built biotherapeutics expressing the cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) using the same logic. The propionate biotherapeutic expressed larger amounts of mouse GM-CSF in the absence of propionate. The butyrate biotherapeutics presented the expected behavior only at the beginning of the kinetics and an accelerated response in the absence of butyrate. Overall, these genetic systems may function as complementary diagnostic tools for measuring SCFAs and as delivery vehicles for biotherapeutic molecules. IMPORTANCE Short-chain fatty acids are key molecules produced by the gut microbiome. Their concentrations are altered in certain diseases. Here, we created molecular biosensors that quantify the absence of propionate and butyrate, using logic "NOT" gates and bacterial promoters. Finally, we show that these genetic systems could be useful for the delivery of therapeutic molecules in the gut, in the absence of these acids.}, }
@article {pmid36939321, year = {2023}, author = {Sarton-Lohéac, G and Nunes da Silva, CG and Mazel, F and Baud, G and de Bakker, V and Das, S and El Chazli, Y and Ellegaard, K and Garcia-Garcera, M and Glover, N and Liberti, J and Nacif Marçal, L and Prasad, A and Somerville, V and ,  and Bonilla-Rosso, G and Engel, P}, title = {Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees.}, journal = {mBio}, volume = {}, number = {}, pages = {e0353822}, doi = {10.1128/mbio.03538-22}, pmid = {36939321}, issn = {2150-7511}, abstract = {Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees. Specifically, the absence of genomic data from their microbiotas presents an important knowledge gap in understanding the evolution and functional diversity of the social bee microbiota. Here, we combined community profiling with culturing and genome sequencing of gut bacteria from six neotropical stingless bee species from Brazil. Phylogenomic analyses show that most stingless bee gut isolates form deep-branching sister clades of core members of the honey bee and bumblebee gut microbiota with conserved functional capabilities, confirming the common ancestry and ecology of their microbiota. However, our bacterial phylogenies were not congruent with those of the host, indicating that the evolution of the social bee gut microbiota was not driven by strict codiversification but included host switches and independent symbiont gain and losses. Finally, as reported for the honey bee and bumblebee microbiotas, we found substantial genomic divergence among strains of stingless bee gut bacteria, suggesting adaptation to different host species and glycan niches. Our study offers first insights into the genomic diversity of the stingless bee microbiota and highlights the need for broader samplings to understand the evolution of the social bee gut microbiota. IMPORTANCE Stingless bees are the most diverse group of the corbiculate bees and represent important pollinator species throughout the tropics and subtropics. They harbor specialized microbial communities in their gut that are related to those found in honey bees and bumblebees and that are likely important for bee health. Few bacteria have been cultured from the gut of stingless bees, which has prevented characterization of their genomic diversity and functional potential. Here, we established cultures of major members of the gut microbiotas of six stingless bee species and sequenced their genomes. We found that most stingless bee isolates belong to novel bacterial species distantly related to those found in honey bees and bumblebees and encoding similar functional capabilities. Our study offers a new perspective on the evolution of the social bee gut microbiota and presents a basis for characterizing the symbiotic relationships between gut bacteria and stingless bees.}, }
@article {pmid36939272, year = {2023}, author = {Yan, K and Auger, S and Diaz, A and Naman, J and Vemulapalli, R and Hasina, R and Izumchenko, E and Shogan, B and Agrawal, N}, title = {Microbial Changes Associated With Oral Cavity Cancer Progression.}, journal = {Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery}, volume = {}, number = {}, pages = {}, doi = {10.1002/ohn.211}, pmid = {36939272}, issn = {1097-6817}, abstract = {OBJECTIVE: To examine the oral microbiome in the context of oral cavity squamous cell carcinoma.<br><br>STUDY DESIGN: Basic science research.<br><br>SETTING: Academic medical center.<br><br>METHODS: Oral swabs were collected from patients presenting to the operating room for management of oral cavity squamous cell carcinoma and from age- and sex-matched control patients receiving surgery for unrelated benign conditions. 16S ribosomal RNA (rRNA) sequencing was performed on genetic material obtained from swabs. A bacterial rRNA gene library was created and sequence reads were sorted into taxonomic units.<br><br>RESULTS: Thirty-one control patients (17 males) and 35 cancer patients (21 males) were enrolled. Ages ranged from 23 to 89 (median 63) for control patients and 35 to 86 (median 66) for cancer patients. Sixty-one percent of control patients and 63% of cancer patients were smokers. 16S analyses demonstrated a significant decrease in Streptococcus genera in oral cancer patients (34.11% vs 21.74% of the population, p&#x2009;=&#x2009;.04). Increases in Fusobacterium, Peptostreptococcus, Parvimonas, and Neisseria were also found. The abundance of these bacteria correlated with tumor T-stage.<br><br>CONCLUSION: 16S rRNA sequencing demonstrated changes in bacterial populations in oral cavity cancer and its progression compared to noncancer controls. We found increases in bacteria genera that correspond with tumor stage-Fusobacteria, Peptostreptococcus, Parvimonas, Neisseria, and Treponema. These data suggest that oral cancer creates an environment to facilitate foreign bacterial growth, rather than implicating a specific bacterial species in carcinogenesis. These bacteria can be employed as a potential marker for tumor progression or interrogated to better characterize the tumor microenvironment.}, }
@article {pmid36939199, year = {2023}, author = {Suresh, DS and Guruvayoorappan, C}, title = {Molecular principles of tissue invasion and metastasis.}, journal = {American journal of physiology. Cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpcell.00348.2022}, pmid = {36939199}, issn = {1522-1563}, abstract = {Cancer associated metastasis is the primary cause of morbidity and mortality. Yet, its underlying biological mechanism remains poorly understood. Efforts to prevent or delay metastasis require a deep understanding of the underlying molecular mechanisms. However, continues advancement in cancer biology research has improved the comprehensive understanding of some of the molecular keystones of dissemination process. However, the emergence of new paradigms in the study of metastasis intuitively recognizes the involvement of genetics, epigenetics, extrinsic traits and tumor microenvironment in metastatic initiation, progression and colonization. On its way to the target site, the disseminated tumor cells interact with multiplex of proteins and cells. Identification of mechanisms underlying metastatic program is crucial for developing effective and efficient therapeutic interventions. In this review, we discuss details about recent advancements in the field of metastasis and organotropism, also highlights the role of genetics, epigenetics, exosomes, circadian rhythm, microbiome, integrins and other adhesion molecules, and chemokines in the regulation of metastatic events.}, }
@article {pmid36939179, year = {2023}, author = {Hamilton, E and Twigg, S}, title = {Diabetes-related foot disease: new insights with an Antipodean focus.}, journal = {The Journal of endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1530/JOE-22-0238}, pmid = {36939179}, issn = {1479-6805}, abstract = {Diabetes-related foot disease (DFD), defined as ulceration, infection, or destruction of tissues of the foot in a person with current or previously diagnosed diabetes mellitus, is associated with a heavy burden for both patients and the healthcare system with high morbidity, mortality and costs. Improved outcomes for people with DFD are achieved with an interdisciplinary approach and adherence to best practice clinical guidelines, however in the Australian context, the vastness of the country presents unique challenges in achieving optimal outcomes for all people with DFD, with variation in service delivery, availability and accessibility between metropolitan, rural and remote areas. Aboriginal and Torres Strait Islander Australians and people with diabetes living in rural and remote areas experience higher rates of lower extremity amputation and further efforts and resources are required to improve outcomes for these high risk groups. In recent years, there have been advances in knowledge, including the understanding of the pathogenesis of diabetes-related peripheral neuropathy, genetic polymorphisms and mechanisms of disease associated with acute Charcot neuroarthropathy, biomarkers and potential mediators of diabetes-related foot ulcer (DFU) healing, the microbiology and microbiome profile of DFUs, pressure assessment and management as well as an expanded understanding of DFU sequelae and comorbidities. In this review, we describe new insights into pathophysiology, sequelae and comorbidities of DFD with a focus on basic and translational aspects and contributions to the field from Australian and New Zealand DFD researchers.}, }
@article {pmid36938958, year = {2023}, author = {Dedon, LR and Hilliard, MA and Rani, A and Daza-Merchan, ZT and Story, G and Briere, CE and Sela, DA}, title = {Fucosylated human milk oligosaccharides drive structure-specific syntrophy between Bifidobacterium infantis and Eubacterium hallii within a modeled infant gut microbiome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2200851}, doi = {10.1002/mnfr.202200851}, pmid = {36938958}, issn = {1613-4133}, abstract = {SCOPE: Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood.<br><br>METHODS AND RESULTS: Metabolite production and microbial populations were tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This was also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites were quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations were quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gave rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure did not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition was dependent on fHMO structure.<br><br>CONCLUSION: Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, fHMOs influences the composition of the gut microbiome. This article is protected by copyright. All rights reserved.}, }
@article {pmid36938940, year = {2023}, author = {Martindale, RG}, title = {Novel nutrition strategies to enhance recovery after surgery.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.2485}, pmid = {36938940}, issn = {1941-2444}, abstract = {Surgery and traumatic injury set off a cascade of metabolic changes that are becoming better understood. Recently, strategies and protocols have been developed for optimizing outcomes, and this has yielded beneficial results. This brief review evaluates three specific nutrition or metabolic interventions in the postoperative setting that attempt to optimize outcomes. We limited this to three subspecialty areas including oncologic surgery, orthopedic surgery, and cardiac surgery. These agents included fish oils, factors to prevent dysbiosis, and resistance exercise and its role in enhancing protein update. Where these novel agents fit into the basic tenets of postoperative nutrition interventions does not change the narrative: deliver graduated early enteral feeding to attenuate the metabolic response to surgical stress, maintain the gastrointestinal mucosal barrier, use immune/metabolic modulation to enhance immune response while attenuating excessive inflammation, and support the microbiome.}, }
@article {pmid36938877, year = {2023}, author = {Singal, AK and Shah, VH and Malhi, H}, title = {Emerging targets for therapy in ALD: lessons from NASH.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/HEP.0000000000000381}, pmid = {36938877}, issn = {1527-3350}, abstract = {Alcohol-associated liver disease due to harmful alcohol use and non-alcoholic fatty liver disease associated with metabolic syndrome are the two most common liver diseases worldwide. Control of respective risk factors is the cornerstone in the long-term management of these diseases. Furthermore, there are no effective therapies. Both diseases are characterized by metabolic derangements, thus, the focus of this review is to broaden our understanding of metabolic targets investigated in non-alcoholic fatty liver disease, and how these can be applied to alcohol-associated liver disease. Conserved pathogenic pathways such as dysregulated lipid metabolism, cell death pathways including apoptosis, activation of innate immune cells and stellate cells mediate both alcohol and non-alcoholic fatty liver diseases, resulting in histological abnormalities of steatosis, inflammation, fibrosis, and cirrhosis. However, pathways such as gut microbiome changes, glucose metabolism and insulin resistance, inflammatory signaling, and micro-RNA abnormalities are distinct in these two diseases. In this review article, we describe conserved and distinct pathogenic pathways highlighting therapeutic targets which may be of potential in both diseases, and those which are unique to each disease.}, }
@article {pmid36938621, year = {2023}, author = {Drobner, JC and Lichtbroun, BJ and Singer, EA and Ghodoussipour, S}, title = {Examining the Role of Microbiota-Centered Interventions in Cancer Therapeutics: Applications for Urothelial Carcinoma.}, journal = {Technology in cancer research &amp; treatment}, volume = {22}, number = {}, pages = {15330338231164196}, doi = {10.1177/15330338231164196}, pmid = {36938621}, issn = {1533-0338}, mesh = {Humans ; *Urinary Bladder Neoplasms ; *Carcinoma, Transitional Cell ; Dysbiosis/therapy/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {Modern advances in genomic and molecular technologies have sparked substantial research on the human intestinal microbiome over the past decade. A deeper understanding of the microbiome has illuminated that dysbiosis, or a disruption in the microbiome, is associated with inflammatory disease states and carcinogenesis. Novel therapies that target the microbiome and restore healthy flora may have value in dampening the immunopathologic state induced by dysbiosis. A narrative review of the literature on the use of microbiota-centered interventions (MCIs) was conducted. Several randomized clinical trials show that MCIs can augment response to immune checkpoint inhibitor (ICI) therapy in patients with metastatic cancer. Clinical trials have also demonstrated that modulation of the intestinal microbiome can enhance recovery and reduce infectious complications in the surgical management of colorectal adenocarcinoma. Overall, these major discoveries suggest future clinical applications of MCIs for a wide range of immune-mediated conditions. These results may also translate to improved patient outcomes in systemic immunotherapy for urothelial carcinoma as well as in patients recovering from radical cystectomy (RC), which is complicated by high infection rates. Further research is needed to evaluate the optimal bacterial composition of microbiota-centered therapies and the specific cellular changes that lead to improved tumor antigen recognition after microbiota-centered therapies.}, }
@article {pmid36938477, year = {2023}, author = {Ghalandari, N and Assarzadegan, F and Mahdavi, H and Jamshidi, E and Esmaily, H}, title = {Evaluating the effectiveness of probiotics in relieving constipation in Parkinson's disease: A systematic review and meta-analysis.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14312}, pmid = {36938477}, issn = {2405-8440}, abstract = {OBJECTIVES: The aim of this study was to evaluate the effects of probiotics on the treatment of constipation in patients with Parkinson's disease (PD) by analyzing data from published randomized clinical trials (RCTs). PD is a neurodegenerative disease characterized by clinical symptoms such as rigidity, bradykinesia, and resting tremor. Constipation is a common complaint reported by PD patients. Probiotics are often used to treat functional constipation. The potential mechanisms behind PD-related constipation include dysfunction of the enteric nervous system due to alpha-synuclein aggregation, dyssynergic contractions of the puborectalis muscle, and alterations of the gut microbiome.<br><br>METHOD: To conduct this study, we searched Scopus, PubMed, and Google Scholar for published articles on PD, probiotics, and constipation. We selected RCTs from 944 studies, and ultimately included 3 RCTs in our meta-analysis. The frequency of bowel movements per week was the only index that could be summarized among the records. We extracted and analyzed the results as means and standard deviations.<br><br>RESULT: We calculated a standardized mean difference (SMD) of 0.92 (95% CI, 0.65 to 1.19; I-squared&#xa0;=&#xa0;57.0%; p&#xa0;<&#xa0;0.001) to determine the treatment effect in terms of frequency of bowel movements per week in the RCTs.<br><br>CONCLUSION: Our results show that probiotic intake has beneficial effects on constipation in PD patients. Further research, including multicenter studies, is needed to assess the long-term efficacy and safety of probiotic supplements in neurodegenerative diseases.}, }
@article {pmid36938237, year = {2023}, author = {Desai, D and Desai, A and Jamil, A and Csendes, D and Gutlapalli, SD and Prakash, K and Swarnakari, KM and Bai, M and Manoharan, MP and Raja, R and Khan, S}, title = {Re-defining the Gut Heart Axis: A Systematic Review of the Literature on the Role of Gut Microbial Dysbiosis in Patients With Heart Failure.}, journal = {Cureus}, volume = {15}, number = {2}, pages = {e34902}, pmid = {36938237}, issn = {2168-8184}, abstract = {Heart failure (HF) contributes to the cardiovascular health burden worldwide. Patients with heart failure have been recently studied to possess unique changes in the gut microbiome that affect immune homeostasis and metabolism. In this systematic review of the literature, we aim to identify the impact of gut dysbiosis on heart failure. We used Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines to conduct our systematic review. We searched the literature on databases such as PubMed, PubMed Central (PMC), Medline, and ScienceDirect. Ten articles were included for review. There were significant differences in the gut microbiome composition in heart failure. Relative abundance of Ruminococcus gnavus, Escherichia Shigella, Streptococcus sp, Veillonella sp, and Actinobacteria, and relative depletion of Eubacterium, Prevotella, Faecalibacterium, SMB53, and Megamonas. The composition varied according to age, heart failure stage, and decompensation level. The composition remained unaltered with ejection fraction. There was an increased expression of genes responsible for the metabolism of amino acids, carbohydrates, choline trimethylamine-lyase (TMA-lyase), lipopolysaccharide (LPS) biosynthesis, tryptophan, and lipid metabolism. The resultant changes affected the levels of metabolites, such as trimethylamine N-oxide (TMAO), indoxyl sulfate (IS), and LPS, and inflammatory markers in the feces and plasma, which contributed to heart failure. These biomarkers of heart failure could serve as targets for the prevention and treatment of heart failure. Patients with heart failure harbor a unique constellation of gut microbiota that affect the pathogenesis of heart failure. Further studies are needed to understand the causal relationship between dysbiosis and heart failure.}, }
@article {pmid36938132, year = {2022}, author = {Klassen, L and Reintjes, G and Li, M and Jin, L and Amundsen, C and Xing, X and Dridi, L and Castagner, B and Alexander, TW and Abbott, DW}, title = {Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1020250}, pmid = {36938132}, issn = {1664-302X}, abstract = {Rapid dietary changes, such as switching from high-forage to high-grain diets, can modify the rumen microbiome and initiate gastrointestinal distress, such as bloating. In such cases, feed additives, including prebiotics and live microbials, can be used to mitigate these negative consequences. Bio-Mos® is a carbohydrate-based prebiotic derived from yeast cells that is reported to increase livestock performance. Here, the responses of rumen bacterial cells to Bio-Mos® were quantified, sorted by flow cytometry using fluorescently-labeled yeast mannan, and taxonomically characterized using fluorescence in situ hybridization and 16S rRNA sequencing. Further, to evaluate the effects of bovine-adapted Bacteroides thetaiotaomicron administration as a live microbial with and without Bio-Mos® supplementation, we analyzed microbial fermentation products, changes to carbohydrate profiles, and shifts in microbial composition of an in vitro rumen community. Bio-Mos® was shown to be an effective prebiotic that significantly altered microbial diversity, composition, and fermentation; while addition of B. thetaiotaomicron had no effect on community composition and resulted in fewer significant changes to microbial fermentation. When combined with Bio-Mos®, there were notable, although not significant, changes to major bacterial taxa, along with increased significant changes in fermentation end products. These data suggest a synergistic effect is elicited by combining Bio-Mos® and B. thetaiotaomicron. This protocol provides a new in vitro methodology that could be extended to evaluate prebiotics and probiotics in more complex artificial rumen systems and live animals.}, }
@article {pmid36937955, year = {2023}, author = {Sajankila, N and Wala, SJ and Ragan, MV and Volpe, SG and Dumbauld, Z and Purayil, N and Mihi, B and Besner, GE}, title = {Current and future methods of probiotic therapy for necrotizing enterocolitis.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1120459}, pmid = {36937955}, issn = {2296-2360}, abstract = {Necrotizing enterocolitis (NEC) is a complex intestinal disease that primarily affects premature neonates. Given its significant mortality and morbidity, there is an urgent need to develop improved prophylactic measures against the disease. One potential preventative strategy for NEC is the use of probiotics. Although there has been significant interest for decades in probiotics in neonatal care, no clear guidelines exist regarding which probiotic to use or for which patients, and no FDA-approved products exist on the market for NEC. In addition, there is lack of agreement regarding the benefits of probiotics in neonates, as well as some concerns about the safety and efficacy of available products. We discuss currently available probiotics as well as next-generation probiotics and novel delivery strategies which may offer an avenue to capitalize on the benefits of probiotics, while minimizing the risks. Thus, probiotics may still prove to be an effective prevention strategy for NEC, although further product development and research is needed to support use in the preterm population.}, }
@article {pmid36937721, year = {2023}, author = {Zhang, J and Zhu, G and Wan, L and Liang, Y and Liu, X and Yan, H and Zhang, B and Yang, G}, title = {Effect of fecal microbiota transplantation in children with autism spectrum disorder: A systematic review.}, journal = {Frontiers in psychiatry}, volume = {14}, number = {}, pages = {1123658}, pmid = {36937721}, issn = {1664-0640}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) may be helpful in the treatment of autism spectrum disorder (ASD) as rebalancing the gut microbiome has been shown to potentially improve behavioral symptoms in children with ASD.<br><br>METHODS: This systematic review was conducted to assess the effect of FMT for children with ASD. The Embase, PubMed, Web of Science, and Cochrane Library databases were searched for articles published from inception to October 6, 2022. Two reviewers independently screened the identified records and undertook data extraction.<br><br>RESULTS: The search identified a total of five studies: two prospective open-label studies, two retrospective observational studies, and a case report; however, no randomized controlled trial was identified. All five studies reported a significant post-FMT-treatment improvement in neuropsychological assessment of ASD. The two prospective open-label studies suggested that the Autism Behavior Checklist (ABC) score, and the Social Responsiveness Scale (SRS) score at the posttreatment assessment decreased from the baseline (Wilcoxon signed-rank test; all p < 0.01]). The two retrospective observational studies suggested that FMT helped to improve the ASD symptoms. One observational study reported that the Childhood Autism Rating Scale (CARS) score and ABC score of the constipation group decreased from the baseline after the second course assessment (CARS [baseline: mean 35.25 &#xb1; standard deviation 4.36, second course: 32.5 &#xb1; 3.1, p = 0.015]; ABC [baseline: 56.21 &#xb1; 16.08, second course: 46.54 &#xb1; 16.54, p = 0.046]). Another observational study found that both ABC and CARS scores decreased as the number of FMT courses increased, and significant differences were found at the end of each course as compared with the baseline.<br><br>CONCLUSION: Compared with the baseline, FMT significantly improved symptoms of autism in children with ASD in observational studies. However, rigorously designed randomized controlled clinical trials are needed to establish the safety and efficacy of FMT as a treatment for ASD.}, }
@article {pmid36937662, year = {2023}, author = {Wang, J and Liu, X and Li, Q}, title = {Interventional strategies for ischemic stroke based on the modulation of the gut microbiota.}, journal = {Frontiers in neuroscience}, volume = {17}, number = {}, pages = {1158057}, pmid = {36937662}, issn = {1662-4548}, abstract = {The microbiota-gut-brain axis connects the brain and the gut in a bidirectional manner. The organism's homeostasis is disrupted during an ischemic stroke (IS). Cerebral ischemia affects the intestinal flora and microbiota metabolites. Microbiome dysbiosis, on the other hand, exacerbates the severity of IS outcomes by inducing systemic inflammation. Some studies have recently provided novel insights into the pathogenesis, efficacy, prognosis, and treatment-related adverse events of the gut microbiome in IS. In this review, we discussed the view that the gut microbiome is of clinical value in personalized therapeutic regimens for IS. Based on recent non-clinical and clinical studies on stroke, we discussed new therapeutic strategies that might be developed by modulating gut bacterial flora. These strategies include dietary intervention, fecal microbiota transplantation, probiotics, antibiotics, traditional Chinese medication, and gut-derived stem cell transplantation. Although the gut microbiota-targeted intervention is optimistic, some issues need to be addressed before clinical translation. These issues include a deeper understanding of the potential underlying mechanisms, conducting larger longitudinal cohort studies on the gut microbiome and host responses with multiple layers of data, developing standardized protocols for conducting and reporting clinical analyses, and performing a clinical assessment of multiple large-scale IS cohorts. In this review, we presented certain opportunities and challenges that might be considered for developing effective strategies by manipulating the gut microbiome to improve the treatment and prevention of ischemic stroke.}, }
@article {pmid36937520, year = {2023}, author = {DuPont, HL and Suescun, J and Jiang, ZD and Brown, EL and Essigmann, HT and Alexander, AS and DuPont, AW and Iqbal, T and Utay, NS and Newmark, M and Schiess, MC}, title = {Fecal microbiota transplantation in Parkinson's disease-A randomized repeat-dose, placebo-controlled clinical pilot study.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1104759}, pmid = {36937520}, issn = {1664-2295}, abstract = {BACKGROUND AND PURPOSE: The intestinal microbiome plays a primary role in the pathogenesis of neurodegenerative disorders and may provide an opportunity for disease modification. We performed a pilot clinical study looking at the safety of fecal microbiota transplantation (FMT), its effect on the microbiome, and improvement of symptoms in Parkinson's disease.<br><br>METHODS: This was a randomized, double-blind placebo-controlled pilot study, wherein orally administered lyophilized FMT product or matching placebo was given to 12 subjects with mild to moderate Parkinson's disease with constipation twice weekly for 12 weeks. Subjects were followed for safety and clinical improvement for 9 additional months (total study duration 12 months).<br><br>RESULTS: Fecal microbiota transplantation caused non-severe transient upper gastrointestinal symptoms. One subject receiving FMT was diagnosed with unrelated metastatic cancer and was removed from the trial. Beta diversity (taxa) of the microbiome, was similar comparing placebo and FMT groups at baseline, however, for subjects randomized to FMT, it increased significantly at 6 weeks (p = 0.008) and 13 weeks (p = 0.0008). After treatment with FMT, proportions of selective families within the phylum Firmicutes increased significantly, while proportion of microbiota belonging to Proteobacteria were significantly reduced. Objective motor findings showed only temporary improvement while subjective symptom improvements were reported compared to baseline in the group receiving FMT. Constipation, gut transient times (NS), and gut motility index (p = 0.0374) were improved in the FMT group.<br><br>CONCLUSIONS: Subjects with Parkinson's disease tolerated multi-dose-FMT, and experienced increased diversity of the intestinal microbiome that was associated with reduction in constipation and improved gut transit and intestinal motility. Fecal microbiota transplantation administration improved subjective motor and non-motor symptoms.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrial.gov, identifier: NCT03671785.}, }
@article {pmid36937503, year = {2023}, author = {Uzochukwu, I and Moyes, D and Proctor, G and Ide, M}, title = {The key players of dysbiosis in Noma disease; A systematic review of etiological studies.}, journal = {Frontiers in oral health}, volume = {4}, number = {}, pages = {1095858}, pmid = {36937503}, issn = {2673-4842}, abstract = {Noma is a rapidly progressing periodontal disease with up to 90% mortality in developing countries. Poor, immunocompromised and severely malnourished children (2 to 6 years old) are mostly affected by Noma. Prevention and effective management of Noma is hindered by the lack of sufficient cohesive studies on the microbial etiology of the disease. Research efforts have not provided a comprehensive unified story of the disease. Bridging the gap between existing studies gives an insight on the disease pathogenesis. This current systematic review of etiological studies focuses on the key players of dysbiosis in Noma disease. This review was performed in accordance with the Preferred Reporting Items for Systemic review and Meta-Analyses (PRISMA) statement. Web of Science, MEDLINE via PubMed, Cochrane Library, Scopus, and Science Direct were searched electronically for clinical trials which applied culture dependent or molecular techniques to identify oral microbiota from Noma patients. Trials which involved periodontal diseases except Noma were excluded. After screening 275 articles, 153 full-texts articles were assessed for eligibility of which eight full text articles were selected for data extraction and analysis. The results show that 308 samples from 169 Noma participants (6 months to 15 years old) have been used in clinical trials. There was some variance in the microbiome identified due to the use of 3 different types of samples (crevicular fluid, subgingival plaque, and swabbed pus) and the ambiguity of the stage or advancement of Noma in the studies. Other limitations of the studies included in this review were: the absence of age-matched controls in some studies; the constraints of colony morphology as a tool in distinguishing between virulent fusobacterium genus at the species level; the difficulty in culturing spirochaetes in the laboratory; the choice of primers in DNA amplification; and the selection of probe sets in gene sequencing. This systematic review highlights spirochaetes and P. intermedia as putative trigger organisms in Noma dysbiosis, shows that F. nucleatum promotes biofilms formation in late stages of the disease and suggests that future studies should be longitudinal, with high throughput genome sequencing techniques used with gingival plaque samples from early stages of Noma.}, }
@article {pmid36937417, year = {2023}, author = {Crespin, A and Le Bescop, C and de Gunzburg, J and Vitry, F and Zalcman, G and Cervesi, J and Bandinelli, PA}, title = {A systematic review and meta-analysis evaluating the impact of antibiotic use on the clinical outcomes of cancer patients treated with immune checkpoint inhibitors.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1075593}, pmid = {36937417}, issn = {2234-943X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have considerably improved patient outcomes in various cancer types, but their efficacy remains poorly predictable among patients. The intestinal microbiome, whose balance and composition can be significantly altered by antibiotic use, has recently emerged as a factor that may modulate ICI efficacy. The objective of this systematic review and meta-analysis is to investigate the impact of antibiotics on the clinical outcomes of cancer patients treated with ICIs.<br><br>METHODS: PubMed and major oncology conference proceedings were systematically searched to identify all studies reporting associations between antibiotic use and at least one of the following endpoints: Overall Survival (OS), Progression-Free Survival (PFS), Objective Response Rate (ORR) and Progressive Disease (PD) Rate. Pooled Hazard Ratios (HRs) for OS and PFS, and pooled Odds Ratios (ORs) for ORR and PD were calculated. Subgroup analyses on survival outcomes were also performed to investigate the potential differential effect of antibiotics according to cancer types and antibiotic exposure time windows.<br><br>RESULTS: 107 articles reporting data for 123 independent cohorts were included, representing a total of 41,663 patients among whom 11,785 (28%) received antibiotics around ICI initiation. The pooled HRs for OS and PFS were respectively of 1.61 [95% Confidence Interval (CI) 1.48-1.76] and 1.45 [95% CI 1.32-1.60], confirming that antibiotic use was significantly associated with shorter survival. This negative association was observed consistently across all cancer types for OS and depending on the cancer type for PFS. The loss of survival was particularly strong when antibiotics were received shortly before or after ICI initiation. The pooled ORs for ORR and PD were respectively of 0.59 [95% CI 0.47-0.76] and 1.86 [95% CI 1.41-2.46], suggesting that antibiotic use was significantly associated with worse treatment-related outcomes.<br><br>CONCLUSION: As it is not ethically feasible to conduct interventional, randomized, controlled trials in which antibiotics would be administered to cancer patients treated with ICIs to demonstrate their deleterious impact versus control, prospective observational studies and interventional trials involving microbiome modifiers are crucially needed to uncover the role of microbiome and improve patient outcomes. Such studies will reduce the existing publication bias by allowing analyses on more homogeneous populations, especially in terms of treatments received, which is not possible at this stage given the current state of the field. In the meantime, antibiotic prescription should be cautiously considered in cancer patients receiving ICIs.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD42019145675.}, }
@article {pmid36937384, year = {2023}, author = {Yu, C and Zhou, Z and Liu, B and Yao, D and Huang, Y and Wang, P and Li, Y}, title = {Investigation of trends in gut microbiome associated with colorectal cancer using machine learning.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1077922}, pmid = {36937384}, issn = {2234-943X}, abstract = {BACKGROUND: The rapid growth of publications on the gut microbiome and colorectal cancer (CRC) makes it feasible for text mining and bibliometric analysis.<br><br>METHODS: Publications were retrieved from the Web of Science. Bioinformatics analysis was performed, and a machine learning-based Latent Dirichlet Allocation (LDA) model was used to identify the subfield research topics.<br><br>RESULTS: A total of 5,696 publications related to the gut microbiome and CRC were retrieved from the Web of Science Core Collection from 2000 to 2022. China and the USA were the most productive countries. The top 25 references, institutions, and authors with the strongest citation bursts were identified. Abstracts from all 5,696 publications were extracted for a text mining analysis that identified the top 50 topics in this field with increasing interest. The colitis animal model, expression of cytokines, microbiome sequencing and 16s, microbiome composition and dysbiosis, and cell growth inhibition were increasingly noticed during the last two years. The 50 most intensively investigated topics were identified and further categorized into four clusters, including "microbiome sequencing and tumor," "microbiome compositions, interactions, and treatment," "microbiome molecular features and mechanisms," and "microbiome and metabolism."<br><br>CONCLUSION: This bibliometric analysis explores the historical research tendencies in the gut microbiome and CRC and identifies specific topics of increasing interest. The developmental trajectory, along with the noticeable research topics characterized by this analysis, will contribute to the future direction of research in CRC and its clinical translation.}, }
@article {pmid36937312, year = {2023}, author = {Chen, X and Han, Z and Dong, J and Xiao, J and Zhao, W and Rong, J and Aschalew, ND and Zhang, X and Qin, G and Zhen, Y and Sun, Z and Wang, T}, title = {Dietary protein to starch metabolizable energy ratios alter growth performance and gastrointestinal microbiota of calves.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1065721}, pmid = {36937312}, issn = {1664-302X}, abstract = {The diet structure is very important for the growth and development of calves. This study aimed to investigate the effects of dietary protein-to-starch metabolizable energy ratios (DPSRs) on growth performance, blood index, and gastrointestinal microbiota of calves. Forty-eight Holstein bull calves were fed six dietary DPSRs including A20-35 (20% CP and 35% starch), B20-30, C20-25, D22-35, E22-30, and F22-25 at d 4 to d 60, and then changed to another six dietary DPSRs at d 61 to d 180 (A18-30, B18-27, C18-24, D20-30, E20-27, and F20-24). Twelve calves (d 60) from groups A20-35, C20-25, D22-35, and F22-25 (n = 3) and another twelve calves (d 180) from groups A18-30, C18-24, D20-30, and F20-24 (n = 3) were euthanized. The growth performance parameters were measured. Blood, ruminal fluid, and cecum digesta were collected for further analysis. Results showed heart girth gain of B18-27 was significantly higher than A18-30, C18-24, and heart girth gain (d 180) was significantly affected by protein × starch (DPSRs; p < 0.05). Blood urea nitrogen (BUN; d 60) in C20-25 was significantly higher than A20-35 and B20-30 (p < 0.05). The BUN (d 180) in D20-30 was significantly higher than A18-30 (p < 0.05). The BUN was significantly affected by protein × starch (p < 0.05) on d 60. The albumin (ALB) levels in C20-25 and C18-24 were significantly higher than that in A20-35 on d 60 and A18-30 on d 180, respectively (p < 0.05). The ALB level in D22-35 on d 60 and E20-27 on d 180 was significantly higher than that in other groups (p < 0.05). The ALB level was significantly affected by protein and starch, respectively, on d 60 (p < 0.05). In the rumen, the genera Roseburia (C20-25) and Dialister (D22-35), Prevotellaceae UCG-001 (C18-24), Erysipelotrichaceae UCG-002, and Anaerovorax (F20-24) were found in significant higher relative abundances than those in other groups (p < 0.05). In the cecum, the genera Bacteroides and Eisenbergiella (F22-25), Ruminiclostridium_1 and Candidatus Stoquefichus (A18-30), Erysipelotrichaceae UCG-004 and Tyzzerella 4 (D20-30), and Prevotellaceae UCG-003 and Klebsiella (F20-24) were found in significant higher abundances than those in other groups (p < 0.05). Collectively, these results indicated that the heart girth, BUN, ALB, and gastrointestinal microbiota responded distinctly to differing DPSRs.}, }
@article {pmid36937305, year = {2023}, author = {Rocha, LO and Silva, NCC}, title = {Editorial: Application of omics-based technologies and the impact on food science.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1155757}, pmid = {36937305}, issn = {1664-302X}, }
@article {pmid36937301, year = {2023}, author = {Agyekum, DVA and Kobayashi, T and Dastogeer, KMG and Yasuda, M and Sarkodee-Addo, E and Ratu, STN and Xu, Q and Miki, T and Matsuura, E and Okazaki, S}, title = {Diversity and function of soybean rhizosphere microbiome under nature farming.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1130969}, pmid = {36937301}, issn = {1664-302X}, abstract = {Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.}, }
@article {pmid36937300, year = {2023}, author = {Yoon, SJ and Yu, JS and Min, BH and Gupta, H and Won, SM and Park, HJ and Han, SH and Kim, BY and Kim, KH and Kim, BK and Joung, HC and Park, TS and Ham, YL and Lee, DY and Suk, KT}, title = {Bifidobacterium-derived short-chain fatty acids and indole compounds attenuate nonalcoholic fatty liver disease by modulating gut-liver axis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1129904}, pmid = {36937300}, issn = {1664-302X}, abstract = {Emerging evidences about gut-microbial modulation have been accumulated in the treatment of nonalcoholic fatty liver disease (NAFLD). We evaluated the effect of Bifidobacterium breve and Bifidobacterium longum on the NAFLD pathology and explore the molecular mechanisms based on multi-omics approaches. Human stool analysis [healthy subjects (n = 25) and NAFLD patients (n = 32)] was performed to select NAFLD-associated microbiota. Six-week-old male C57BL/6 J mice were fed a normal chow diet (NC), Western diet (WD), and WD with B. breve (BB) or B. longum (BL; 109 CFU/g) for 8 weeks. Liver/body weight ratio, histopathology, serum/tool analysis, 16S rRNA-sequencing, and metabolites were examined and compared. The BB and BL groups showed improved liver histology and function based on liver/body ratios (WD 7.07 ± 0.75, BB 5.27 ± 0.47, and BL 4.86 ± 0.57) and NAFLD activity scores (WD 5.00 ± 0.10, BB 1.89 ± 1.45, and BL 1.90 ± 0.99; p < 0.05). Strain treatment showed ameliorative effects on gut barrier function. Metagenomic analysis showed treatment-specific changes in taxonomic composition. The community was mainly characterized by the significantly higher composition of the Bacteroidetes phylum among the NC and probiotic-feeding groups. Similarly, the gut metabolome was modulated by probiotics treatment. In particular, short-chain fatty acids and tryptophan metabolites were reverted to normal levels by probiotics, whereas bile acids were partially normalized to those of the NC group. The analysis of gene expression related to lipid and glucose metabolism as well as the immune response indicated the coordinative regulation of β-oxidation, lipogenesis, and systemic inflammation by probiotic treatment. BB and BL attenuate NAFLD by improving microbiome-associated factors of the gut-liver axis.}, }
@article {pmid36937288, year = {2023}, author = {Wang, C and Li, Y and Wang, H and Li, M and Rong, J and Liao, X and Wu, Y and Wang, Y}, title = {Differences in peripheral and central metabolites and gut microbiome of laying hens with different feather-pecking phenotypes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1132866}, pmid = {36937288}, issn = {1664-302X}, abstract = {BACKGROUND: Feather pecking (FP) is a maladaptive behavior in laying hens that is associated with numerous physiological traits, including those involving the central neurotransmitter system and the immune system, which have been identified in many species as being regulated by the gut microbiota via the "microbiota-gut-brain" (MGB) axis. Yet, it is unknown whether and how gut microbiota influences FP by regulating multiple central neurotransmission systems and immune system.<br><br>METHODS: This study was measured the prevalence of severe FP (SFP) in the commercial layer farm. The chicken flock with the highest frequency of SFP were selected for FP phenotype identification. Nontargeted metabolomics was performed to investigated the differences in the peripheral and central metabolites and 16S rDNA sequencing was performed to investigated the differences in gut microbiome of laying hens with different FP phenotypes. Correlation analysis was performed to determine the potential mechanism by which the disturbed gut microbiota may modulate host physiology and behavior.<br><br>RESULTS: The results showed that pullets (12&#x2009;weeks of age) showed significantly higher SFP frequencies than chicks (6&#x2009;weeks of age) and adults (22&#x2009;weeks of age; p&#x2009;<&#x2009;0.05). Compared to neutrals (N), peckers (P) exhibited the stress-induced immunosuppression with the increased plasma levels of corticosterone and norepinephrine, and the decreased plasma levels of IgA, IL-1, IL-6 and tumor necrosis factor &#x3b1; (p&#x2009;<&#x2009;0.05). In the cecum, the relative abundances of Bacteroides and Gemmiger were higher in the P group, while Roseburia, Ruminococcus2, Anaerostipes, Lachnospiracea_incertae_sedis and Methanobrevibacter were more enriched in the N group. Moreover, increased plasma levels of L-tryptophan, beta-tyrosine and L-histidine were found in the P group (p&#x2009;<&#x2009;0.05). Notably, in the P group, hippocampal levels of L-tryptophan, xanthurenic acid, L-histidine and histamine were improved and showed a positive association with L-glutamic acid levels. Plasma levels of L-tryptophan, beta-tyrosine and L-histidine were both positively correlated with Bacteroides abundance but negatively correlated with Methanobrevibacter abundance.<br><br>CONCLUSION: Overall, these findings suggest that the development of FP may be affected by the gut microbiota, which regulates the central glutamatergic nerve system by altering the metabolism of tryptophan, histidine and tyrosine.}, }
@article {pmid36937279, year = {2023}, author = {Kerr, EN and Papudeshi, B and Haggerty, M and Wild, N and Goodman, AZ and Lima, LFO and Hesse, RD and Skye, A and Mallawaarachchi, V and Johri, S and Parker, S and Dinsdale, EA}, title = {Stingray epidermal microbiomes are species-specific with local adaptations.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1031711}, pmid = {36937279}, issn = {1664-302X}, abstract = {Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.}, }
@article {pmid36937276, year = {2023}, author = {Hossain, MS and DeLaune, PB and Gentry, TJ}, title = {Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1075575}, pmid = {36937276}, issn = {1664-302X}, abstract = {Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.}, }
@article {pmid36937258, year = {2023}, author = {Qu, S and Zheng, Y and Huang, Y and Feng, Y and Xu, K and Zhang, W and Wang, Y and Nie, K and Qin, M}, title = {Excessive consumption of mucin by over-colonized Akkermansia muciniphila promotes intestinal barrier damage during malignant intestinal environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111911}, pmid = {36937258}, issn = {1664-302X}, abstract = {Gut microbiota disorders damage the intestinal barrier, which causes intestinal disease. Thus, we screened the microbiota with significant changes using an in situ malignant colorectal cancer (CRC) model. Among the colonies with increased abundance, Akkermansia muciniphila (A. muciniphila) is known for its characteristic of breaking down mucin, which is an essential component of the intestinal barrier. The role of A. muciniphila remains controversial. To investigate the effect of excess A. muciniphila on the intestinal barrier, we established an over-colonized A. muciniphila mouse model by administering a live bacterial suspension after disrupting the original gut microbiome with antibiotics. The results showed that over-colonization of A. muciniphila decreased intestinal mucin content. The mRNA and protein expression levels of tight junction proteins also decreased significantly in the over-colonized A. muciniphila mouse model. Our findings reveal that excess colonization by A. muciniphila breaks the dynamic balance between mucin secretion and degradation, reduces the thickness of the intestinal mucus layer, and damages the intestinal barrier, which would eventually aggravate the development of colitis and CRC. These results will raise awareness about the safety of A. muciniphila serving as a probiotic.}, }
@article {pmid36937253, year = {2023}, author = {Blyton, MDJ and Pascoe, J and Hynes, E and Soo, RM and Hugenholtz, P and Moore, BD}, title = {The koala gut microbiome is largely unaffected by host translocation but rather influences host diet.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1085090}, pmid = {36937253}, issn = {1664-302X}, abstract = {INTRODUCTION: Translocation is a valuable and increasingly used strategy for the management of both threatened and overabundant wildlife populations. However, in some instances the translocated animals fail to thrive. Differences in diet between the source and destination areas may contribute to poor translocation outcomes, which could conceivably be exacerbated if the animals' microbiomes are unsuited to the new diet and cannot adapt.<br><br>METHODS: In this study we tracked how the faecal microbiome of a specialist Eucalyptus folivore, the koala (Phascolarctos cinereus), changed over the course of a year after translocation. We assessed microbiome composition by 16S rRNA amplicon sequencing of faecal pellets.<br><br>RESULTS: We found no significant overall changes in the faecal microbiomes of koalas post-translocation (n&#x2006;=&#x2006;17) in terms of microbial richness, diversity or composition when compared to the faecal microbiomes of koalas from an untranslocated control group (n&#x2006;=&#x2006;12). This was despite the translocated koalas feeding on a greater variety of Eucalyptus species after translocation. Furthermore, while differences between koalas accounted for half of the microbiome variation, estimated diets at the time of sampling only accounted for 5% of the variation in the koala microbiomes between sampling periods. By contrast, we observed that the composition of koala faecal microbiomes at the time of translocation accounted for 37% of between koala variation in post-translocation diet. We also observed that translocated koalas lost body condition during the first month post-translocation and that the composition of the koalas' initial microbiomes were associated with the magnitude of that change.<br><br>DISCUSSION: These findings suggest that the koala gut microbiome was largely unaffected by dietary change and support previous findings suggesting that the koala gut microbiome influences the tree species chosen for feeding. They further indicate that future research is needed to establish whether the koalas' gut microbiomes are directly influencing their health and condition or whether aspects of the koala gut microbiomes are an indicator of underlying physiological differences or pathologies. Our study provides insights into how animal microbiomes may not always be affected by the extreme upheaval of translocation and highlights that responses may be host species-specific. We also provide recommendations to improve the success of koala translocations in the future.}, }
@article {pmid36937222, year = {2023}, author = {Cannizzaro, S and Maiorani, C and Scribante, A and Butera, A}, title = {Personalized Treatment of Periodontitis in a Patient with McArdle's Disease: The Benefits from Probiotics.}, journal = {Case reports in dentistry}, volume = {2023}, number = {}, pages = {5080384}, pmid = {36937222}, issn = {2090-6447}, abstract = {INTRODUCTION: McArdle's disease is a severe glycogen storage disease characterized by intolerance to exercise; patients have a syndrome of muscle intolerance to stress, associated with myalgia, cramps, fatigue, and muscle weakness. Periodontal disease is a multifactorial pathology of the supporting tissues of the teeth: one of the main factors is the formation of bacterial biofilm; its control favors the prevention and the maintenance of good health of the oral cavity; and some systemic pathologies can worsen the periodontal disease and hinder its therapy. This case report concerns a woman with McArdle's disease diagnosed with periodontal disease. Material and Methods. A 54-year-old female patient with McArdle's disease has been diagnosed with Stage 3 generalized periodontitis, Grade B. At the baseline, the patient had 82 pockets with probing pocket depth (PPD) equal to or greater than 4 mm. The patient was instructed in the correct methods of oral hygiene and was advised toothpaste and mouthwash based on probiotics; subsequently, a debridement was performed to remove etiological factors using Dental-Biofilm Detection Topographic Technique (D-BioTECH).<br><br>RESULTS: After 60 days, the number of pockets was reduced from 82 to 14 overall with PPD &#x2265; 4&#x2009;mm and from 50 to 2 pockets with PPD &#x2265; 5&#x2009;mm. Full mouth bleeding score (FMBS) increased from 48% to 15% and full mouth plaque score (FMPS) from 73% to 15%.<br><br>CONCLUSIONS: In this case, the use of a correct brushing method combined with the D-BioTECH has reduced the disease state, with the use of probiotics at home to restore and maintain a healthy oral microbiome.}, }
@article {pmid36937014, year = {2023}, author = {Zhang, L and Shen, H and Zhang, J and Mao, S}, title = {Variety of rumen microbial populations involved in biohydrogenation related to individual milk fat percentage of dairy cows.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1106834}, pmid = {36937014}, issn = {2297-1769}, abstract = {Our objective was to investigate the contribution of the rumen microbiome on the individual milk fat percentage (MFP) of Holstein dairy cows under the same nutritional and management conditions. From 92 early lactation dairy cows, the top 10 with the highest MFP (HF; n = 10) and the last 10 with the lowest MFP (LF; n = 10) were selected for the study. As a result, the milk trans-10, cis-12 C18:2 content was significant lower in the HF group than that in the LF group (P < 0.001). The rumen acetate to propionate ratio was significant higher in the HF group than that in the LF group (P = 0.035). According to the results of 16S rRNA gene sequencing, a minor but significant difference existed between the groups (P = 0.040). Three genera of the family Lachnospiraceae and four genera of the order Bacteroidales were identified to be the biomarkers for the LF group and HF group in the LEfSe analysis, respectively. Three microbial modules enriched by the family Lachnospiraceae were positively related to the milk trans-10, cis-12 C18:2 content (r s > 0.60, P < 0.05). According to the results of shotgun metagenome sequencing, three kinds of linoleic acid (LA) isomerase genes were present in the gene pools of the rumen microbiome. Among them, the relative abundance of Bifidobacterium LA isomerase (BBI) was higher in the HF group than that in the LF group (P = 0.007). Three metagenome-assembled genomes (MAGs) with LA isomerase genes were positively correlated to the milk trans-10, cis-12 C18:2 content (r s > 0.40, P < 0.05). Furthermore, all of these three MAGs were found to be able to produce lactate. Taken together, these results indicate that the increased relative abundance of microbial population with the trans-10 biohydrogenation pathway within the rumen microbiome contributes to the decrease of MFP via the increase of rumen trans-10, cis-12 C18:2 production. This study provides a new perspective for the development of measures for improving the milking performance of dairy cows.}, }
@article {pmid36936939, year = {2023}, author = {Li, L and Wang, Y and Huang, Y and Wang, C}, title = {Multi-omics approach to study the dual effects of novel proteins on the intestinal health of juvenile largemouth bass (Micropterus salmoides) under an alternate feeding strategy.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1110696}, pmid = {36936939}, issn = {1664-3224}, abstract = {INTRODUCTION: In an effort to minimize the usage of fishmeal in aquaculture, novel protein diets, including Tenebrio molitor, cottonseed protein concentrate, Clostridium autoethanogenum, and Chlorella vulgaris were evaluated for their potential to replace fishmeal. Nevertheless, comprehensive examinations on the gut health of aquatic animals under an alternate feeding strategy when fed novel protein diets are vacant.<br><br>METHODS: Five isonitrogenous and isolipidic diets containing various proteins were manufactured, with a diet consisting of whole fishmeal serving as the control and diets containing novel proteins serving as the experimental diets. Largemouth bass (Micropterus salmoides) with an initial body weight of 4.73 &#xb1; 0.04g employed as an experimental animal and given these five diets for the first 29 days followed by a fishmeal diet for the next 29 days.<br><br>RESULTS: The results of this study demonstrated that the growth performance of novel protein diets in the second stage was better than in the first stage, even though only the C. vulgaris diet increased antioxidant capacity and the cottonseed protein concentrate diet decreased it. Concerning the intestinal barriers, the C. autoethanogenum diet lowered intestinal permeability and plasma IL-1&#x3b2;/TNF-&#x3b1;. In addition, the contents of intestinal immunological factors, namely LYS and sIgA-like, were greater in C. vulgaris than in fishmeal. From the data analysis of microbiome and metabolome, the levels of short chain fatty acids (SCFAs), anaerobic bacteria, Lactococcus, and Firmicutes were significantly higher in the C. autoethanogenum diet than in the whole fishmeal diet, while the abundance of Pseudomonas, aerobic bacteria, Streptococcus, and Proteobacteria was lowest. However, no extremely large differences in microbiota or short chain fatty acids were observed between the other novel protein diets and the whole fishmeal diet. In addition, the microbiota were strongly connected with intestinal SCFAs, lipase activity, and tight junctions, as shown by the Mantel test and Pearson's correlation.<br><br>DISCUSSION: Taken together, according to Z-score, the ranking of advantageous functions among these protein diets was C. autoethanogenum diet > C. vulgaris diet > whole fishmeal diet > cottonseed protein concentrate > T. molitor diet. This study provides comprehensive data illustrating a mixed blessing effect of novel protein diets on the gut health of juvenile largemouth bass under an alternate feeding strategy.}, }
@article {pmid36936930, year = {2023}, author = {Aries, ML and Hensley-McBain, T}, title = {Neutrophils as a potential therapeutic target in Alzheimer's disease.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1123149}, pmid = {36936930}, issn = {1664-3224}, abstract = {Alzheimer's disease (AD) is the leading cause of dementia in the United States. Sporadic or late-onset AD remains incompletely understood, with age as the current greatest risk factor. Inflammation in general and neutrophils, a potent mediator of inflammation, have been shown to exacerbate AD associated dementia. This review explores the latest research on neutrophils in AD mouse models and in human cohort studies and discusses current gaps in research and needs for future studies. AD mouse models have shown neutrophil chemotactic migration towards amyloid beta plaques in the brain. Capillary blood flow stalling decreases blood perfusion to associated brain regions and mouse studies have demonstrated that anti-Ly6G antibodies lead to a decrease in capillary blood flow stalling and memory improvement. Several recent transcriptomic studies of blood and brain tissue from persons with AD have shown an upregulation in neutrophil-related genes, and studies have demonstrated neutrophil involvement in brain capillary adhesion, blood brain barrier breaching, myeloperoxidase release, and the propensity for neutrophil extracellular trap release in AD. Neutrophil-derived inflammation and regulation are a potential potent novel therapeutic target for AD progression. Future studies should further investigate neutrophil functionality in AD. In addition, other aspects of AD that may impact neutrophils including the microbiome and the APOE4 allele should be studied.}, }
@article {pmid36936475, year = {2022}, author = {Yan, M and Guo, X and Ji, G and Huang, R and Huang, D and Li, Z and Zhang, D and Chen, S and Cao, R and Yang, X and Wu, W}, title = {Mechanismbased role of the intestinal microbiota in gestational diabetes mellitus: A systematic review and meta-analysis.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1097853}, pmid = {36936475}, issn = {1664-3224}, abstract = {BACKGROUND: Metabolic disorders caused by intestinal microbial dysregulation are considered to be important causes of gestational diabetes mellitus (GDM). Increasing evidence suggests that the diversity and composition of gut microbes are altered in disease states, yet the critical microbes and mechanisms of disease regulation remain unidentified.<br><br>METHODS: PubMed[&#xae;] (National Library of Medicine, Bethesda, MD, USA), Embase[&#xae;] (Elsevier, Amsterdam, the Netherlands), the Web of Science&#x2122; (Clarivate&#x2122;, Philadelphia, PA, USA), and the Cochrane Library databases were searched to identify articles published between 7 July 2012 and 7 July 2022 reporting on case-control and controlled studies that analyzed differences in enterobacteria between patients with GDM and healthy individuals. Information on the relative abundance of enterobacteria was collected for comparative diversity comparison, and enterobacterial differences were analyzed using random effects to calculate standardized mean differences at a p-value of 5%.<br><br>RESULTS: A total of 22 studies were included in this review, involving a total of 965 GDM patients and 1,508 healthy control participants. Alpha diversity did not differ between the participant groups, but beta diversity was significantly different. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the dominant bacteria, but there was no significant difference between the two groups. Qualitative analysis showed differences between the groups in the Firmicutes/Bacteroidetes ratio, Blautia, and Collinsella, but these differences were not statistically different.<br><br>CONCLUSION: Enterobacterial profiles were significantly different between the GDM and non-GDM populations. Alpha diversity in patients with GDM is similar to that in healthy people, but beta diversity is significantly different. Firmicutes/Bacteroidetes ratios were significantly increased in GDM, and this, as well as changes in the abundance of species of Blautia and Collinsella, may be responsible for changes in microbiota diversity. Although the results of our meta-analysis are encouraging, more well-conducted studies are needed to clarify the role of the gut microbiome in GDM. The systematic review was registered with PROSPERO (https://www.crd.york.ac.uk/prospero/) as CRD42022357391.}, }
@article {pmid36936168, year = {2023}, author = {Kung, CP and Barnoud, T and Yao, CH and Murphy, ME}, title = {Editorial: Double-edged swords: Important factors connecting metabolic disorders and cancer development - from basic research to translational applications.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1168700}, pmid = {36936168}, issn = {1664-2392}, }
@article {pmid36936020, year = {2023}, author = {Han, M and Wang, N and Han, W and Ban, M and Sun, T and Xu, J}, title = {Vaginal and tumor microbiomes in gynecological cancer (Review).}, journal = {Oncology letters}, volume = {25}, number = {4}, pages = {153}, pmid = {36936020}, issn = {1792-1082}, abstract = {Cervical, ovarian and endometrial cancer are the three most common types of gynecologic cancer. As a hub, the vagina connects the site of gynecological cancer with the external environment. Lactobacilli participate in the formation of a healthy vaginal microenvironment as the first line of defense against pathogen invasion; a dysbiotic vaginal microenvironment loses its original protective function and is associated with the onset, metastasis, poor efficacy and poor prognosis of gynecological cancer. The early diagnosis of cancer is the key to improve the survival time of patients with cancer. The screening of Porphyromonas, Sneathia and Atopobium vaginae, and other microbial markers, can assist the diagnosis of gynecological cancer, and screen out the high-risk population as early as possible. With the in-depth study of the microbes in tumor tissues, reasearchers have analyzed the immunological associations of microorganisms in tumor tissues. Due to the structural-functional interconnection between the organ of gynecological tumorigenesis and the vagina, the present study aims to review the relationship between vaginal and tumor microorganisms and gynecological cancer in terms of occurrence, screening, treatment and prognosis.}, }
@article {pmid36935758, year = {2023}, author = {Shen, Y and Wang, P and Yang, X and Chen, M and Dong, Y and Li, J}, title = {Untargeted metabolomics unravel serum metabolic alterations in smokers with hypertension.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1127294}, pmid = {36935758}, issn = {1664-042X}, abstract = {Background: Cigarette smoking is an important environmental risk factor for cardiovascular events of hypertension (HTN). Existing studies have provided evidence supporting altered gut microbiota by cigarette smoking, especially in hypertensive patients. Metabolic biomarkers play a central role in the functional potentials of the gut microbiome but are poorly characterized in hypertensive smokers. To explore whether serum metabolomics signatures and compositions of HTN patients were varied in smokers, and investigate their connecting relationship to gut microbiota, the serum metabolites were examined in untreated hypertensive patients using untargeted liquid chromatography-mass spectrometry (LC/MS) analysis. Results: A dramatic difference and clear separation in community features of circulating metabolomics members were seen in smoking HTN patients compared with the non-smoking controls, according to partial least squares discrimination analysis (PLS-DA) and orthogonal partial least squares discrimination analysis (OPLS-DA). Serum metabolic profiles and compositions of smoking patients with HTN were significantly distinct from the controls, and were characterized by enrichment of 12-HETE, 7-Ketodeoxycholic acid, Serotonin, N-Stearoyl tyrosine and Deoxycholic acid glycine conjugate, and the depletion of Tetradecanedioic acid, Hippuric acid, Glyceric acid, 20-Hydroxyeicosatetraenoic acid, Phenylpyruvic acid and Capric acid. Additionally, the metabolome displayed prominent functional signatures, with a majority proportion of the metabolites identified to be discriminating between groups distributed in Starch and sucrose metabolism, Caffeine metabolism, Pyruvate metabolism, Glycine, serine and threonine metabolism, and Phenylalanine metabolic pathways. Furthermore, the observation of alterations in metabolites associated with intestinal microbial taxonomy indicated that these metabolic members might mediate the effects of gut microbiome on the smoking host. Indeed, the metabolites specific to smoking HTNs were strongly organized into co-abundance networks, interacting with an array of clinical parameters, including uric acid (UA), low-denstiy lipoprotein cholesterol (LDLC) and smoking index. Conclusions: In conclusion, we demonstrated disparate circulating blood metabolome composition and functional potentials in hypertensive smokers, showing a linkage between specific metabolites in blood and the gut microbiome.}, }
@article {pmid36935743, year = {2023}, author = {Zwirzitz, B and Oladeinde, A and Johnson, J and Zock, G and Milfort, MC and Fuller, AL and Ghareeb, AFA and Foutz, JC and Teran, JA and Woyda, R and Abdo, Z and Looft, T and Lawrence, JP and Cudnik, D and Aggrey, SE}, title = {Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1083192}, pmid = {36935743}, issn = {1664-042X}, abstract = {In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).}, }
@article {pmid36935607, year = {2023}, author = {Zhou, X and Zhang, J and Khashi U Rahman, M and Gao, D and Wei, Z and Wu, F and Dini-Andreote, F}, title = {Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes.}, journal = {Molecular plant}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molp.2023.03.009}, pmid = {36935607}, issn = {1752-9867}, abstract = {Terrestrial plants can affect the growth and health of adjacent plants via interspecific interaction. Here, we studied the mechanism by which plant root exudates affect the recruitment of the rhizosphere microbiome in adjacent plants - with implications for plant protection - using a tomato (Solanum lycopersicum)-potatoonion (Allium cepa var. agrogatum Don.) intercropping system. First, we showed the intercropping system to result in a disease-suppressive rhizosphere microbiome in tomato plants against Verticillium wilt disease, caused by the soilborne pathogen Verticillium dahliae. Second, 16S rRNA gene sequencing found that intercropping with potatoonion altered the composition of the tomato rhizosphere microbiome, by promoting the colonization of specific Bacillus sp. This taxon was isolated and shown to inhibit V. dahliae growth and induce systemic resistance in tomato plants. Third, a belowground segregation experiment found that root exudates mediated the interspecific interaction between potatoonion and tomato. Moreover, experiments using split-root tomato plants found root exudates from potatoonion, especially taxifolin - a flavonoid compound - to stimulate tomato plants to recruit plant-beneficial bacteria, such as Bacillus sp. Last, UPLC-MS analysis found taxifolin to alter tomato root exudates chemistry, thus acting as an indirect compound modulating the root colonization of Bacillus sp. Our results revealed that this intercropping system can improve tomato plant fitness by changing the rhizosphere microbiome recruitment via utilizing signaling chemicals released by root exudates of potatoonion. This study revealed a novel mechanism by which interspecific plant interaction modulates the establishment of a disease-suppressive microbiome, thus opening up new avenues of research for precision plant microbiome manipulations.}, }
@article {pmid36935537, year = {2023}, author = {Elfiky, SA and Mahmoud Ahmed, S and Elmenshawy, AM and Sultan, GM and Asser, SL}, title = {Study of the gut microbiome as a novel target for prevention of hospital-associated infections in intensive care unit patients.}, journal = {Acute and critical care}, volume = {38}, number = {1}, pages = {76-85}, doi = {10.4266/acc.2022.01116}, pmid = {36935537}, issn = {2586-6060}, abstract = {BACKGROUND: Hospital-acquired infections (HAIs) are increasing due to the spread of multi-drugresistant organisms. Gut dysbiosis in an intensive care unit (ICU) patients at admission showed an altered abundance of some bacterial genera associated with the occurrence of HAIs and mortality. In the present study, we investigated the pattern of the gut microbiome in ICU patients at admission to correlate it with the development of HAIs during ICU stay.<br><br>METHODS: Twenty patients admitted to an ICU with a cross-matched control group of 30 healthy subjects of matched age and sex. Quantitative SYBR green real-time polymerase chain reaction was done for the identification and quantitation of selected bacteria.<br><br>RESULTS: Out of those twenty patients, 35% developed ventilator-associated pneumonia during their ICU stay. Gut microbiome analysis showed a significant decrease in Firmicutes and Firmicutes to Bacteroidetes ratio in ICU patients in comparison to the control and in patients who developed HAIs in comparison to the control group and patients who did not develop HAIs. There was a statistically significant increase in Bacteroides in comparison to the control group. There was a statistically significant decrease in Bifidobacterium and Faecalibacterium prausnitzii and an increase in Lactobacilli in comparison to the control group with a negative correlation between Acute Physiology and Chronic Health Evaluation (APACHE) II score and Firmicutes to Bacteroidetes and Prevotella to Bacteroides ratios.<br><br>CONCLUSIONS: Gut dysbiosis of patients at the time of admission highlights the importance of identification of the microbiome of patients admitted to the ICU as a target for preventing of HAIs.}, }
@article {pmid36934910, year = {2023}, author = {Greses, S and De Bernardini, N and Treu, L and Campanaro, S and González-Fernández, C}, title = {Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128920}, doi = {10.1016/j.biortech.2023.128920}, pmid = {36934910}, issn = {1873-2976}, abstract = {Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25°C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H2 production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.}, }
@article {pmid36934717, year = {2023}, author = {Marissen, J and Gomez de Agüero, M and Chandorkar, P and Reichert, L and Glaser, K and Speer, CP and Härtel, C}, title = {The Delicate Skin of Preterm Infants: Barrier Function, Immune-Microbiome Interaction, and Clinical Implications.}, journal = {Neonatology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1159/000529026}, pmid = {36934717}, issn = {1661-7819}, abstract = {The skin of preterm infants is a delicate organ with critical structural and functional differences as compared to term born infants. Unique features contribute to an increased susceptibility to injury, infection, thermal instability, and water loss. During rapid, often accelerated adaption of the physical barrier function of preterm skin, a parallel and mutual development of host skin immunity and skin microbiome seem to be crucial for skin homeostasis. Recent advances in molecular biology have enabled researchers to gain a deeper understanding of the microbial community composition of preterm skin and the important relationship with microbiome composition of other body sites. Nevertheless, several questions remain to be answered, including niche factors and environmental influences on skin maturation. In line with that, evidence-based guidelines on skin care practice in preterm infants are missing. This review articles aims to provide an overview of the current knowledge of preterm infant skin development including immune and barrier function, host-microbial interactions, and potential clinical implications.}, }
@article {pmid36934642, year = {2023}, author = {Yasir, M and Al-Sharif, HA and Al-Subhi, T and Sindi, AA and Bokhary, DH and El-Daly, MM and Alosaimi, B and Hamed, ME and Karim, AM and Hassan, AM and AlShawdari, MM and Alawi, M and El-Kafrawy, SA and Azhar, EI}, title = {Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia.}, journal = {Journal of infection and public health}, volume = {16}, number = {5}, pages = {680-688}, doi = {10.1016/j.jiph.2023.03.001}, pmid = {36934642}, issn = {1876-035X}, abstract = {BACKGROUND: Infection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health.<br><br>METHODS: A total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens.<br><br>RESULTS: No significant (p&#xa0;>&#xa0;0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p&#xa0;<&#xa0;0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1.<br><br>CONCLUSIONS: Overall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.}, }
@article {pmid36934439, year = {2023}, author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM}, title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjad031}, pmid = {36934439}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.<br><br>METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.<br><br>RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.<br><br>CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.}, }
@article {pmid36934269, year = {2023}, author = {Kim, BH and Yim, SV and Hwang, SD and Kim, YS and Kim, JH}, title = {A clinical trial on anti-diabetic efficacy of submerged culture medium of Ceriporia lacerata mycelium.}, journal = {BMC complementary medicine and therapies}, volume = {23}, number = {1}, pages = {83}, pmid = {36934269}, issn = {2662-7671}, abstract = {BACKGROUND: Increased glucose level and insulin resistance are major factors in Type 2 diabetes mellitus (T2M), which is chronic and debilitating disease worldwide. Submerged culture medium of Ceriporia lacerata mycelium (CLM) is known to have glucose lowering effects and improving insulin resistance in a mouse model in our previous studies. The main purpose of this clinical trial was to evaluate the functional efficacy and safety of CLM in enrolled participants with impaired fasting blood sugar or mild T2D for 12 weeks.<br><br>METHODS: A total of 72 participants with impaired fasting blood sugar or mild T2D were participated in a randomized, double-blind, placebo-controlled clinical trial. All participants were randomly assigned into the CLM group or placebo group. Fasting blood glucose (FBG), HbA1c, insulin, C-peptide, HOMA-IR, and HOMA-IR by C-peptide were used to assess the anti-diabetic efficacy of CLM for 12&#xa0;weeks.<br><br>RESULTS: In this study, the effectiveness of CLM on lowering the anti-diabetic indicators (C-peptide levels, insulin, and FBG) was confirmed. CLM significantly elicited anti-diabetic effects after 12&#xa0;weeks of ingestion without showing any side effects in both groups of participants. After the CLM treatment, FBG levels were effectively dropped by 63.9% (ITT), while HOMA-IR level in the CLM group with FBG&#x2009;>&#x2009;110&#xa0;mg/dL showed a marked decrease by 34% up to 12&#xa0;weeks. Remarkably, the effect of improving insulin resistance was significantly increased in the subgroup of participants with insulin resistance, exhibiting effective reduction at 6&#xa0;weeks (42.5%) and 12&#xa0;weeks (61%), without observing a recurrence or hypoglycemia. HbA1c levels were also decreased by 50% in the participants with reduced indicators (FBG, insulin, C-peptide, HOMA-IR, and HOMA-IR). Additionally, it is noteworthy that the levels of insulin and C-peptide were significantly reduced despite the CLM group with FBG&#x2009;>&#x2009;110&#xa0;mg/dL. No significant differences were detected in the other parameters (lipids, blood tests, and blood pressure) after 12&#xa0;weeks.<br><br>CONCLUSION: The submerged culture medium of CLM showed clinical efficacy in the improvement of FBG, insulin, C-peptide, HbAc1, and HOMA-index. The microbiome-based medium could benefit patients with T2D, FBG disorders, or pre-diabetes, which could guide a new therapeutic pathway in surging the global diabetes epidemic.}, }
@article {pmid36934265, year = {2023}, author = {Dragojević, M and Stankovic, N and Djokic, L and Raičević, V and Jovičić-Petrović, J}, title = {Endorhizosphere of indigenous succulent halophytes: a valuable resource of plant growth promoting bacteria.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {20}, pmid = {36934265}, issn = {2524-6372}, abstract = {The adaptability of halophytes to increased soil salinity is related to complex rhizosphere interactions. In this study, an integrative approach, combining culture-independent and culture-dependent techniques was used to analyze the bacterial communities in the endorizosphere of indigenous succulent halophytes Salicornia europaea, Suaeda maritima, and Camphorosma annua from the natural salt marshes of Slano Kopovo (Serbia). The 16 S rDNA analyses gave, for the first time, an insight into the composition of the endophytic bacterial communities of S. maritima and C. annua. We have found that the composition of endophyte microbiomes in the same habitat is to some extent influenced by plant species. A cultivable portion of the halophyte microbiota was tested at different NaCl concentrations for the set of plant growth promoting (PGP) traits. Through the mining of indigenous halotolerant endophytes, we obtained a collection representing a core endophyte microbiome conferring desirable PGP traits. The majority (65%) of the selected strains belonged to the common halotolerant/halophilic genera Halomonas, Kushneria, and Halobacillus, with representatives exhibiting multiple PGP traits, and retaining beneficial traits in conditions of the increased salinity. The results suggest that the root endosphere of halophytes is a valuable source of PGP bacteria supporting plant growth and fitness in salt-affected soils.}, }
@article {pmid36934246, year = {2023}, author = {Chen, X and Xue, D and Zhao, Y and Cui, P and Wang, P and Wang, Y and Lu, SB}, title = {Association between periodontitis and disc structural failure in older adults with lumbar degenerative disorders: A prospective cohort study.}, journal = {BMC surgery}, volume = {23}, number = {1}, pages = {57}, pmid = {36934246}, issn = {1471-2482}, abstract = {BACKGROUND: Bacterial microbiome as a putative trigger of inflammation might indicate the cascade of mouth-gut-disc axis for causing intervertebral disc (IVD) structural failures (such as IVD degeneration and endplate change) processed. However, direct evidence for the mouth-gut-disc axis still unclear. Therefore, it is interesting to explore periodontal inflammation related to IVD structural failures and clinical outcomes.<br><br>METHODS: This prospective cohort study enrolled older adults (aged&#x2009;&#x2265;&#x2009;75 years) who scheduled to undergo elective open lumbar spine surgery. Demographic, radiological, clinical, and periodontal parameters were recorded. Independent samples t-test and Pearson's correlation analysis were calculated.<br><br>RESULTS: A total of 141 patients with lumbar degenerative disorders (56 males and 85 females; age 79.73&#x2009;&#xb1;&#x2009;3.34 years) were divided into edentulous group (19 patients), No/Mild group (84 patients), and Moderate/Severe group (38 patients). The incidence rates of IVD degeneration in each lumbar segmental level based on Pfirrmann grade and endplate change in the fourth and fifth lumbar vertebrae, and Visual Analogue Scale (VAS) low back pain (LBP) and leg pain of patients at preoperative in dentate group was significantly higher compared with edentulous group, especially the comparisons between Moderate/Severe and edentulous groups. There were no significant differences in the range of motion, lumbar lordosis, pelvic incidence, pelvic tilt, sacral slope, and disc height between dentate and edentulous groups. There was a positive association between plaque index (PLI) and pain scores (VAS LBP: r&#x2009;=&#x2009;0.215, P&#x2009;=&#x2009;0.030 and VAS leg pain: r&#x2009;=&#x2009;0.309, P&#x2009;=&#x2009;0.005), but no significant difference in Oswestry disability index (ODI) score.<br><br>CONCLUSION: Results show that the severity of periodontitis is associated with higher incidence rates of IVD degeneration and endplate change and clinical outcomes in older adults with lumbar degenerative disorders. Furthermore, the discovery of these relationships unveils a novel mechanism through which the alterations in oral microbiome composition potentially promote IVD degeneration and pain.}, }
@article {pmid36934229, year = {2023}, author = {Panzer, JJ and Romero, R and Greenberg, JM and Winters, AD and Galaz, J and Gomez-Lopez, N and Theis, KR}, title = {Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {76}, pmid = {36934229}, issn = {1471-2180}, abstract = {The existence of a placental microbiota is debated. The human placenta has historically been considered sterile and microbial colonization was associated with adverse pregnancy outcomes. Yet, recent DNA sequencing investigations reported a microbiota in typical human term placentas. However, this detected microbiota could represent background DNA or delivery-associated contamination. Using fifteen publicly available 16S rRNA gene datasets, existing data were uniformly re-analyzed with DADA2 to maximize comparability. While Amplicon Sequence Variants (ASVs) identified as Lactobacillus, a typical vaginal bacterium, were highly abundant and prevalent across studies, this prevalence disappeared after applying likely DNA contaminant removal to placentas from term cesarean deliveries. A six-study sub-analysis targeting the 16S rRNA gene V4 hypervariable region demonstrated that bacterial profiles of placental samples and technical controls share principal bacterial ASVs and that placental samples clustered primarily by study origin and mode of delivery. Contemporary DNA-based evidence does not support the existence of a placental microbiota.ImportanceEarly-gestational microbial influences on human development are unclear. By applying DNA sequencing technologies to placental tissue, bacterial DNA signals were observed, leading some to conclude that a live bacterial placental microbiome exists in typical term pregnancy. However, the low-biomass nature of the proposed microbiome and high sensitivity of current DNA sequencing technologies indicate that the signal may alternatively derive from environmental or delivery-associated bacterial DNA contamination. Here we address these alternatives with a re-analysis of 16S rRNA gene sequencing data from 15 publicly available placental datasets. After identical DADA2 pipeline processing of the raw data, subanalyses were performed to control for mode of delivery and environmental DNA contamination. Both environment and mode of delivery profoundly influenced the bacterial DNA signal from term-delivered placentas. Aside from these contamination-associated signals, consistency was lacking across studies. Thus, placentas delivered at term are unlikely to be the original source of observed bacterial DNA signals.}, }
@article {pmid36934156, year = {2023}, author = {Ma, Y and He, J and Sieber, M and von Frieling, J and Bruchhaus, I and Baines, JF and Bickmeyer, U and Roeder, T}, title = {The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {289}, pmid = {36934156}, issn = {2399-3642}, abstract = {The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates.}, }
@article {pmid36934111, year = {2023}, author = {Kim, JE and Tun, HM and Bennett, DC and Leung, FC and Cheng, KM}, title = {Microbial diversity and metabolic function in duodenum, jejunum and ileum of emu (Dromaius novaehollandiae).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4488}, pmid = {36934111}, issn = {2045-2322}, abstract = {Emus (Dromaius novaehollandiae), a large flightless omnivorous ratite, are farmed for their fat and meat. Emu fat can be rendered into oil for therapeutic and cosmetic use. They are capable of gaining a significant portion of its daily energy requirement from the digestion of plant fibre. Despite of its large body size and low metabolic rate, emus have a relatively simple gastroinstetinal (GI) tract with a short mean digesta retention time. However, little is known about the GI microbial diversity of emus. The objective of this study was to characterize the intraluminal intestinal bacterial community in the different segments of small intestine (duodenum, jejunum, and ileum) using pyrotag sequencing and compare that with the ceca. Gut content samples were collected from each of four adult emus (2 males, 2 females; 5-6 years old) that were free ranged but supplemented with a barley-alfalfa-canola based diet. We amplified the V3-V5 region of 16S rRNA gene to identify the bacterial community using Roche 454 Junior system. After quality trimming, a total of 165,585 sequence reads were obtained from different segments of the small intestine (SI). A total of 701 operational taxonomic units (OTUs) were identified in the different segments of small intestine. Firmicutes (14-99%) and Proteobacteria (0.5-76%) were the most predominant bacterial phyla in the small intestine. Based on species richness estimation (Chao1 index), the average number of estimated OTUs in the small intestinal compartments were 148 in Duodenum, 167 in Jejunum, and 85 in Ileum, respectively. Low number of core OTUs identified in each compartment of small intestine across individual birds (Duodenum: 13 OTUs, Jejunum: 2 OTUs, Ileum: 14 OTUs) indicated unique bacterial community in each bird. Moreover, only 2 OTUs (Escherichia and Sinobacteraceae) were identified as core bacteria along the whole small intestine. PICRUSt analysis has indicated that the detoxification of plant material and environmental chemicals seem to be performed by SI microbiota, especially those in the jejunum. The emu cecal microbiome has more genes than SI segments involving in protective or immune response to enteric pathogens. Microbial digestion and fermentation is mostly in the jejunum and ceca. This is the first study to characterize the microbiota of different compartments of the emu intestines via gut samples and not fecal samples. Results from this study allow us to further investigate the influence of the seasonal and physiological changes of intestinal microbiota on the nutrition of emus and indirectly influence the fatty acid composition of emu fat.}, }
@article {pmid36934020, year = {2023}, author = {Berthouzoz, E and Lazarevic, V and Zekeridou, A and Castro, M and Debove, I and Aybek, S and Schrenzel, J and Burkhard, PR and Fleury, V}, title = {Oral and intestinal dysbiosis in Parkinson's disease.}, journal = {Revue neurologique}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neurol.2022.12.010}, pmid = {36934020}, issn = {0035-3787}, abstract = {The suspicion of an origin of Parkinson's disease (PD) at the periphery of the body and the involvement of environmental risk factors in the pathogenesis of PD have directed the attention of the scientific community towards the microbiota. The microbiota represents all the microorganisms residing both in and on a host. It plays an essential role in the physiological functioning of the host. In this article, we review the dysbiosis repeatedly demonstrated in PD and how it influences PD symptoms. Dysbiosis is associated with both motor and non-motor PD symptoms. In animal models, dysbiosis only promotes symptoms in individuals genetically susceptible to Parkinson's disease, suggesting that dysbiosis is a risk factor but not a cause of Parkinson's disease. We also review how dysbiosis contributes to the pathophysiology of PD. Dysbiosis induces numerous and complex metabolic changes, resulting in increased intestinal permeability, local and systemic inflammation, production of bacterial amyloid proteins that promote α-synuclein aggregation, as well as a decrease in short-chain fatty acid-producing bacteria that have anti-inflammatory and neuroprotective potential. In addition, we review how dysbiosis decreases the efficacy of dopaminergic treatments. We then discuss the interest of dysbiosis analysis as a biomarker of Parkinson's disease. Finally, we give an overview of how interventions modulating the gut microbiota such as dietary interventions, pro-biotics, intestinal decontamination and fecal microbiota transplantation could influence the course of PD.}, }
@article {pmid36933563, year = {2023}, author = {Massironi, S and Viganò, C and Palermo, A and Pirola, L and Mulinacci, G and Allocca, M and Peyrin-Biroulet, L and Danese, S}, title = {Inflammation and malnutrition in inflammatory bowel disease.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2468-1253(23)00011-0}, pmid = {36933563}, issn = {2468-1253}, abstract = {Inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis, has become increasingly prevalent worldwide in the past decade. The nutritional status of patients with IBD is often impaired, with malnutrition presenting as imbalanced energy or nutrient intake, including protein-energy malnutrition, disease-related malnutrition, sarcopenia, and micronutrient deficiency. Additionally, malnutrition can manifest as overweight, obesity, and sarcopenic obesity. Malnutrition can lead to disturbances in gut microbiome composition that might alter homoeostasis and cause a dysbiotic state, potentially triggering inflammatory responses. Despite the clear link between IBD and malnutrition, little is known about the pathophysiological mechanisms beyond protein-energy malnutrition and micronutrient deficiencies that could promote inflammation through malnutrition, and vice versa. This Review focuses on potential mechanisms that trigger a vicious cycle between malnutrition and inflammation, and their clinical and therapeutic implications.}, }
@article {pmid36933557, year = {2023}, author = {Hajishengallis, G and Lamont, RJ and Koo, H}, title = {Oral polymicrobial communities: Assembly, function, and impact on diseases.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2023.02.009}, pmid = {36933557}, issn = {1934-6069}, abstract = {Oral microbial communities assemble into complex spatial structures. The sophisticated physical and chemical signaling systems underlying the community enable their collective functional regulation as well as the ability to adapt by integrating environmental information. The combined output of community action, as shaped by both intra-community interactions and host and environmental variables, dictates homeostatic balance or dysbiotic disease such as periodontitis and dental caries. Oral polymicrobial dysbiosis also exerts systemic effects that adversely affect comorbidities, in part due to ectopic colonization of oral pathobionts in extra-oral tissues. Here, we review new and emerging concepts that explain the collective functional properties of oral polymicrobial communities and how these impact health and disease both locally and systemically.}, }
@article {pmid36933555, year = {2023}, author = {Li, D and Sun, T and Tong, Y and Le, J and Yao, Q and Tao, J and Liu, H and Jiao, W and Mei, Y and Chen, J and Liu, Z and Wang, G and Li, Y}, title = {Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2023.02.017}, pmid = {36933555}, issn = {1932-7420}, abstract = {Estradiol decline can result in depressive disorders in females; nevertheless, the causes of this decline are unclear. In this study, we isolated estradiol-degrading Klebsiella aerogenes from the feces of premenopausal females with depression. In mice, gavaging with this strain led to estradiol decline and depression-like behaviors. The gene encoding the estradiol-degrading enzyme in K. aerogenes was identified as 3β-hydroxysteroid dehydrogenase (3β-HSD). Heterologously expressing 3β-HSD resulted in Escherichia coli obtaining the ability to degrade estradiol. Gavaging mice with 3β-HSD-expressing E. coli decreased their serum estradiol levels, causing depression-like behaviors. The prevalence of K. aerogene and 3β-HSD was higher in premenopausal women with depression than in those without depression. These results suggest that the estradiol-degrading bacteria and 3β-HSD enzymes are potential intervention targets for depression treatment in premenopausal women.}, }
@article {pmid36933489, year = {2023}, author = {Chen, L and Huang, Z and Li, Q and Chen, C and Luo, Y and Kang, P}, title = {Activated intestinal microbiome-associated tryptophan metabolism upregulates aryl hydrocarbon receptor to promote osteoarthritis in a rat model.}, journal = {International immunopharmacology}, volume = {118}, number = {}, pages = {110020}, doi = {10.1016/j.intimp.2023.110020}, pmid = {36933489}, issn = {1878-1705}, abstract = {OBJECTIVE: To evaluate the role of aryl hydrocarbon receptor in the pathogenesis of osteoarthritis (OA) and its association with intestinal microbiome-related tryptophan metabolism.<br><br>METHODS: Cartilage was isolated from OA patients undergoing total knee arthroplasty and analyzed for expression of aryl hydrocarbon receptor (AhR) and cytochrome P450 of family 1, subfamily A, and polypeptide 1 (CyP1A1). To gain mechanistic insights, OA model was induced in Sprague Dawley rats after antibiotic pretreatment combined with a tryptophan-rich diet (or not). The severity of OA was assessed eight weeks after surgery according to the Osteoarthritis Research Society International grading system. Expression of AhR, CyP1A1 as well as markers of bone and cartilage metabolism, inflammation, and intestinal microbiome-related tryptophan metabolism was assessed.<br><br>RESULTS: Severity of OA in cartilage from patients positively correlated with expression of AhR and CyP1A1 in chondrocytes. In the rat model of OA, antibiotic pretreatment led to lower expression of AhR and CyP1A1 and lower serum levels of lipopolysaccharide (LPS). Conversely, antibiotics upregulated Col2A1 and SOX9 in cartilage, which mitigated the cartilage damage and synovitis, reduced the relative abundance of Lactobacillus. Additional tryptophan supplementation activated intestinal microbiome-related tryptophan metabolism, antagonizing the effects of antibiotics, exacerbating OA synovitis.<br><br>CONCLUSION: Our study established an underlying intestinal microbiome associated tryptophan metabolism-OA connection which sets a new target for exploring OA pathogenesis. The alteration of tryptophan metabolism might prompt the activation and synthesis of AhR, accelerating the development of OA.}, }
@article {pmid36933182, year = {2023}, author = {Li, J and Huang, T and Zhang, M and Tong, X and Chen, J and Zhang, Z and Huang, F and Ai, H and Huang, L}, title = {Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {36933182}, issn = {1618-1905}, abstract = {Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.}, }
@article {pmid36933165, year = {2023}, author = {Peng, Y and Chen, Y and Wang, Y and Wang, W and Qiao, S and Lan, J and Wang, M}, title = {Dysbiosis and primary B-cell immunodeficiencies: current knowledge and future perspective.}, journal = {Immunologic research}, volume = {}, number = {}, pages = {}, pmid = {36933165}, issn = {1559-0755}, abstract = {According to Elie Metchnikoff, an originator of modern immunology, several pivotal functions for disease and health are provided by indigenous microbiota. Nonetheless, important mechanistic insights have been elucidated more recently, owing to the growing availability of DNA sequencing technology. There are 10 to 100 trillion symbiotic microbes (such as viruses, bacteria, and yeast) in each human gut microbiota. Both locally and systemically, the gut microbiota has been demonstrated to impact immune homeostasis. Primary B-cell immunodeficiencies (PBIDs) are a group of primary immunodeficiency diseases (PIDs) referring to the dysregulated antibody production due to either intrinsic genetic defects or failures in functions of B cells. Recent studies have found that PBIDs cause disruptions in the gut's typical homeostatic systems, resulting in inadequate immune surveillance in the gastrointestinal (GI) tract, which is linked to increased dysbiosis, which is characterized by a disruption in the microbial homeostasis. This study aimed to review the published articles in this field to provide a comprehensive view of the existing knowledge about the crosstalk between the gut microbiome and PBID, the factors shaping the gut microbiota in PBID, as well as the potential clinical approaches for restoring a normal microbial community.}, }
@article {pmid36933058, year = {2023}, author = {Balachandran, KRS and Sankara Subramanianan, SH and Dhassiah, MP and Rengarajan, A and Chandrasekaran, M and Rangamaran, VR and Gopal, D}, title = {Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments.}, journal = {Molecular genetics and genomics : MGG}, volume = {}, number = {}, pages = {}, pmid = {36933058}, issn = {1617-4623}, abstract = {Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.}, }
@article {pmid36932313, year = {2023}, author = {Yuan, J and Wen, T and Yang, S and Zhang, C and Zhao, M and Niu, G and Xie, P and Liu, X and Zhao, X and Shen, Q and Bezemer, TM}, title = {Growth substrates alter aboveground plant microbial and metabolic properties thereby influencing insect herbivore performance.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {36932313}, issn = {1869-1889}, abstract = {The gut microbiome of plant-eaters is affected by the food they eat, but it is currently unclear how the plant metabolome and microbiome are influenced by the substrate the plant grows in and how this subsequently impacts the feeding behavior and gut microbiomes of insect herbivores. Here, we use Plutella xylostella caterpillars and show that the larvae prefer leaves of cabbage plants growing in a vermiculite substrate to those from plants growing in conventional soil systems. From a plant metabolomics analysis, we identified 20 plant metabolites that were related to caterpillar feeding performance. In a bioassay, the effects of these plant metabolites on insects' feeding were tested. Nitrate and compounds enriched with leaves of soilless cultivation promoted the feeding of insects, while compounds enriched with leaves of plants growing in natural soil decreased feeding. Several microbial groups (e.g., Sporolactobacillus, Haliangium) detected inside the plant correlated with caterpillar feeding performance and other microbial groups, such as Ramlibacter and Methylophilus, correlated with the gut microbiome. Our results highlight the role of growth substrates on the food metabolome and microbiome and on the feeding performance and the gut microbiome of plant feeders. It illustrates how belowground factors can influence the aboveground properties of plant-animal systems, which has important implications for plant growth and pest control.}, }
@article {pmid36932240, year = {2023}, author = {Valles-Colomer, M and Menni, C and Berry, SE and Valdes, AM and Spector, TD and Segata, N}, title = {Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {36932240}, issn = {1546-170X}, abstract = {Cardiometabolic diseases have become a leading cause of morbidity and mortality globally. They have been tightly linked to microbiome taxonomic and functional composition, with diet possibly mediating some of the associations described. Both the microbiome and diet are modifiable, which opens the way for novel therapeutic strategies. High-throughput omics techniques applied on microbiome samples (meta-omics) hold the unprecedented potential to shed light on the intricate links between diet, the microbiome, the metabolome and cardiometabolic health, with a top-down approach. However, effective integration of complementary meta-omic techniques is an open challenge and their application on large cohorts is still limited. Here we review meta-omics techniques and discuss their potential in this context, highlighting recent large-scale efforts and the novel insights they provided. Finally, we look to the next decade of meta-omics research and discuss various translational and clinical pathways to improving cardiometabolic health.}, }
@article {pmid36932227, year = {2023}, author = {Llovet, JM and Willoughby, CE and Singal, AG and Greten, TF and Heikenwälder, M and El-Serag, HB and Finn, RS and Friedman, SL}, title = {Nonalcoholic steatohepatitis-related hepatocellular carcinoma: pathogenesis and treatment.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {36932227}, issn = {1759-5053}, abstract = {Nonalcoholic fatty liver disease (NAFLD), including its more severe manifestation, nonalcoholic steatohepatitis (NASH), has a global prevalence of 20-25% and is a major public health problem. Its incidence is increasing in parallel to the rise in obesity, diabetes and metabolic syndrome. Progression from NASH to NASH-related hepatocellular carcinoma (HCC) (~2% of cases per year) is influenced by many factors, including the tissue and immune microenvironment, germline mutations in PNPLA3, and the microbiome. NASH-HCC has unique molecular and immune traits compared with other aetiologies of HCC and is equally prevalent in men and women. Comorbidities associated with NASH, such as obesity and diabetes mellitus, can prevent the implementation of potentially curative therapies in certain patients; nonetheless, outcomes are similar in patients who receive treatment. NASH-HCC at the early to intermediate stages is managed with surgery and locoregional therapies, whereas advanced HCC is treated with systemic therapies, including anti-angiogenic therapies and immune-checkpoint inhibitors. In this Review, we present the latest knowledge of the pathogenic mechanisms and clinical management of NASH-HCC. We discuss data highlighting the controversy over varying responses to immune-checkpoint inhibitors according to underlying aetiology and suggest that the future of NASH-HCC management lies in improved surveillance, targeted combination therapies to overcome immune evasion, and identifying biomarkers to recognize treatment responders.}, }
@article {pmid36932179, year = {2023}, author = {Lakosa, A and Rahimian, A and Tomasi, F and Marti, F and Reynolds, LM and Tochon, L and David, V and Danckaert, A and Canonne, C and Tahraoui, S and de Chaumont, F and Forget, B and Maskos, U and Besson, M}, title = {Impact of the gut microbiome on nicotine's motivational effects and glial cells in the ventral tegmental area in male mice.}, journal = {Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology}, volume = {}, number = {}, pages = {}, pmid = {36932179}, issn = {1740-634X}, abstract = {A link between gut dysbiosis and the pathogenesis of brain disorders has been identified. A role for gut bacteria in drug reward and addiction has been suggested but very few studies have investigated their impact on brain and behavioral responses to addictive drugs so far. In particular, their influence on nicotine's addiction-like processes remains unknown. In addition, evidence shows that glial cells shape the neuronal activity of the mesolimbic system but their regulation, within this system, by the gut microbiome is not established. We demonstrate that a lack of gut microbiota in male mice potentiates the nicotine-induced activation of sub-regions of the mesolimbic system. We further show that gut microbiota depletion enhances the response to nicotine of dopaminergic neurons of the posterior ventral tegmental area (pVTA), and alters nicotine's rewarding and aversive effects in an intra-VTA self-administration procedure. These effects were not associated with gross behavioral alterations and the nicotine withdrawal syndrome was not impacted. We further show that depletion of the gut microbiome modulates the glial cells of the mesolimbic system. Notably, it increases the number of astrocytes selectively in the pVTA, and the expression of postsynaptic density protein 95 in both VTA sub-regions, without altering the density of the astrocytic glutamatergic transporter GLT1. Finally, we identify several sub-populations of microglia in the VTA that differ between its anterior and posterior sub-parts, and show that they are re-organized in conditions of gut microbiota depletion. The present study paves the way for refining our understanding of the pathophysiology of nicotine addiction.}, }
@article {pmid36935840, year = {2022}, author = {Sugino, KY and Mandala, A and Janssen, RC and Gurung, S and Trammell, M and Day, MW and Brush, RS and Papin, JF and Dyer, DW and Agbaga, MP and Friedman, JE and Castillo-Castrejon, M and Jonscher, KR and Myers, DA}, title = {Western diet-induced shifts in the maternal microbiome are associated with altered microRNA expression in baboon placenta and fetal liver.}, journal = {Frontiers in clinical diabetes and healthcare}, volume = {3}, number = {}, pages = {}, pmid = {36935840}, issn = {2673-6616}, abstract = {Maternal consumption of a high-fat, Western-style diet (WD) disrupts the maternal/infant microbiome and contributes to developmental programming of the immune system and nonalcoholic fatty liver disease (NAFLD) in the offspring. Epigenetic changes, including non-coding miRNAs in the fetus and/or placenta may also underlie this risk. We previously showed that obese nonhuman primates fed a WD during pregnancy results in the loss of beneficial maternal gut microbes and dysregulation of cellular metabolism and mitochondrial dysfunction in the fetal liver, leading to a perturbed postnatal immune response with accelerated NAFLD in juvenile offspring. Here, we investigated associations between WD-induced maternal metabolic and microbiome changes, in the absence of obesity, and miRNA and gene expression changes in the placenta and fetal liver. After ~8-11 months of WD feeding, dams were similar in body weight but exhibited mild, systemic inflammation (elevated CRP and neutrophil count) and dyslipidemia (increased triglycerides and cholesterol) compared with dams fed a control diet. The maternal gut microbiome was mainly comprised of Lactobacillales and Clostridiales, with significantly decreased alpha diversity (P = 0.0163) in WD-fed dams but no community-wide differences (P = 0.26). At 0.9 gestation, mRNA expression of IL6 and TNF in maternal WD (mWD) exposed placentas trended higher, while increased triglycerides, expression of pro-inflammatory CCR2, and histological evidence for fibrosis were found in mWD-exposed fetal livers. In the mWD-exposed fetus, hepatic expression levels of miR-204-5p and miR-145-3p were significantly downregulated, whereas in mWD-exposed placentas, miR-182-5p and miR-183-5p were significantly decreased. Notably, miR-1285-3p expression in the liver and miR-183-5p in the placenta were significantly associated with inflammation and lipid synthesis pathway genes, respectively. Blautia and Ruminococcus were significantly associated with miR-122-5p in liver, while Coriobacteriaceae and Prevotellaceae were strongly associated with miR-1285-3p in the placenta; both miRNAs are implicated in pathways mediating postnatal growth and obesity. Our findings demonstrate that mWD shifts the maternal microbiome, lipid metabolism, and inflammation prior to obesity and are associated with epigenetic changes in the placenta and fetal liver. These changes may underlie inflammation, oxidative stress, and fibrosis patterns that drive NAFLD and metabolic disease risk in the next generation.}, }
@article {pmid36937379, year = {2021}, author = {Bondarenko, O and Mortimer, M and Kahru, A and Feliu, N and Javed, I and Kakinen, A and Lin, S and Xia, T and Song, Y and Davis, TP and Lynch, I and Parak, WJ and Leong, DT and Ke, PC and Chen, C and Zhao, Y}, title = {Nanotoxicology and Nanomedicine: The Yin and Yang of Nano-Bio Interactions for the New Decade.}, journal = {Nano today}, volume = {39}, number = {}, pages = {}, pmid = {36937379}, issn = {1748-0132}, abstract = {Nanotoxicology and nanomedicine are two sub-disciplines of nanotechnology focusing on the phenomena, mechanisms, and engineering at the nano-bio interface. For the better part of the past three decades, these two disciplines have been largely developing independently of each other. Yet recent breakthroughs in microbiome research and the current COVID-19 pandemic demonstrate that holistic approaches are crucial for solving grand challenges in global health. Here we show the Yin and Yang relationship between the two fields by highlighting their shared goals of making safer nanomaterials, improved cellular and organism models, as well as advanced methodologies. We focus on the transferable knowledge between the two fields as nanotoxicological research is moving from pristine to functional nanomaterials, while inorganic nanomaterials - the main subjects of nanotoxicology - have become an emerging source for the development of nanomedicines. We call for a close partnership between the two fields in the new decade, to harness the full potential of nanotechnology for benefiting human health and environmental safety.}, }
@article {pmid36937228, year = {2017}, author = {Navas-Molina, JA and Hyde, ER and Sanders, J and Knight, R}, title = {The Microbiome and Big Data.}, journal = {Current opinion in systems biology}, volume = {4}, number = {}, pages = {92-96}, pmid = {36937228}, issn = {2452-3100}, abstract = {Microbiome datasets have expanded rapidly in recent years. Advances in DNA sequencing, as well as the rise of shotgun metagenomics and metabolomics, are producing datasets that exceed the ability of researchers to analyze them on their personal computers. Here we describe what Big Data is in the context of microbiome research, how this data can be transformed into knowledge about microbes and their functions in their environments, and how the knowledge can be applied to move microbiome research forward. In particular, the development of new high-resolution tools to assess strain-level variability (moving away from OTUs), the advent of cloud computing and centralized analysis resources such as Qiita (for sequences) and GNPS (for mass spectrometry), and better methods for curating and describing "metadata" (contextual information about the sequence or chemical information) are rapidly assisting the use of microbiome data in fields ranging from human health to environmental studies.}, }
@article {pmid36932092, year = {2023}, author = {Cao, Z and Zuo, W and Wang, L and Chen, J and Qu, Z and Jin, F and Dai, L}, title = {Spatial profiling of microbial communities by sequential FISH with error-robust encoding.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1477}, pmid = {36932092}, issn = {2041-1723}, abstract = {Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.}, }
@article {pmid36931952, year = {2023}, author = {Lin, L and Zhang, K and Xiong, Q and Zhang, J and Cai, B and Huang, Z and Yang, B and Wei, B and Chen, J and Niu, Q}, title = {Gut microbiota in pre-clinical rheumatoid arthritis: From pathogenesis to preventing progression.}, journal = {Journal of autoimmunity}, volume = {}, number = {}, pages = {103001}, doi = {10.1016/j.jaut.2023.103001}, pmid = {36931952}, issn = {1095-9157}, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by progressive polyarthritis that leads to cartilage and bone damage. Pre-clinical RA is a prolonged state before clinical arthritis and RA develop, in which autoantibodies (antibodies against citrullinated proteins, rheumatoid factors) can be present due to the breakdown of immunologic self-tolerance. As early treatment initiation before the onset of polyarthritis may achieve sustained remission, optimize clinical outcomes, and even prevent RA progression, the pre-clinical RA stage is showing the prospect to be the window of opportunity for RA treatment. Growing evidence has shown the role of the gut microbiota in inducing systemic inflammation and polyarthritis via multiple mechanisms, which may involve molecular mimicry, impaired intestinal barrier function, gut microbiota-derived metabolites mediated immune regulation, modulation of the gut microbiota's effect on immune cells, intestinal epithelial cells autophagy, and the interaction between the microbiome and human leukocyte antigen alleles as well as microRNAs. Since gut microbiota alterations in pre-clinical RA have been reported, potential therapies for modifying the gut microbiota in pre-clinical RA, including natural products, antibiotic therapy, fecal microbiota transplantation, probiotics, microRNAs therapy, vitamin D supplementation, autophagy inducer-based treatment, prebiotics, and diet, holds great promise for the successful treatment and even prevention of RA via altering ongoing inflammation. In this review, we summarized current studies that include pathogenesis of gut microbiota in RA progression and promising therapeutic strategies to provide novel ideas for the management of pre-clinical RA and possibly preventing arthritis progression.}, }
@article {pmid36931898, year = {2023}, author = {Luna, N and Herrera, G and Muñoz, M and Sánchez-Herrera, M and Brown, A and Khazan, E and Pardo-Diaz, C and Ramírez, JD and Salazar, C}, title = {Geography shapes the microbial community in Heliconius butterflies.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad028}, pmid = {36931898}, issn = {1574-6941}, abstract = {Heliconius butterflies are an ideal organism for studying ecology, behavior, adaptation, and speciation. These butterflies can be found in various locations and habitats in Central and South America, where they encounter and interact with different sources of pollen, nectar, and host plants. However, there is limited knowledge on how geographic and habitat variations affect the microbiota of these insects, and whether microbial associates play a role in their ability to exploit different habitats. To date, research on the microbial communities associated with Heliconius has mainly focused on host phylogenetic signal in microbiomes or microbiome characterization in specific communities of butterflies. In this study we characterized the microbiomes of several species and populations of Heliconius from distant locations that represent contrasting environments. We found that the microbiota of different Heliconius species is taxonomically similar but vary in abundance. Notably, this variation is associated with a major geographic barrier-the Central Cordillera of Colombia. Additionally, we confirmed that this microbiota is not associated with pollen-feeding. Therefore, it seems likely that geography shapes the abundance of microbiota that the butterfly carries, but not the taxonomic diversity of the microbial community. Based on the current evidence, the bacterial microbiota associated with Heliconius does not appear to play a beneficial role for these butterflies.}, }
@article {pmid36931888, year = {2023}, author = {van Leeuwen, PT and Brul, S and Zhang, J and Wortel, MT}, title = {Synthetic microbial communities (SynComs) of the human gut: design, assembly, and applications.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuad012}, pmid = {36931888}, issn = {1574-6976}, abstract = {The human gut harbors native microbial communities, forming a highly complex ecosystem. Synthetic microbial communities (SynComs) of the human gut are an assembly of microorganisms isolated from human mucosa or fecal samples. In recent decades, the ever-expanding culturing capacity and affordable sequencing, together with advanced computational modeling, started a ''golden age'' for harnessing the beneficial potential of SynComs to fight gastrointestinal disorders, such as infections and chronic inflammatory bowel diseases. As simplified and completely defined microbiota, SynComs offer a promising reductionist approach to understanding the multi-species and multi-kingdom interactions in the microbe-host-immune axis. However, there are still many challenges to overcome before we can precisely construct SynComs of designed function and efficacy that allow the translation of scientific findings to patients' treatments. Here we discussed the strategies used to design, assemble, and test a SynCom, and address the significant challenges, which are of microbiological, engineering, and translational nature, that stand in the way of using SynComs as live bacterial therapeutics.}, }
@article {pmid36931881, year = {2023}, author = {Kleinová, P and Beliančinová, M and Vnučák, M and Graňák, K and Dedinská, I}, title = {Gut microbiome and renal transplantation.}, journal = {Vnitrni lekarstvi}, volume = {69}, number = {1}, pages = {41-46}, doi = {10.36290/vnl.2023.006}, pmid = {36931881}, issn = {0042-773X}, abstract = {Gut microbiome research has been a surge of interest in many branches of medicine in the last decade. Our main aim is to show ability of microbes to infuence the functions of human body, especially in the immune system, and on the other hand to clarify changes in composition of gut microbiome in the post-transplantation period and their function for the long-term survival of the graft and the patient in the context of the occurrence of a wide range of complications. Kidney transplantation with the subsequent use of immunosuppressants and antibiotics affects the composition of gut microbiome. The subsequent development of dysbiosis significantly increases the risk of acute rejection, interstitial fibrosis and tubular atrophy of the graft, post-transplant diarrhoea, organ´s infections and metabolic complications such as post-transplant diabetes mellitus. Also important is the influence of the microorganisms of the gut microbiome on metabolism of immunosuppressants with the production of less effective components and the subsequent necessity of modifying their levels with a higher risk of underdosing and the occurrence of graft rejection. Support of the composition of the gut microbiome in the post-transplantation period in favor of bacteria producing short chain fatty acids (SCFA) is possible by changing of diet with predominance of fiber, the application of probiotics, prebiotics. According to available studies, it can lead to benefits in term of metabolic compensation, to the induction of donor-specific tolerance and many others, with an overall improvement in the quality of patient and graft survival.}, }
@article {pmid36931530, year = {2023}, author = {Li, J and Zhu, S and Wang, Y and Fan, M and Dai, J and Zhu, C and Xu, K and Cui, M and Suo, C and Jin, L and Jiang, Y and Chen, X}, title = {Metagenomic association analysis of cognitive impairment in community-dwelling older adults.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106081}, doi = {10.1016/j.nbd.2023.106081}, pmid = {36931530}, issn = {1095-953X}, abstract = {The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.}, }
@article {pmid36931236, year = {2023}, author = {Walter, J and Shanahan, F}, title = {Fecal microbiota-based treatment for recurrent Clostridioides difficile infection.}, journal = {Cell}, volume = {186}, number = {6}, pages = {1087}, doi = {10.1016/j.cell.2023.02.034}, pmid = {36931236}, issn = {1097-4172}, abstract = {Rebyota is a rectally administered fecal microbiota suspension for prevention of recurrence of Clostridioides difficile infection. The mechanism of action of Rebyota probably involves competitive exclusion of C. difficile by donor microbes with reduced toxin production; other factors may include restoration of protective taxa and modulation of the recipient's microbiome by phage, donor microbes, or metabolites.}, }
@article {pmid36931204, year = {2023}, author = {Ai, D and Zhang, X and Zhang, Q and Li, X and Wang, Y and Liu, X and Xia, LC}, title = {Tumor tissue microorganisms are closely associated with tumor immune subtypes.}, journal = {Computers in biology and medicine}, volume = {157}, number = {}, pages = {106774}, doi = {10.1016/j.compbiomed.2023.106774}, pmid = {36931204}, issn = {1879-0534}, abstract = {Studies have found that different immune subtypes are present in the same tumor. Different tumor subtypes have different tumor microenvironments (TME). This means that the efficacy of immunotherapy in actual applications will, therefore, have different results. Existing tumor immune subtype studies have mostly focused on immune cells, stromal cells, genes and molecules without considering the presence of microbes. Some studies have shown that microflora can strongly promote many gastrointestinal cancers. The microbiome has, therefore, become an important biomarker and regulatory factor of cancer progression and therapeutic responses. In addition, the presence of microflora can strongly regulate the host immune system, indirectly affecting tumor growth. Taken together, it is important to study the relationships that develop among tumor tissue microorganisms, tumor immune subtype, and the TME. In this study, correlations between microbial abundance, immune cell infiltration, immune gene expression and tumor immune subtype were studied. To accomplish this, tissue microorganisms and immune cell ratios with significant differences between the different cancers were obtained by comparing 203 gastric cancer and intestinal cancer samples. Two immune subtypes of intestinal samples were obtained by K-means clustering algorithm and tissue microorganisms, immune cell ratios and immune-related genes with significant differences between different immune subtypes were screened through Wilcoxon rank sum test. The results showed that Clostridioides difficile, Aspergillus fumigatus, Yarrowia lipolytica, and Fusarium pseudograminearum were all closely associated with the identified tumor immune subtypes. Our open-source software is freely available from GitHub at https://github.com/gutmicrobes/IMM-subtype.git.}, }
@article {pmid36931138, year = {2023}, author = {Kruse, S and Becker, S and Pierre, F and Morlock, GE}, title = {Metabolic profiling of bacterial co-cultures reveals intermicrobiome interactions and dominant species.}, journal = {Journal of chromatography. A}, volume = {1694}, number = {}, pages = {463911}, doi = {10.1016/j.chroma.2023.463911}, pmid = {36931138}, issn = {1873-3778}, abstract = {In animal production, the use of probiotic microorganisms has increased since the ban on antibiotic growth promoters in 2006. The added microorganisms interact with the microbiome of the animals, whereby the probiotic activity is not fully understood. Several microorganisms of the genus Bacillus are already known for their probiotic activity and are applied as feed supplements to increase the health status of the animals. They are thought to interact with Escherichia coli, one of the most abundant bacteria in the animal gut. In biotechnological applications, co-culturing enables the regulation of bacterial interaction or the production of target metabolites. The basic principles of multi-imaging high-performance thin-layer chromatography (HPTLC) with upstream cultivation were further developed to analyze the metabolic profiles of three axenic bacilli cultures compared to their co-cultures with E. coli DSM 18039 (K12). The comparative profiling visualized bacteria's metabolic interactions and showed how the presence of E. coli affects the metabolite formation of bacilli. The characteristic metabolic profile images showed not only the influence of microbiomes but also of inoculation, cultivation and nutrients on the commercial probiotic. The formation of antimicrobially active metabolites, detected via three different planar bioassays, was influenced by the presence of other microorganisms, especially in the probiotic. This first application of multi-imaging HPTLC in the field of co-culturing enabled visualization of metabolic interactions of bacteria via their produced chemical as well as bioactive metabolite profiles. The metabolic profiling provided evidence of bacterial interactions, intermicrobiome influences and dominant species in the co-culture.}, }
@article {pmid36931094, year = {2023}, author = {Correia, GD and Marchesi, JR and MacIntyre, DA}, title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102292}, doi = {10.1016/j.mib.2023.102292}, pmid = {36931094}, issn = {1879-0364}, abstract = {Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.}, }
@article {pmid36931087, year = {2023}, author = {Zhang, S and Chen, A and Deng, H and Jiang, L and Liu, X and Chai, L}, title = {Intestinal response of Rana chensinensis larvae exposed to Cr and Pb, alone and in combination.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114774}, doi = {10.1016/j.ecoenv.2023.114774}, pmid = {36931087}, issn = {1090-2414}, abstract = {Although numerous investigations on the adverse impact of Cr and Pb have been performed, studies on intestinal homeostasis in amphibians are limited. Here, single and combined effects of Cr (104 μg/L) and Pb (50 μg/L) on morphological and histological features, bacterial community, digestive enzymes activities, as well as transcriptomic profile of intestines in Rana chensinensis tadpoles were assessed. Significant decrease in the relative intestine length (intestine length/snout-to-vent length, IL/SVL) was observed after exposure to Pb and Cr/Pb mixture. Intestinal histology and digestive enzymes activities were altered in metal treatment groups. In addition, treatment groups showed significantly increased bacterial richness and diversity. Tadpoles in treatment groups were observed to have differential gut bacterial composition from controls, especially for the abundance of phylum Proteobacteria, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria as well as genus Citrobacter, Anaerotruncus, Akkermansia, and Alpinimonas. Moreover, transcriptomic analysis showed that the transcript expression profiles of GPx and SOD isoforms responded differently to Cr and/or Pb exposure. Besides, transcriptional activation of pro-apoptotic and glycolysis-related genes, such as Bax, Apaf 1, Caspase 3, PK, PGK, TPI, and GPI were detected in all treatment groups but downregulation of Bcl2 in Pb and Cr/Pb mixture groups. Collectively, these results suggested that Cr and Pb exposure at environmental relevant concentration, alone and in combination, could disrupt intestinal homeostasis of R. chensinensis tadpoles.}, }
@article {pmid36930714, year = {2023}, author = {Geng, Z and Wang, X and Wu, F and Cao, Z and Liu, J}, title = {Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics.}, journal = {Science advances}, volume = {9}, number = {11}, pages = {eade0997}, doi = {10.1126/sciadv.ade0997}, pmid = {36930714}, issn = {2375-2548}, abstract = {Despite the fact that oral microecologics are effective in modulating the gut microbiome, they always suffer from multiple insults during the journey from manufacture to arrival at the intestine. Inspired by the protective mechanism of mineralization, we describe a cytocompatible approach of biointerface mineralization that can generate an ultraresistant and self-removable coating on bacterial surface to solve these challenges. Mineral coating endows bacteria with robust resistances against manufacture-associated oxygen exposure, ultraviolet irradiation, and 75% ethanol. Following oral ingestion, the coating is able to actively neutralize gastric acid and release encapsulated bacteria through spontaneous yet rapid double-decomposition reaction. In addition to acid neutralization, the generated calcium ions can trigger micellar aggregation of bile acid, enabling dual exemptions from the insults of gastric acid and bile acid to achieve uncompromised bacterial viability. Further supported by the therapeutic efficacy of coated bacteria toward colitis mice, biointerface mineralization provides a versatile platform for developing next-generation living oral biotherapeutics.}, }
@article {pmid36930679, year = {2023}, author = {Puschhof, J and Elinav, E}, title = {Human microbiome research: Growing pains and future promises.}, journal = {PLoS biology}, volume = {21}, number = {3}, pages = {e3002053}, doi = {10.1371/journal.pbio.3002053}, pmid = {36930679}, issn = {1545-7885}, abstract = {Human microbiome research is evolving from describing associations to understanding the impact of bioactive strains on humans. Despite challenges, progress is being made to apply data-driven microbiome diagnostics and interventions, potentially leading to precision medicine breakthroughs in the next decade.}, }
@article {pmid36930202, year = {2023}, author = {Amaro, A and Leão, C and Guerra, V and Albuquerque, T and Clemente, L}, title = {Plasmid-Mediated Colistin Resistance Genes mcr-1 and mcr-4 in Multidrug-Resistant Escherichia coli Strains Isolated from a Healthy Pig in Portugal.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {29}, number = {3}, pages = {78-84}, doi = {10.1089/mdr.2022.0228}, pmid = {36930202}, issn = {1931-8448}, abstract = {Antimicrobial resistance encoded by mobile colistin resistance (mcr) genes is a global and emergent threat. In this study, we report the occurrence of two different populations of colistin-resistant Escherichia coli harboring mcr-1 and mcr-4 variants in the intestinal microbiome of a healthy pig. Following antimicrobial susceptibility determination, the presence of mcr genes in two E. coli strains, isolated according to different selective microbiological procedures, was screened by PCR. Whole-genome sequencing confirmed that both strains were multidrug-resistant; INIAV_002EC was an AmpC producer carrying blaCMY-2, blaTEM-1B, qnrS1, mcr-1.1 genes, and INIAV_001EC carrying blaTEM-1A, tetB, and mcr-4.1 genes, along with mutations in quinolone resistance-determining regions. In addition, both strains harbored sul3, dfrA, and aadA1 determinants. Further genome analysis revealed different plasmid replicons associated with the mcr genes, IncX4 associated with mcr-1.1, and ColE10 with mcr-4.1. In addition, other replicons, including IncFIA, IncI1-Iγ, IncX1, IncY, in INIAV_002EC, and IncX1, IncI1, and p0111, in INIAV_001EC, were identified. Furthermore, both strains belonged to ST215 serotype O68:H12 and ST156 serotype O25:H28, respectively. This finding highlights the pig gut flora as a potential reservoir of mobile colistin resistance genes and reports the presence of the mcr-4.1 gene found for the first time in Portugal.}, }
@article {pmid36930056, year = {2023}, author = {Njunge, JM and Walson, JL}, title = {Microbiota and growth among infants and children in low-income and middle-income settings.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCO.0000000000000927}, pmid = {36930056}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: Adequate nutrition is essential but insufficient for optimal childhood growth and development. Increasingly, it is clear that the gut microbiota modulates childhood growth and may be particularly important in low-income and middle-income countries (LMIC), where growth faltering, undernutrition, environmental contamination and enteric pathogens are more common. We summarize recent evidence demonstrating the role of the gut microbiota in impacting childhood growth and interventions targeting the gut microbiota to impact growth in children in LMIC settings.<br><br>RECENT FINDINGS: Recent studies show that maturation of the infant microbiota is linked with the development of the immune system, which is key to host-microbe symbiosis. Infants lacking Bifidobacterium longum subsp. Infantis, which predominates breastfed microbiome, display immune activation while supplementation is linked to increased immune tolerance and among undernourished children, promotes growth. Microbiome-directed complimentary foods (MDCF) containing local ingredients is a novel strategy to promote gut microbiota development, especially among undernourished children and improve growth. Dietary patterns during pregnancy may drive selection of gut microbial species that impact infant health and growth.<br><br>SUMMARY: Growth patterns among children in LMIC settings are closely associated with the diversity and maturity of the infant microbiome. Prebiotics, probiotics, and synbiotics targeting microbiota dysbiosis may impact birth outcomes, infant immune development and infections, and childhood growth in LMIC settings.}, }
@article {pmid36929933, year = {2023}, author = {Zou, H and Sun, T and Jin, B and Wang, S}, title = {sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad131}, pmid = {36929933}, issn = {1367-4811}, abstract = {SUMMARY: Microbial secondary metabolites exhibit potential medicinal value. A large number of secondary metabolite biosynthetic gene clusters (BGCs) in the human gut microbiome, which exhibit essential biological activity in microbe-microbe and microbe-host interactions, have not been adequately characterised, making it difficult to prioritise these BGCs for experimental characterization. Here, we present the sBGC-hm, an atlas of secondary metabolite BGCs allows researchers to explore the potential therapeutic benefits of these natural products. One of its key features is the ability to assist in optimizing the BGC structure by utilizing the gene co-occurrence matrix obtained from HMP data. Results are viewable online and can be downloaded as spreadsheets.<br><br>The database is openly available at https://www.wzubio.com/sbgc. The website is powered by Apache 2 server with PHP and MariaDB.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36929926, year = {2023}, author = {Dinleyici, M and Barbieur, J and Dinleyici, EC and Vandenplas, Y}, title = {Functional effects of human milk oligosaccharides (HMOs).}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2186115}, doi = {10.1080/19490976.2023.2186115}, pmid = {36929926}, issn = {1949-0984}, abstract = {Human milk oligosaccharides (HMOs) are the third most important solid component in human milk and act in tandem with other bioactive components. Individual HMO levels and distribution vary greatly between mothers by multiple variables, such as secretor status, race, geographic region, environmental conditions, season, maternal diet, and weight, gestational age and mode of delivery. HMOs improve the gastrointestinal barrier and also promote a bifidobacterium-rich gut microbiome, which protects against infection, strengthens the epithelial barrier, and creates immunomodulatory metabolites. HMOs fulfil a variety of physiologic functions including potential support to the immune system, brain development, and cognitive function. Supplementing infant formula with HMOs is safe and promotes a healthy development of the infant revealing benefits for microbiota composition and infection prevention. Because of limited data comparing the effect of non-human oligosaccharides to HMOs, it is not known if HMOs offer an additional clinical benefit over non-human oligosaccharides. Better knowledge of the factors influencing HMO composition and their functions will help to understand their short- and long-term benefits.}, }
@article {pmid36929894, year = {2023}, author = {Qi, S and Zhang, J and Luan, X and Li, J and He, Z and Long, J and Xu, M and Li, P and Chen, Z and Wei, J and Yan, J}, title = {Chlorine Dioxide Reprograms Rhizosphere Microbial Communities to Enrich Interactions with Tobacco (Nicotiana tabacum).}, journal = {Polish journal of microbiology}, volume = {72}, number = {1}, pages = {47-60}, doi = {10.33073/pjm-2023-009}, pmid = {36929894}, issn = {2544-4646}, abstract = {For decades chlorine dioxide has been used in water disinfection with excellent results. As the scope of application expands, chlorine dioxide has the potential for soil disinfection. We used amplicon sequencing and gas chromatography-mass spectrometry to compare the changes of four mixed rhizosphere microbial community samples and 12 tobacco leaf volatile samples four months after the flood irrigation with chlorine dioxide in different concentrations (0, 2, 4, 8 mg/l). Phenotypic data of 60 tobacco plants were also collected. The effects of chlorine dioxide on rhizosphere microorganisms were positively correlated with dose gradients. Bacteria responded more strongly in both community structure and metabolic pathways than fungi. Five new bacterial phyla (Firmicutes, Bacteroidota, Myxococcota, Patescibacteria, Verrucomicroboata) appeared in chlorine dioxide treatment groups, while the fungal community only appeared as one new fungal phylum (Basidomycota). Alterations in 271 predicted metabolic bacterial pathways were found. However, in the fungal community were only 10 alternations. The correlations between leaf volatile compounds and rhizosphere microorganisms under the influence of chlorine dioxide treatment could be observed based on network results. However, natural connectivity had already been declining rapidly when less than 20% of the network's nodes were removed. Therefore, the microbe-metabolite network is not stable. It might be why chlorine dioxide treatments did not significantly affect tobacco quality (p = 0.754) and phenotype (p = 0.867). As a comprehensive investigation of chlorine dioxide in agriculture, this study proves the effectiveness and safety of chlorine dioxide soil disinfection and widens the application range of chlorine dioxide.}, }
@article {pmid36929079, year = {2023}, author = {Kim, Y}, title = {Bioinformatic and Statistical Analysis of Microbiome Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {183-229}, pmid = {36929079}, issn = {1940-6029}, abstract = {Since advances in next-generation sequencing (NGS) technique enabled to investigate uncultured microbiota and their genomes in unbiased manner, many microbiome researches have been reporting strong evidences for close links of microbiome to human health and disease. Bioinformatic and statistical analysis of NGS-based microbiome data are essential components in those microbiome researches to explore the complex composition of microbial community and understand the functions of community members in relation to host and environment. This chapter introduces bioinformatic analysis methods that generate taxonomy and functional feature count table along with phylogenetic tree from raw NGS microbiome data and then introduce statistical methods and machine learning approaches for analyzing the outputs of the bioinformatic analysis to infer the biodiversity of a microbial community and unravel host-microbiome association. Understanding the advantages and limitations of the analysis methods will help readers use the methods correctly in microbiome data analysis and may give a new opportunity to develop new analytic techniques for microbiome research.}, }
@article {pmid36929070, year = {2023}, author = {Wang, X and Fridley, BL}, title = {Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {1-9}, pmid = {36929070}, issn = {1940-6029}, abstract = {In the current era of multi-omics, new sequencing and molecular profiling technologies have facilitated our quest for a deeper and broader understanding of the variations and dynamic regulations in human genomes. However, analyzing and integrating data generated from diverse platforms, modalities, and large-scale heterogeneous samples to extract functional and clinically valuable information remains a significant challenge. Here, we first discuss recent advances in methods and algorithms for analyzing data at the genome, transcriptome, proteome, metabolome, and microbiome levels, followed by emerging methods for leveraging single-cell sequencing and spatial transcriptomic data. We also highlight the mechanistic insights that these advances can bring to the field, as well as the current challenges and outlooks relating to their translational and reproducible adoption at the population level. It is evident that novel statistical methods, which were inspired by new assays, will enable the associated molecular profiling pipelines and experimental designs to continuously improve our understanding of the human genome and the downstream consequences in the transcriptome, epigenome, proteome, metabolome, regulome, and microbiome.}, }
@article {pmid36928429, year = {2023}, author = {Austin, GI and Park, H and Meydan, Y and Seeram, D and Sezin, T and Lou, YC and Firek, BA and Morowitz, MJ and Banfield, JF and Christiano, AM and Pe'er, I and Uhlemann, AC and Shenhav, L and Korem, T}, title = {Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36928429}, issn = {1546-1696}, abstract = {Sequencing-based approaches for the analysis of microbial communities are susceptible to contamination, which could mask biological signals or generate artifactual ones. Methods for in silico decontamination using controls are routinely used, but do not make optimal use of information shared across samples and cannot handle taxa that only partially originate in contamination or leakage of biological material into controls. Here we present Source tracking for Contamination Removal in microBiomes (SCRuB), a probabilistic in silico decontamination method that incorporates shared information across multiple samples and controls to precisely identify and remove contamination. We validate the accuracy of SCRuB in multiple data-driven simulations and experiments, including induced contamination, and demonstrate that it outperforms state-of-the-art methods by an average of 15-20 times. We showcase the robustness of SCRuB across multiple ecosystems, data types and sequencing depths. Demonstrating its applicability to microbiome research, SCRuB facilitates improved predictions of host phenotypes, most notably the prediction of treatment response in melanoma patients using decontaminated tumor microbiome data.}, }
@article {pmid36928160, year = {2023}, author = {Bhatt, A and Haslam, A and Prasad, V}, title = {The effect of gastrointestinal microbiome supplementation on immune checkpoint inhibitor immunotherapy: a systematic review.}, journal = {Journal of cancer research and clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {36928160}, issn = {1432-1335}, abstract = {PURPOSE: Gastrointestinal (GI) microbiome modulators, such as fecal microbiome transplants (FMTs), are being considered as supplements to standard immune checkpoint inhibitor (ICI) treatment to improve efficacy. This systematic review aims to assess the study design and outcomes of clinical trials that use FMTs to enhance ICI treatment.<br><br>METHODS: Systematic literature searches were conducted on PubMed and Embase using search terms that included names of ICIs and gastrointestinal microbiome. A first search identified interventional trials, and the second search identified interventional, retrospective, and observational studies.<br><br>RESULTS: The search for interventional trials produced 205 articles, 3&#xa0;of which met the inclusion criteria. All studies had sample sizes ranging between 10 and 30 participants. 2 of the studies were single-arm studies with no control&#xa0;arm. One study reported an overall response rate (ORR) of 3 out of 15 (20%), a median progression-free survival (PFS) of 3&#xa0;months, and a median overall survival (OS) of 7&#xa0;months. The second study reported 1 complete response out of 10 (10%) and 2 partial responses out of 10 (20%). The third study reported an ORR of 58% vs. 20%, a median PFS of 12.7&#xa0;months vs. 2.5&#xa0;months in patients receiving nivolumab-ipilimumab plus CBM588 compared with patients receiving nivolumab-ipilimumab alone respectively, and an undefined median OS.<br><br>CONCLUSION: Current studies on the microbiome modulators with ICI use are limited in study design. Future clinical trials should be randomized, use larger sample sizes, and use an appropriate control arm to better ascertain the clinical effect of the GI microbiome on ICI treatment.}, }
@article {pmid36928026, year = {2023}, author = {Seymour, CO and Palmer, M and Becraft, ED and Stepanauskas, R and Friel, AD and Schulz, F and Woyke, T and Eloe-Fadrosh, E and Lai, D and Jiao, JY and Hua, ZS and Liu, L and Lian, ZH and Li, WJ and Chuvochina, M and Finley, BK and Koch, BJ and Schwartz, E and Dijkstra, P and Moser, DP and Hungate, BA and Hedlund, BP}, title = {Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {36928026}, issn = {2058-5276}, abstract = {Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.}, }
@article {pmid36927871, year = {2023}, author = {Doulidis, PG and Galler, AI and Hausmann, B and Berry, D and Rodríguez-Rojas, A and Burgener, IA}, title = {Gut microbiome signatures of Yorkshire Terrier enteropathy during disease and remission.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4337}, pmid = {36927871}, issn = {2045-2322}, abstract = {The role of the gut microbiome in developing Inflammatory Bowel Disease (IBD) in humans and dogs has received attention in recent years. Evidence suggests that IBD is associated with alterations in gut microbial composition, but further research is needed in veterinary medicine. The impact of IBD treatment on the gut microbiome needs to be better understood, especially in a breed-specific form of IBD in Yorkshire Terriers known as Yorkshire Terrier Enteropathy (YTE). This study aimed to investigate the difference in gut microbiome composition between YTE dogs during disease and remission and healthy Yorkshire Terriers. Our results showed a significant increase in specific taxa such as Clostridium sensu stricto 1, Escherichia-Shigella, and Streptococcus, and a decrease in Bacteroides, Prevotella, Alloprevotella, and Phascolarctobacterium in YTE dogs compared to healthy controls. No significant difference was found between the microbiome of dogs in remission and those with active disease, suggesting that the gut microbiome is affected beyond clinical recovery.}, }
@article {pmid36927795, year = {2023}, author = {Yi, X and Huang, C and Huang, C and Zhao, M and Lu, Q}, title = {Fecal microbiota from MRL/lpr mice exacerbates pristane-induced lupus.}, journal = {Arthritis research &amp; therapy}, volume = {25}, number = {1}, pages = {42}, pmid = {36927795}, issn = {1478-6362}, abstract = {BACKGROUND: The roles of gut microbiota in the pathogenesis of SLE have been receiving much attention during recent years. However, it remains unknown how fecal microbiota transplantation (FMT) and microbial metabolites affect immune responses and lupus progression.<br><br>METHODS: We transferred fecal microbiota from MRL/lpr (Lpr) mice and MRL/Mpj (Mpj) mice or PBS to pristane-induced lupus mice and observed disease development. We also screened gut microbiota and metabolite spectrums of pristane-induced lupus mice with FMT via 16S rRNA sequencing, metagenomic sequencing, and metabolomics, followed by correlation analysis.<br><br>RESULTS: FMT from MRL/lpr mice promoted the pathogenesis of pristane-induced lupus and affected immune cell profiles in the intestine, particularly the plasma cells. The structure and composition of microbial communities in the gut of the FMT-Lpr mice were different from those of the FMT-Mpj mice and FMT-PBS mice. The abundances of specific microbes such as prevotella taxa were predominantly elevated in the gut microbiome of the FMT-Lpr mice, which were positively associated with functional pathways such as cyanoamino acid metabolism. Differential metabolites such as valine and L-isoleucine were identified with varied abundances among the three groups. The abundance alterations of the prevotella taxa may affect the phenotypic changes such as proteinuria levels in the pristane-induced lupus mice.<br><br>CONCLUSION: These findings further confirm that gut microbiota play an important role in the pathogenesis of lupus. Thus, altering the gut microbiome may provide a novel way to treat lupus.}, }
@article {pmid36927689, year = {2023}, author = {Hou, X and Du, H and Deng, Y and Wang, H and Liu, J and Qiao, J and Liu, W and Shu, X and Sun, B and Liu, Y}, title = {Gut microbiota mediated the individualized efficacy of Temozolomide via immunomodulation in glioma.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {198}, pmid = {36927689}, issn = {1479-5876}, abstract = {BACKGROUND: Temozolomide (TMZ) is the preferred chemotherapy strategy for glioma therapy. As a second-generation alkylating agent, TMZ provides superior oral bio-availability. However, limited response rate (less than 50%) and high incidence of drug resistance seriously restricts TMZ's application, there still lack of strategies to increase the chemotherapy sensitivity.<br><br>METHODS: Luci-GL261 glioma orthotopic xenograft model combined bioluminescence imaging was utilized to evaluate the anti-tumor effect of TMZ and differentiate TMZ sensitive (S)/non-sensitive (NS) individuals. Integrated microbiomics and metabolomics analysis was applied to disentangle the involvement of gut bacteria in TMZ sensitivity. Spearman's correlation analysis was applied to test the association between fecal bacteria levels and pharmacodynamics indices. Antibiotics treatment combined TMZ treatment was used to confirm the involvement of gut microbiota in TMZ response. Flow cytometry&#xa0;analysis, ELISA and histopathology were used to explore the potential role of immunoregulation in gut microbiota mediated TMZ response.<br><br>RESULTS: Firstly, gut bacteria composition was significantly altered during glioma development and TMZ treatment. Meanwhile, in vivo anti-cancer evaluation suggested a remarkable difference in chemotherapy efficacy after TMZ administration. Moreover, 16s rRNA gene sequencing and non-targeted metabolomics analysis revealed distinct different gut microbiota and immune infiltrating state between TMZ sensitive and non-sensitive mice, while abundance of differential gut bacteria and related metabolites was significantly correlated with TMZ pharmacodynamics indices. Further verification suggested that gut microbiota deletion by antibiotics treatment could accelerate glioma development, attenuate TMZ efficacy and inhibit immune cells (macrophage and CD8&#x3b1;[+] T cell) recruitment.<br><br>CONCLUSIONS: The current study confirmed the involvement of gut microbiota in glioma development and individualized TMZ efficacy via immunomodulation, hence gut bacteria may serve as a predictive biomarker as well as a therapeutic target for clinical TMZ application.}, }
@article {pmid36927582, year = {2023}, author = {Cao, X and Yang, Y and Zhang, Y and Ji, R and Zhao, X and Zheng, W and Yang, A}, title = {Impact of Helicobacter pylori on the gastric microbiome in patients with chronic gastritis: a systematic review and meta-analysis protocol.}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e050476}, doi = {10.1136/bmjopen-2021-050476}, pmid = {36927582}, issn = {2044-6055}, abstract = {INTRODUCTION: Chronic gastritis is a common disease worldwide. Studies have consistently shown that chronic gastritis is usually associated with gastric microbial dysbiosis, especially the infection of Helicobacter pylori. However, the interaction between H. pylori and non-H. pylori bacteria in patients with chronic gastritis has not been clearly identified yet. Consequently, we designed a protocol for a systematic review and meta-analysis, which focused on identifying the changes in gastrointestinal microbiota composition between patients with H. pylori-infective and non-infective chronic gastritis.<br><br>METHOD AND ANALYSIS: We will search PubMed, EMBASE and Cochrane Library databases to retrieve observational studies on humans. The eligible studies must include data about the relative abundance of the gastrointestinal microbiome in patients with H. pylori-infective or non-infective chronic gastritis. Only the data of adults aged over 18 years will be analysed. Two researchers will extract the data independently, and Newcastle-Ottawa Scale will be used to assess the risk of bias. Random-effects model will be performed in quantitative analyses. Correlation analysis, bioinformatics analysis and function analysis will be performed.<br><br>DISCUSSION: Currently, numerous studies have revealed the role of H. pylori in chronic gastritis. However, the alterations of non-H. pylori bacteria in patients with chronic gastritis remain an open question. The results of our study might provide new insights into future diagnosis and treatments.<br><br>ETHICS AND DISSEMINATION: This study is based on published documents, unrelated to personal data, so ethical approval is not in need. The results of this study are expected to be published in journals or conference proceedings.<br><br>PROSPERO REGISTRATION NUMBER: CRD42020205260; Pre-results.}, }
@article {pmid36927522, year = {2023}, author = {Silamiķele, L and Saksis, R and Silamiķelis, I and Kotoviča, PP and Brīvība, M and Kalniņa, I and Kalniņa, Z and Fridmanis, D and Kloviņš, J}, title = {Spatial variation of the gut microbiome in response to long-term metformin treatment in high-fat diet-induced type 2 diabetes mouse model of both sexes.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2188663}, doi = {10.1080/19490976.2023.2188663}, pmid = {36927522}, issn = {1949-0984}, abstract = {Antidiabetic drug metformin alters the gut microbiome composition in the context of type 2 diabetes and other diseases; however, its effects have been mainly studied using fecal samples, which offer limited information about the intestinal site-specific effects of this drug. Our study aimed to characterize the spatial variation of the gut microbiome in response to metformin treatment by using a high-fat diet-induced type 2 diabetes mouse model of both sexes. Four intestinal parts, each at the luminal and mucosal layer level, were analyzed in this study by performing 16S rRNA sequencing covering six variable regions (V1-V6) of the gene and thus allowing to obtain in-depth information about the microbiome composition. We identified significant differences in gut microbiome diversity in each of the intestinal parts regarding the alpha and beta diversities. Metformin treatment altered the abundance of different genera in all studied intestinal sites, with the most pronounced effect in the small intestine, where Lactococcus increased remarkably. The abundance of Lactobacillus was substantially lower in male mice compared to female mice in all locations, in addition to an enrichment of opportunistic pathogens. Diet type and intestinal layer had significant effects on microbiome composition at each of the sites studied. We observed a different effect of metformin treatment on the analyzed subsets, indicating the multiple dimensions of metformin's effect on the gut microbiome.}, }
@article {pmid36927481, year = {2023}, author = {Cornelisse, VJ and Ong, JJ and Ryder, N and Ooi, C and Wong, A and Kenchington, P and Giola, M and Donovan, B and Dean, JA and Molina, JM and Medland, NA}, title = {Interim position statement on doxycycline post-exposure prophylaxis (Doxy-PEP) for the prevention of bacterial sexually transmissible infections in Australia and Aotearoa New Zealand - the Australasian Society for HIV, Viral Hepatitis and Sexual Health Medicine (ASHM).}, journal = {Sexual health}, volume = {}, number = {}, pages = {}, doi = {10.1071/SH23011}, pmid = {36927481}, issn = {1449-8987}, abstract = {Recent studies have provided evidence for the effectiveness of using doxycycline (Doxy-PEP) to prevent bacterial sexually transmissible infections (STI), namely chlamydia, gonorrhoea, and syphilis, among gay, bisexual, and other men who have sex with men who have experienced multiple STIs. However, there remain several unanswered questions around potential adverse outcomes from Doxy-PEP, including the possibility of inducing antimicrobial resistance in STIs and other organisms, and the possibility of disrupting the microbiome of people who choose to use Doxy-PEP. This interim position statement from the Australasian Society for HIV, Viral Hepatitis and Sexual Health Medicine aims to outline the current evidence for Doxy-PEP, and to highlight potential adverse outcomes, to enable clinicians to conduct evidence-based conversations with patients in Australia and Aotearoa New Zealand who intend to use Doxy-PEP.}, }
@article {pmid36927367, year = {2023}, author = {Hoang, T and Kim, M and Park, JW and Jeong, SY and Lee, J and Shin, A}, title = {Correction to: Dysbiotic microbiome variation in colorectal cancer patients is linked to lifestyles and metabolic diseases.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {72}, pmid = {36927367}, issn = {1471-2180}, }
@article {pmid36927287, year = {2023}, author = {Neves, LL and Hair, AB and Preidis, GA}, title = {A systematic review of associations between gut microbiota composition and growth failure in preterm neonates.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2190301}, doi = {10.1080/19490976.2023.2190301}, pmid = {36927287}, issn = {1949-0984}, abstract = {Growth failure is among the most prevalent and devastating consequences of prematurity. Up to half of all extremely preterm neonates struggle to grow despite modern nutrition practices. Although elegant preclinical models suggest causal roles for the gut microbiome, these insights have not yet translated into biomarkers that identify at-risk neonates or therapies that prevent or treat growth failure. This systematic review aims to identify features of the neonatal gut microbiota that are positively or negatively associated with early postnatal growth. We identified 860 articles, of which 14 were eligible for inclusion. No two studies used the same definitions of growth, ages at stool collection, and statistical methods linking microbiota to metadata. In all, 58 different taxa were associated with growth, with little consensus among studies. Two or more studies reported positive associations with Enterobacteriaceae, Bacteroides, Bifidobacterium, Enterococcus, and Veillonella, and negative associations with Citrobacter, Klebsiella, and Staphylococcus. Streptococcus was positively associated with growth in five studies and negatively associated with growth in three studies. To gain insight into how the various definitions of growth could impact results, we performed an exploratory secondary analysis of 245 longitudinally sampled preterm infant stools, linking microbiota composition to multiple clinically relevant definitions of neonatal growth. Within this cohort, every definition of growth was associated with a different combination of microbiota features. Together, these results suggest that the lack of consensus in defining neonatal growth may limit our capacity to detect consistent, meaningful clinical associations that could be leveraged into improved care for preterm neonates.}, }
@article {pmid36927206, year = {2023}, author = {Dougherty, MW and Jobin, C}, title = {Intestinal bacteria and colorectal cancer: etiology and treatment.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2185028}, doi = {10.1080/19490976.2023.2185028}, pmid = {36927206}, issn = {1949-0984}, abstract = {The etiology of colorectal cancer (CRC) is influenced by bacterial communities that colonize the gastrointestinal tract. These microorganisms derive essential nutrients from indigestible dietary or host-derived compounds and activate molecular signaling pathways necessary for normal tissue and immune function. Associative and mechanistic studies have identified bacterial species whose presence may increase CRC risk, including notable examples such as Fusobacterium nucleatum, Enterotoxigenic Bacteroides fragilis, and pks[+] E. coli. In recent years this work has expanded in scope to include aspects of host mutational status, intra-tumoral microbial heterogeneity, transient infection, and the cumulative influence of multiple carcinogenic bacteria after sequential or co-colonization. In this review, we will provide an updated overview of how host-bacteria interactions influence CRC development, how this knowledge may be utilized to diagnose or prevent CRC, and how the gut microbiome influences CRC treatment efficacy.}, }
@article {pmid36926875, year = {2023}, author = {Wang, H and Jurasinski, G and Täumer, J and Kuß, AW and Groß, V and Köhn, D and Günther, A and Urich, T}, title = {Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c07461}, pmid = {36926875}, issn = {1520-5851}, abstract = {Rewetted peatlands are reestablished hot spots for CH4 emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH4 fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH4 fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH4 fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH4 fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH4 turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.}, }
@article {pmid36926663, year = {2023}, author = {Nikitina, D and Lehr, K and Vilchez-Vargas, R and Jonaitis, LV and Urba, M and Kupcinskas, J and Skieceviciene, J and Link, A}, title = {Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals.}, journal = {World journal of gastroenterology}, volume = {29}, number = {7}, pages = {1202-1218}, pmid = {36926663}, issn = {2219-2840}, abstract = {BACKGROUND: Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis, and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease. There are two common modalities for microbiome analysis: DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing. The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer (GC) are poorly studied.<br><br>AIM: To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.<br><br>METHODS: In this study, 316 DNA and RNA samples extracted from 105 individual stomach biopsies were included. The study cohort consisted of 29 healthy control individuals and 76 patients with GC. Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue. From the controls, healthy stomach mucosa biopsies were collected. From all biopsies RNA and DNA were extracted. RNA was reverse transcribed into cDNA. V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform. Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.<br><br>RESULTS: Microbial analysis revealed that only a portion of phylotypes (18%-30%) overlapped between microbial profiles obtained from DNA and RNA samples. Detailed analysis revealed differences between GC and controls depending on the chosen modality, identifying 17 genera at the DNA level and 27 genera at the RNA level. Ten of those bacteria were found to be different from the control group at both levels. The key taxa showed congruent results in various tests used; however, differences in 7 bacteria taxa were found uniquely only at the DNA level, and 17 uniquely only at the RNA level. Furthermore, RNA sequencing was more sensitive for detecting differences in bacterial richness, as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group (control, tumor, and tumor adjacent) were found differences between DNA and RNA bacterial profiles.<br><br>CONCLUSION: Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile, as well as on the identified differences between case and control.}, }
@article {pmid36925756, year = {2023}, author = {Macaya-Sanz, D and Witzell, J and Collada, C and Gil, L and Martín, JA}, title = {Core endophytic mycobiome in Ulmus minor and its relation to Dutch elm disease resistance.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1125942}, pmid = {36925756}, issn = {1664-462X}, abstract = {The core microbiota of plants exerts key effects on plant performance and resilience to stress. The aim of this study was to identify the core endophytic mycobiome in U. minor stems and disentangle associations between its composition and the resistance to Dutch elm disease (DED). We also defined its spatial variation within the tree and among distant tree populations. Stem samples were taken i) from different heights of the crown of a 168-year-old elm tree, ii) from adult elm trees growing in a common garden and representing a gradient of resistance to DED, and iii) from trees growing in two distant natural populations, one of them with varying degrees of vitality. Endophyte composition was profiled by high throughput sequencing of the first internal transcribed spacer region (ITS1) of the ribosomal DNA. Three families of yeasts (Buckleyzymaceae, Trichomeriaceae and Bulleraceae) were associated to DED-resistant hosts. A small proportion (10%) of endophytic OTUs was almost ubiquitous throughout the crown while tree colonization by most fungal taxa followed stochastic patterns. A clear distinction in endophyte composition was found between geographical locations. By combining all surveys, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.}, }
@article {pmid36924444, year = {2023}, author = {Rieder, F and Mukherjee, PK}, title = {Skin microbiome in atopic dermatitis: New insights from clinical trials.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {37}, number = {4}, pages = {649-650}, doi = {10.1111/jdv.18991}, pmid = {36924444}, issn = {1468-3083}, }
@article {pmid36924244, year = {2023}, author = {He, D and Wang, X and Ye, J and Yao, Y and Wen, Y and Jia, Y and Meng, P and Yang, X and Wu, C and Ning, Y and Wang, S and Zhang, F}, title = {Evaluating the genetic interaction effects of gut microbiome and diet on the risk of neuroticism in the UK Biobank cohort.}, journal = {Psychiatric genetics}, volume = {33}, number = {2}, pages = {59-68}, doi = {10.1097/YPG.0000000000000334}, pmid = {36924244}, issn = {1473-5873}, abstract = {OBJECTIVES: In this study designed to investigate the effect of diet and gut microbiome on neuropsychiatric disorders, we explored the mechanisms of the interaction between diet and gut microbiome on the risk of neuroticism.<br><br>METHODS: First, using the individual genotype data from the UK Biobank cohort (N&#x2009;=&#x2009;306&#x2009;165), we calculated the polygenic risk score (PRS) based on 814 dietary habits single nucleotide polymorphisms (SNPs), 21 diet compositions SNPs and 1001 gut microbiome SNPs, respectively. Gut microbiome and diet-associated SNPs were collected from three genome-wide association studies (GWAS), including the gut microbiome (N&#x2009;=&#x2009;3890), diet compositions (over 235&#x2009;000 subjects) and dietary habits (N&#x2009;=&#x2009;449&#x2009;210). The neuroticism score was calculated by 12 questions from the Eysenck Personality Inventory Neuroticism scale. Then, regression analysis was performed to evaluate the interaction effects between diet and the gut microbiome on the risk of neuroticism.<br><br>RESULTS: Our studies demonstrated multiple candidate interactions between diet and gut microbiome, such as protein vs. Bifidobacterium (&#x3b2;&#x2009;=&#x2009;4.59&#x2009;&#xd7;&#x2009;10-3; P&#x2009;=&#x2009;9.45&#x2009;&#xd7;&#x2009;10-3) and fat vs. Clostridia (&#x3b2;&#x2009;=&#x2009;3.67&#x2009;&#xd7;&#x2009;10-3; P&#x2009;=&#x2009;3.90&#x2009;&#xd7;&#x2009;10-2). In addition, pieces of fresh fruit per day vs. Ruminococcus (&#x3b2;&#x2009;=&#x2009;-5.79&#x2009;&#xd7;&#x2009;10-3, P&#x2009;=&#x2009;1.10&#x2009;&#xd7;&#x2009;10-3) and pieces of dried fruit per day vs. Clostridiales (&#x3b2;&#x2009;=&#x2009;-5.63&#x2009;&#xd7;&#x2009;10-3, P&#x2009;=&#x2009;1.49&#x2009;&#xd7;&#x2009;10-3) were found to be negatively associated with neuroticism in fruit types. We also identified several positive interactions, such as tablespoons of raw vegetables per day vs. Veillonella (&#x3b2;&#x2009;=&#x2009;5.92&#x2009;&#xd7;&#x2009;10-3, P&#x2009;=&#x2009;9.21&#x2009;&#xd7;&#x2009;10-4) and cooked vegetables per day vs. Acidaminococcaceae (&#x3b2;&#x2009;=&#x2009;5.69&#x2009;&#xd7;&#x2009;10-3, P&#x2009;=&#x2009;1.24&#x2009;&#xd7;&#x2009;10-3).<br><br>CONCLUSIONS: Our results provide novel clues for understanding the roles of diet and gut microbiome in the development of neuroticism.}, }
@article {pmid36923929, year = {2023}, author = {Shim, JA and Ryu, JH and Jo, Y and Hong, C}, title = {The role of gut microbiota in T cell immunity and immune mediated disorders.}, journal = {International journal of biological sciences}, volume = {19}, number = {4}, pages = {1178-1191}, pmid = {36923929}, issn = {1449-2288}, abstract = {Gut microbiota was only considered as a commensal organism that aids in digestion, but recent studies revealed that the microbiome play a critical role in both physiological and pathological immune system. The gut microbiome composition is altered by environmental factors such as diet and hygiene, and the alteration affects immune cells, especially T cells. Advanced genomic techniques in microbiome research defined that specific microbes regulate T cell responses and the pathogenesis of immune-mediated disorders. Here, we review features of specific microbes-T cell crosstalk and relationship between the microbes and immunopathogenesis of diseases including in cancers, autoimmune disorders and allergic inflammations. We also discuss the limitations of current experimental animal models, cutting-edge developments and current challenges to overcome in the field, and the possibility of considering gut microbiome in the development of new drug.}, }
@article {pmid36923594, year = {2023}, author = {Chen, P and Wang, K and Zhuang, M and Fu, X and Liu, S and Chen, M and Lei, Y}, title = {An insight into gut microbiota and metabolites in the mice with adenomyosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1075387}, pmid = {36923594}, issn = {2235-2988}, abstract = {BACKGROUND: Adenomyosis (AM) is a benign uterine disease characterized pathologically by the invasion of endometrial tissue into the myometrium. The pathogenesis of AM is still far from clear. Although the gut microbiome and metabolomics are thought to contribute to a variety of diseases, the role of them in AM has not been revealed.<br><br>OBJECTIVE: To investigate changes in the gut microbiota and derived metabolites in AM mice.<br><br>METHOD: Female ICR mice were randomly assigned to AM and control groups, and pituitary transplantation was employed to perform AM modeling. Then, the fecal samples were obtained for microbial (16S rRNA gene sequencing) and metabolomic (liquid chromatography mass spectrometry, LC-MS) analysis.<br><br>RESULT: The results of gut microbiota analysis showed that the intestinal microbiota composition of AM mice was altered. The ratio of Firmicutes/Bacteroidetes and the relative abundance of Lactobacillus in AM group increased compared with the control group. Sixty differential expressed metabolites were identified in intestinal metabolites, mainly involved in steroid hormone biosynthesis, cysteine and methionine metabolism, and alanine, aspartate, and glutamate metabolism. Further, correlation analysis verified that L-methionine and L-cystine were negatively correlated with Bacteroides and positively correlated with Desulfovibrio. The Pregnenolone, Androsterone glucuronide, and Testosterone glucuronide were negatively correlated with Unidentified_Ruminococcaceae and Alistipes, whereas they positively correlated with Bacteroides.<br><br>CONCLUSION: AM mice have a unique gut microbiome and intestinal metabolites.}, }
@article {pmid36923591, year = {2023}, author = {Zhang, J and Zheng, YC and Chu, YL and Cui, XM and Wei, R and Bian, C and Liu, HB and Yao, NN and Jiang, RR and Huo, QB and Yuan, TT and Li, J and Zhao, L and Li, LF and Wang, Q and Wei, W and Zhu, JG and Chen, MC and Gao, Y and Wang, F and Ye, JL and Song, JL and Jiang, JF and Lam, TT and Ni, XB and Jia, N}, title = {Skin infectome of patients with a tick bite history.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1113992}, pmid = {36923591}, issn = {2235-2988}, abstract = {INTRODUCTION: Ticks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people.<br><br>METHODS: A total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings.<br><br>RESULTS: Four bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins.<br><br>DISCUSSION: Advances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients' skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness.}, }
@article {pmid36923492, year = {2023}, author = {Peng, Y and Chiu, ATG and Li, VWY and Zhang, X and Yeung, WL and Chan, SHS and Tun, HM}, title = {The role of the gut-microbiome-brain axis in metabolic remodeling amongst children with cerebral palsy and epilepsy.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1109469}, pmid = {36923492}, issn = {1664-2295}, abstract = {BACKGROUND: Epilepsy-associated dysbiosis in gut microbiota has been previously described, but the mechanistic roles of the gut microbiome in epileptogenesis among children with cerebral palsy (CP) have yet to be illustrated.<br><br>METHODS: Using shotgun metagenomic sequencing coupled with untargeted metabolomics analysis, this observational study compared the gut microbiome and metabolome of eight children with non-epileptic cerebral palsy (NECP) to those of 13 children with cerebral palsy with epilepsy (CPE). Among children with CPE, 8 had drug-sensitive epilepsy (DSE) and five had drug-resistant epilepsy (DRE). Characteristics at enrollment, medication history, and 7-day dietary intake were compared between groups.<br><br>RESULTS: At the species level, CPE subjects had significantly lower abundances of Bacteroides fragilis and Dialister invisus but higher abundances of Phascolarctobacterium faecium and Eubacterium limosum. By contrast, DRE subjects had a significantly higher colonization of Veillonella parvula. Regarding microbial functional pathways, CPE subjects had decreased abundances of pathways for serine degradation, quinolinic acid degradation, glutamate degradation I, glycerol degradation, sulfate reduction, and nitrate reduction but increased abundances of pathways related to ethanol production. As for metabolites, CPE subjects had higher concentrations of kynurenic acid, 2-oxindole, dopamine, 2-hydroxyphenyalanine, 3,4-dihydroxyphenylglycol, L-tartaric acid, and D-saccharic acid; DRE subjects had increased concentrations of indole and homovanilic acid.<br><br>CONCLUSIONS: In this study, we found evidence of gut dysbiosis amongst children with cerebral palsy and epilepsy in terms of gut microbiota species, functional pathways, and metabolites. The combined metagenomic and metabolomic analyses have shed insights on the potential roles of B. fragilis and D. invisus in neuroprotection. The combined analyses have also provided evidence for the involvement of GMBA in the epilepsy-related dysbiosis of kynurenine, serotonin, and dopamine pathways and their complex interplay with neuroimmune and neuroendocrinological pathways.}, }
@article {pmid36923410, year = {2023}, author = {Humberg, A and Neuenburg, L and Boeckel, H and Fortmann, MI and Härtel, C and Herting, E and Hinrichs, H and Rademacher, F and Harder, J}, title = {Antimicrobial skin peptides in premature infants: Comparison with term infants and impact of perinatal factors.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1093340}, pmid = {36923410}, issn = {1664-3224}, abstract = {INTRODUCTION: Preterm infants have an immature epidermis barrier function that may lead to an increased permeability to pathogens. On the surface of the human skin, antimicrobial peptides (AMPs) are important molecules of the innate immune system, have broad antimicrobial properties, and provide an essential role in integrity of the microbiome. Given the marked susceptibility of preterm infants to infection, we hypothesize a decreased expression of AMPs on the skin of preterm infants.<br><br>MATERIALS AND METHODS: In a prospective single-center study with 35 preterm and 20 term infants, we analyzed skin rinsing probes for the presence of the AMPs psoriasin (S100A7) and ribonuclease 7 (RNase 7) via enzyme-linked immunosorbent assay. Samples were taken from preterm infants < 34 0/7 weeks gestational age (mean &#xb1; SD gestational age, 28.8 &#xb1; 2.4 weeks) on days 0, 7, 14, and 28 after birth. Term infants (> 36 6/7 weeks) (controls) were washed on days 0 and 28.<br><br>RESULTS: Psoriasin and RNase 7 were both expressed on skin of preterm and term infants and increased in concentration significantly over time. RNase 7 was more expressed in term infants on day 0 [preterm = 1.1 (0.7-2.9) vs. term = 2.0 (1.1-3.4) ng/ml, p = 0.017]. On day 28, premature infants showed higher values of psoriasin [preterm = 10.9 (5.6-14.2) vs. term = 6.3 (3.4-9.0) ng/ml, p < 0.001]. Notably, preterm infants with infectious or inflammatory context driven by histological proof of chorioamnionitis and early-onset or late-onset sepsis had higher concentrations of psoriasin as compared with non-affected preterm infants. After exclusion of infants with inflammatory hit, median concentrations of RNase 7 and psoriasin did not differ between preterm and full-term infants on days 0 and 28.<br><br>DISCUSSION: Psoriasin and RNase 7 concentrations increase over time on the skin of newborn infants and seem to play a role in the first defense against infection. This is of particularly interest as the role of AMPs on a maturing skin microbiome and its possible new prevention strategies is unclear and needs to be determined.}, }
@article {pmid36922976, year = {2023}, author = {Rydal, MP and Gambino, M and Castro-Mejia, JL and Poulsen, LL and Jørgensen, CB and Nielsen, JP}, title = {Post-weaning diarrhea in pigs from a single Danish production herd was not associated with the pre-weaning fecal microbiota composition and diversity.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1108197}, pmid = {36922976}, issn = {1664-302X}, abstract = {INTRODUCTION: The association between the porcine pre-weaning gut microbiota composition and diversity, and subsequent post-weaning diarrhea (PWD) susceptibility is currently being studied. In this longitudinal study, we examined the association between pre-weaning fecal microbiome composition and diversity, and PWD development in a Danish sow herd.<br><br>METHODS: Forty-five pigs were followed from birth until 7 days after weaning (post-natal day (PND) 33). At PND 33, the pigs were categorized as PWD cases or healthy controls based on fecal consistency. We compared their fecal microbiomes at PND 8, late lactation (PND 27) and 7 days post weaning (PND 33) using 16S rRNA V3 region high-throughput sequencing. At PND 27 and 33, we also weighed the pigs, assessed fecal shedding of hemolytic Escherichia coli by culture and characterized hemolytic isolates by ETEC virulence factors with PCR and by whole genome sequencing.<br><br>RESULTS: A total of 25 out of 45 pigs developed PWD and one Enterotoxigenic E. coli strain with F18:LT:EAST1 virotype was isolated from most pigs. At PND 33, we found differences in beta diversity between PWD and healthy pigs (R[2] = 0.027, p = 0.009) and that body weight was associated with both alpha and beta diversity. Pre-weaning fecal microbiome diversity did not differ between PWD and healthy pigs and we found no significant, differentially abundant bacteria between them.<br><br>CONCLUSION: In the production herd under study, pre-weaning fecal microbiome diversity and composition were not useful indicators of PWD susceptibility.}, }
@article {pmid36922974, year = {2023}, author = {Bruno, A and Cafiso, A and Sandionigi, A and Galimberti, A and Magnani, D and Manfrin, A and Petroni, G and Casiraghi, M and Bazzocchi, C}, title = {Red mark syndrome: Is the aquaculture water microbiome a keystone for understanding the disease aetiology?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1059127}, pmid = {36922974}, issn = {1664-302X}, abstract = {Aquaculture significantly contributes to the growing demand for food worldwide. However, diseases associated with intensive aquaculture conditions, especially the skin related syndromes, may have significant implications on fish health and industry. In farmed rainbow trout, red mark syndrome (RMS), which consists of multiple skin lesions, currently lacks recognized aetiological agents, and increased efforts are needed to elucidate the onset of these conditions. Most of the past studies were focused on analyzing skin lesions, but no study focused on water, a medium constantly interacting with fish. Indeed, water tanks are environmental niches colonized by microbial communities, which may be implicated in the onset of the disease. Here, we present the results of water and sediment microbiome analyses performed in an RMS-affected aquaculture facility, bringing new knowledge about the environmental microbiomes harbored under these conditions. On the whole, no significant differences in the bacterial community structure were reported in RMS-affected tanks compared to the RMS-free ones. However, we highlighted significant differences in microbiome composition when analyzing different samples source (i.e., water and sediments). Looking at the finer scale, we measured significant changes in the relative abundances of specific taxa in RMS-affected tanks, especially when analyzing water samples. Our results provide worthwhile insight into a mostly uncharacterized ecological scenario, aiding future studies on the aquaculture built environment for disease prevention and monitoring.}, }
@article {pmid36922970, year = {2023}, author = {Zeng, Y and Cao, S and Yang, H}, title = {Roles of gut microbiome in epilepsy risk: A Mendelian randomization study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115014}, pmid = {36922970}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies have suggested an association between gut microbiomes (GMs) and epilepsy. However, the GM taxa identified in different studies are variable. In addition, observational studies cannot indicate causality. Therefore, our study aimed to explore the causal association of GMs with epilepsy and identify the most influential GM taxa.<br><br>METHODS: We conducted a Mendelian randomization (MR) study using summary statistics from genome-wide association studies (GWAS) of 211 GM taxa and epilepsy. The GWAS summary statistics for 211 GM taxa (from phylum to genus level) were generated by the MiBioGen consortium, while the FinnGen consortium provided the GWAS summary statistics for epilepsy. The primary analytical method to assess causality was the inverse-variance weighted (IVW) approach. To complement the IVW method, we also applied four additional MR methods: MR-Egger, weighted median, simple mode, and weighted. In addition, we conducted sensitivity analyses using Cochrane's Q-test, MR-Egger intercept test, MR-PRESSO global test, and leave-one-out analysis.<br><br>RESULTS: We evaluated the causal effect of 211 GM taxa (from phylum to genus level) on epilepsy, generalized epilepsy, and focal epilepsy. After using the Bonferroni method for multiple testing correction, Class Betaproteobacteria [odds ratio (OR)&#x2009;=&#x2009;1.357, 95% confidence interval (CI): 1.126-1.635, p&#x2009;=&#x2009;0.001] and Order Burkholderiales (OR&#x2009;=&#x2009;1.336, 95% CI: 1.112-1.606, p =&#x2009;0.002). In addition, 21 nominally significant causal relationships were also identified. Further, the MR-Egger intercept test and MR-PRESSO global test suggested that our MR analysis was unaffected by horizontal pleiotropy (p&#x2009;>&#x2009;0.05). Finally, the leave-one-out analysis suggested the robustness of the results.<br><br>CONCLUSION: Through the MR study, we analyzed the causal relationship of 211 GM taxa with epilepsy and determined the specific intestinal flora associated with increased epilepsy risk. Our findings may provide helpful biomarkers for disease progression and potential candidate therapeutic targets for epilepsy. In addition, in-depth analysis of large-scale microbiome GWAS datasets based on metagenomics sequencing is necessary for future studies.}, }
@article {pmid36922895, year = {2023}, author = {Guo, K and Figueroa-Romero, C and Noureldein, M and Hinder, LM and Sakowski, SA and Rumora, AE and Petit, H and Savelieff, MG and Hur, J and Feldman, EL}, title = {Gut microbiota in a mouse model of obesity and peripheral neuropathy associated with plasma and nerve lipidomics and nerve transcriptomics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {52}, pmid = {36922895}, issn = {2049-2618}, support = {U24DK115255/NH/NIH HHS/United States ; R24DK082841/NH/NIH HHS/United States ; R01ES030049/NH/NIH HHS/United States ; R21NS102924/NH/NIH HHS/United States ; R01ES030049/NH/NIH HHS/United States ; F32DK112642/NH/NIH HHS/United States ; R24DK082841/NH/NIH HHS/United States ; R01ES030049/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Peripheral neuropathy (PN) is a common complication in obesity, prediabetes, and type 2 diabetes, though its pathogenesis remains incompletely understood. In a murine high-fat diet (HFD) obesity model of PN, dietary reversal (HFD-R) to a low-fat standard diet (SD) restores nerve function and the nerve lipidome to normal. As the gut microbiome represents a potential link between dietary fat intake and nerve health, the current study assessed shifts in microbiome community structure by 16S rRNA profiling during the paradigm of dietary reversal (HFD-R) in various gut niches. Dietary fat content (HFD versus SD) was also correlated to gut flora and metabolic and PN phenotypes. Finally, PN-associated microbial taxa that correlated with the plasma and sciatic nerve lipidome and nerve transcriptome were used to identify lipid species and genes intimately related to PN phenotypes.<br><br>RESULTS: Microbiome structure was altered in HFD relative to SD but rapidly reversed with HFD-R. Specific taxa variants correlating positively with metabolic health associated inversely with PN, while specific taxa negatively linked to metabolic health positively associated with PN. In HFD, PN-associated taxa variants, including Lactobacillus, Lachnoclostridium, and Anaerotruncus, also positively correlated with several lipid species, especially elevated plasma sphingomyelins and sciatic nerve triglycerides. Negative correlations were additionally present with other taxa variants. Moreover, relationships that emerged between specific PN-associated taxa variants and the sciatic nerve transcriptome were related to inflammation, lipid metabolism, and antioxidant defense pathways, which are all established in PN pathogenesis.<br><br>CONCLUSIONS: The current results indicate that microbiome structure is altered with HFD, and that certain taxa variants correlate with metabolic health and PN. Apparent links between PN-associated taxa and certain lipid species and nerve transcriptome-related pathways additionally provide insight into new targets for microbiota and the associated underlying mechanisms of action in PN. Thus, these findings strengthen the possibility of a gut-microbiome-peripheral nervous system signature in PN and support continuing studies focused on defining the connection between the gut microbiome and nerve health to inform mechanistic insight and therapeutic opportunities. Video Abstract.}, }
@article {pmid36922761, year = {2023}, author = {Marynowska, M and Sillam-Dussès, D and Untereiner, B and Klimek, D and Goux, X and Gawron, P and Roisin, Y and Delfosse, P and Calusinska, M}, title = {A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {115}, pmid = {36922761}, issn = {1471-2164}, abstract = {BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.<br><br>RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.<br><br>CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.}, }
@article {pmid36922572, year = {2023}, author = {Michishita, R and Shimoda, M and Furukawa, S and Uehara, T}, title = {Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4297}, pmid = {36922572}, issn = {2045-2322}, abstract = {The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.}, }
@article {pmid36922385, year = {2023}, author = {Yang, S and Fan, Z and Li, J and Wang, X and Lan, Y and Yue, B and He, M and Zhang, A and Li, J}, title = {Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta).}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2188848}, doi = {10.1080/19490976.2023.2188848}, pmid = {36922385}, issn = {1949-0984}, abstract = {Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.}, }
@article {pmid36921834, year = {2023}, author = {Chen, Y and Pei, C and Chen, Y and Xiao, X and Zhang, X and Cai, K and Deng, S and Liang, R and Xie, Z and Li, P and Liao, Q}, title = {Kidney tea ameliorates hyperuricemia in mice via altering gut microbiota and restoring metabolic profile.}, journal = {Chemico-biological interactions}, volume = {}, number = {}, pages = {110449}, doi = {10.1016/j.cbi.2023.110449}, pmid = {36921834}, issn = {1872-7786}, abstract = {Clerodendranthus spicatus (Thunb.) C. Y. Wu, also known as kidney tea (KT), has been widely employed in kidney protection in Chinese Medicine. It has been reported that KT can lower uric acid (UA) and mitigate gout, while the mechanism remains to be elucidated. Given the close relationship between hyperuricemia (HUA), intestinal flora and host metabolism, this study aimed to explore the mechanism by which KT lowers UA from the perspective of the fecal microbiome and metabolome. Initially, mice were intraperitoneally injected with potassium oxonate to induce the HUA model. The results showed that KT markedly reduced the serum level of UA and impaired renal damage in HUA mice. Subsequently, the result of 16S rRNA gene sequencing analysis indicated that KT administration appeared a significant improvement in the structure of the intestinal flora, especially increased the abundances of Roseburia and Enterorhabdus, while decreased the abundances of Ileibacterium and UBA1819. Moreover, the levels of differential metabolites (including twenty-five in feces and eight in serum) identified by untargeted metabolomics returned to normal after KT intervention. Taken together, the mechanism of KT in alleviating HUA is related to the regulation of the intestinal flora and the remodeling of metabolic disorders, which will lay a theoretical foundation for KT as a UA-lowering drug.}, }
@article {pmid36921804, year = {2023}, author = {Wang, Y and Lindemann, SR and Cross, TL and Tang, M and Clark, CM and Campbell, WW}, title = {Effects of adding lean red meat to a U.S.-Style Healthy Vegetarian Dietary Pattern on gut microbiota and cardiovascular risk factors in young adults: a crossover randomized-controlled trial.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.03.013}, pmid = {36921804}, issn = {1541-6100}, abstract = {BACKGROUND: Limited research evidence exists on the effects of red meat on gut microbiota in human adults.<br><br>OBJECTIVE: We aim to assess the effects of consuming a Healthy U.S.-Style Dietary Pattern (HDP), without or with unprocessed or processed lean red meat, on gut microbiota and fecal short-chain fatty acids levels (SCFA) in healthy young adults. Secondary outcomes are cardiovascular disease risk factors.<br><br>METHODS: We conducted a randomized-controlled, cross-over trial with three 3-week dietary interventions, each separated by a 5-week washout period with habitual dietary intake. Nineteen participants (8 females, age 26 &#xb1; 4 years old, BMI 23 &#xb1; 3 kg/m[2]) consumed three study diets in random order: 1) healthy lacto-ovo vegetarian diet (LOV); 2) LOV plus 3 ounces/day of cooked unprocessed lean red meat (URM); and 3) LOV plus 3 ounces/day of cooked processed lean red meat (PRM). Fecal and fasting blood samples were collected before and during the last 2 weeks of each intervention. We measured fecal bacterial community structure using 16S rRNA amplicon sequencing (V4 region, primers 515F-806R). Community diversity, structure, and taxonomic composition were computed using Mothur v.1.44.3.<br><br>RESULTS: The addition of unprocessed or processed lean red meats to a LOV HDP did not influence short-term changes in bacterial taxonomic composition. Independent of red meat intake, the HDP led to changes in 23 bacteria; reductions in serum total cholesterol (TC) and LDL-C concentrations; but no changes in fecal SCFA, serum triglycerides, HDL-C, TC/HDL-C ratio, or blood pressures. With data from all 3 diet interventions combined, changes in some bacteria were associated with improvements in TC, LDL-C, HDL-C, TC/HDL-C ratio, and triglycerides.<br><br>CONCLUSIONS: Healthy young adults who adopt a HDP that may be vegetarian or omnivorous only including lean red meat experience short-term changes in gut microbial composition, which associate with improvements in multiple lipid-related cardiovascular risk factors.<br><br>NCT03885544, https://clinicaltrials.gov/ct2/show/NCT03885544?cond=NCT03885544&amp;draw=2&amp;rank=1.}, }
@article {pmid36921627, year = {2023}, author = {Maitz, J and Merlino, J and Rizzo, S and McKew, G and Maitz, P}, title = {Burn wound infections microbiome and novel approaches using therapeutic microorganisms in burn wound infection control.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {114769}, doi = {10.1016/j.addr.2023.114769}, pmid = {36921627}, issn = {1872-8294}, }
@article {pmid36921549, year = {2023}, author = {Bortoluzzi, C and Tamburini, I and Geremia, J}, title = {Microbiome modulation, microbiome protein metabolism index, and growth performance of broilers supplemented with a precision biotic.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102595}, doi = {10.1016/j.psj.2023.102595}, pmid = {36921549}, issn = {1525-3171}, abstract = {The objectives of the present studies were to evaluate: 1) the in vivo impact of the supplementation with a precision biotic (PB) on the growth performance and microbiome modulation of broiler chickens; 2) the role of PB on the modulation of functional pathways of the microbiome collected from animals with low and high body weight gain, and 3) to develop a Microbiome Protein Metabolism Index (MPMI) derived from gut metagenomic data to link microbial protein metabolism with performance. The in vivo work consisted of 2 experiments with 2 treatments: Control vs. PB at 1.1 kg/MT of PB with 21 or 14 replicates of 40 birds per replicate, in experiments 1 and 2, respectively. Growth performance was evaluated in both experiments, and from experiment 1, cecal samples from one bird/replicate was collected on d 21 and 42 (n = 21/treatment) to evaluate the microbiome through whole genome sequencing. In the ex vivo assay, 6 cecal samples were collected from low body weight (BW) birds (at 10% below average), and 6 samples from high BW birds (at least 10% above average). The samples were incubated in the presence or absence of PB. After incubation, DNA was isolated to develop a functional genomic assay and the supernatant was separated to measure short-chain fatty acid (SCFA) production. The MPMI is the sum of beneficial genes in the pathways related to protein metabolism. In the in vivo grow out experiments, it was observed that the supplementation improved the BW gain by 3% in both studies, and the corrected feed conversion ratio (cFCR) by 3.7 and 3.4% in studies 1 and 2, respectively (P < 0.05). The functional microbiome analysis revealed that the PB shifted the microbiome pathways toward a beneficial increase in protein utilization, as shown by higher MPMI. In the ex vivo experiment, the PB increased the abundance of genes related to the beneficial metabolism of protein (quantitative MPMI), and the concentration of SCFA, regardless of the underline BW of the birds. Taken together, the microbiome metabolic shift observed in the in vivo study and higher MPMI, plus the observations from the ex vivo assay with higher SFCA production, may explain the improvement in growth performance obtained with the supplementation of PB.}, }
@article {pmid36921537, year = {2023}, author = {Chen, H and Kan, Q and Zhao, L and Ye, G and He, X and Tang, H and Shi, F and Zou, Y and Liang, X and Song, X and Liu, R and Luo, J and Li, Y}, title = {Prophylactic effect of Tongxieyaofang polysaccharide on depressive behavior in adolescent male mice with chronic unpredictable stress through the microbiome-gut-brain axis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {161}, number = {}, pages = {114525}, doi = {10.1016/j.biopha.2023.114525}, pmid = {36921537}, issn = {1950-6007}, abstract = {Major depression disorder is more common among adolescents and is a primary reason for suicide in adolescents. Some antidepressants are ineffective and may possess side effects. Therefore, developing an adolescent antidepressant is the need of the hour. We designed the stress model of adolescent male mice induced by chronic unpredictable stress (CUS). The mice were treated using Tongxieyaofang neutral polysaccharide (TXYF-NP), Tongxieyaofang acidic polysaccharide (TXYF-AP), TXYF-AP + TXYF-NP and fructooligosaccharide + galactooligosaccharides to determine their body weight, behavior, and serum hormone levels. RT-qPCR was used to detect the gene expression of Crhr1, Nr3c1, and Nr3c2 in the hypothalamus and hippocampus and the gene expression of glutamic acid and γ-aminobutyric acid-related receptors in the hippocampus. RT-qPCR, Western blot, and ELISA detected tryptophan metabolism in the colon, serum, and hippocampus. 16s rDNA helped sequence colon microflora, and non-targeted metabolomics enabled the collection of metabolic profiles of colon microflora. In adolescent male mice, CUS induced depression-like behavior, hypothalamic-pituitary-adrenal axis hyperactivity, hippocampal tissue damage, abnormal expression of its related receptors, and dysregulation of tryptophan metabolism. The 16s rDNA and non-targeted metabolomics revealed that CUS led to colon microflora disorder and bile acid metabolism abnormality. Tongxieyaofang polysaccharide could improve the bacterial community and bile acid metabolism disorder by upregulating the relative abundance of Lactobacillus gasseri, Lachnospiraceae bacterium 28-4, Bacteroides and Ruminococcaceae UCG-014 while preventing CUS-induced changes. TXYF-P can inhibit depression-like behavior due to CUS by regulating colonic microflora and restoring bile acid metabolism disorder. Thus, based on the different comparisons, TXYF-NP possessed the best effect.}, }
@article {pmid36921399, year = {2023}, author = {Karim, MR and Iqbal, S and Mohammad, S and Lee, JH and Jung, D and Mathiyalagan, R and Yang, DC and Yang, DU and Kang, SC}, title = {A review on Impact of dietary interventions, drugs, and traditional herbal supplements on the gut microbiome.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127346}, doi = {10.1016/j.micres.2023.127346}, pmid = {36921399}, issn = {1618-0623}, abstract = {The gut microbiome is the community of healthy, and infectious organisms in the gut and its interaction in the host gut intestine (GI) environment. The balance of microbial richness with beneficial microbes is very important to perform healthy body functions like digesting food, controlling metabolism, and precise immune function. Alternately, this microbial dysbiosis occurs due to changes in the physiochemical condition, substrate avidity, and drugs. Moreover, various categories of diet such as "plant-based", "animal-based", "western", "mediterranean", and various drugs (antibiotic and common drugs) also contribute to maintaining microbial flora inside the gut. The imbalance (dysbiosis) in the microbiota of the GI tract can cause several disorders (such as diabetes, obesity, cancer, inflammation, and so on). Recently, the major interest is to use prebiotic, probiotic, postbiotic, and herbal supplements to balance such microbial community in the GI tract. But, there has still a large gap in understanding the microbiome function, and its relation to the host diet, drugs, and herbal supplements to maintain the healthy life of the host. So, the present review is about the updates on the microbiome concerns related to diet, drug, and herbal supplements, and also gives research evidence to improve our daily habits regarding diet, drugs, and herbal supplements. Because our regular dietary plan and traditional herbal supplements can improve our health by balancing the bacteria in our gut.}, }
@article {pmid36920665, year = {2023}, author = {Costa, CJ and Cohen, MW and Goldberg, DC and Mellado, W and Willis, DE}, title = {Nicotinamide Riboside Improves Enteric Neuropathy in Streptozocin-Induced Diabetic Rats Through Myenteric Plexus Neuroprotection.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {36920665}, issn = {1573-2568}, support = {NR010797/NR/NINR NIH HHS/United States ; }, abstract = {BACKGROUND: Diabetes Mellitus causes a systemic oxidative stress due in part to the hyperglycemia and the reactive oxygen species generated. Up to 75% of diabetic patients present with an autonomic neuropathy affecting the Enteric Nervous System. Deficits in the human population are chronic dysmotilities with either increased (i.e., constipation) or decreased (i.e., diarrhea) total gastrointestinal transit times. These are recapitulated in the streptozocin-induced diabetic rat, which is a model of Type I Diabetes Mellitus.<br><br>AIMS: Examine the effects that a precursor of nicotinamide adenosine dinucleotide (NAD), nicotinamide riboside (NR), had on the development of dysmotility in induced diabetic rats and if fecal microbiota transplant (FMT) could produce the same results.<br><br>MATERIALS AND METHODS: Utilizing a 6-week treatment paradigm, NR was administered intraperitoneally every 48&#xa0;h. Total gastrointestinal transit time was assessed weekly utilizing the carmine red method. Three weeks following hyperglycemic induction, FMT was performed between NR-treated animals and untreated animals.<br><br>SIGNIFICANT RESULTS: There is improvement in overall gastrointestinal transit time with the use of NR. 16S microbiome sequencing demonstrated decreased alpha and beta diversity in induced diabetic rats without change in animals receiving FMT. Improvements in myenteric plexus ganglia density in small and large intestines in diabetic animals treated with NR were seen.<br><br>CONCLUSIONS: NR treatment led to functional improvement in total gastrointestinal transit time in induced diabetic animals. This was associated with neuroprotection in the myenteric plexuses of both small and large intestines of induced diabetic rats. This represents an important first step in showing NR's benefit as a treatment for diabetic enteric neuropathy. Streptozocin-induced diabetic rats have improved transit times and increased myenteric plexus ganglia density when treated with intraperitoneal nicotinamide riboside.}, }
@article {pmid36920536, year = {2023}, author = {Kazarina, A and Kuzmicka, J and Bortkevica, S and Zayakin, P and Kimsis, J and Igumnova, V and Sadovska, D and Freimane, L and Kivrane, A and Namina, A and Capligina, V and Poksane, A and Ranka, R}, title = {Oral microbiome variations related to ageing: possible implications beyond oral health.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {116}, pmid = {36920536}, issn = {1432-072X}, abstract = {The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.}, }
@article {pmid36920238, year = {2023}, author = {Kallner, A and Debelius, J and Schuppe-Koistinen, I and Pereira, M and Engstrand, L}, title = {Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {185-192}, doi = {10.1089/jmf.2021.0195}, pmid = {36920238}, issn = {1557-7600}, abstract = {Surströmming, a Swedish fermented fish, loved by some and avoided by others, occurs in many reports on improved or cured gastrointestinal problems even by a single meal. We tested the hypothesis that the microbes of the fermented food might have a potency to modify the gut microbiome. Two groups of voluntary participants (11 male, 8 female; aged 20-80 years) were exposed to a single meal containing the fish. A 7-day dietary intervention was carried out comprising the fish as the main source of protein in a single adult. The microbiome was characterized using 16S rRNA and metagenomic sequencing. Individual community-level changes in the microbiome were compared, as well as the presence of bacteria associated with the fermented fish. We focused on Shannon alpha and UniFrac beta diversity. We did not detect any global changes in the gut microbiome in response to Surströmming, nor were we able to recover and identify any members of Halanaerobium, which were associated with and abundant in the ingested fish, in the stool samples of the participants. Our results suggest that Surströmming consumption does not alter the microbiome of healthy individuals. However, beneficial effects on a diseased gut, impaired gut microbiome, or other effects in disease remain to be studied.}, }
@article {pmid36920187, year = {2023}, author = {Bhandari, P and Hill, JE}, title = {Transport and Utilization of Glycogen Breakdown Products by Gardnerella spp. from the Human Vaginal Microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0443522}, doi = {10.1128/spectrum.04435-22}, pmid = {36920187}, issn = {2165-0497}, abstract = {Multiple Gardnerella species frequently cooccur in vaginal microbiomes, and several factors, including competition for nutrients such as glycogen could determine their population structure. Although Gardnerella spp. can hydrolyze glycogen to produce glucose, maltose, maltotriose, and maltotetraose, how these sugars are transported and utilized for growth is unknown. We determined the distribution of genes encoding transporter proteins associated with the uptake of glucose, maltose, and malto-oligosaccharides and maltodextrins among Gardnerella species. A total of five different ABC transporters were identified in Gardnerella spp. of which MusEFGK2I and MalXFGK were conserved across all 15 Gardnerella isolates. RafEFGK and TMSP (trehalose, maltose, sucrose, and palatinose) operons were specific to G. vaginalis while the MalEFG transporter was identified in G. leopoldii only. Although no glucose specific sugar-symporters were identified, putative "glucose/galactose porters" and components of a phosphotransferase system were identified. In laboratory experiments, all Gardnerella isolates grew more in the presence of glucose, maltose, maltotriose, and maltotetraose compared to unsupplemented media. In addition, most isolates (10/15) showed significantly more growth on maltotetraose compared to glucose (Kruskal Wallis, P < 0.05) suggesting their preference for longer chain malto-oligosaccharides. Our findings show that although putative MusEFGK2I and MalXFGK transporters are found in all Gardnerella spp., some species-specific transporters are also present. Observed distribution of genes encoding transporter systems was consistent with laboratory observations that Gardnerella spp. grow better on longer chain malto-oligosaccharides. IMPORTANCE Increased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community. Gardnerella produces enzymes to digest glycogen, an important nutrient source for vaginal bacteria, but little is known about the mechanisms in Gardnerella for uptake of the products of this digestion, or whether Gardnerella use some or all of the products. Our results indicate that Gardnerella may have evolved to preferentially use a subset of the glycogen breakdown products, which would help them reduce direct competition with some other bacteria in the vagina.}, }
@article {pmid36920074, year = {2023}, author = {Feng, M and Namanja-Magliano, H and Rajagopalan, S and Mishra, T and Ducati, RG and Hirsch, BM and Kelly, L and Szymczak, W and Fajardo, JE and Sidoli, S and Fiser, A and Jacobs, WR and Schramm, VL}, title = {MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with Resistance to MTAN Transition State Analogues.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.2c00644}, pmid = {36920074}, issn = {2373-8227}, abstract = {Helicobacter pylori is found in the gut lining of more than half of the world's population, causes gastric ulcers, and contributes to stomach cancers. Menaquinone synthesis in H. pylori relies on the rare futalosine pathway, where H. pylori 5'-methylthioadenosine nucleosidase (MTAN) is proposed to play an essential role. Transition state analogues of MTAN, including BuT-DADMe-ImmA (BTDIA) and MeT-DADMe-ImmA (MTDIA), exhibit bacteriostatic action against numerous diverse clinical isolates of H. pylori with minimum inhibitory concentrations (MIC's) of <2 ng/mL. Three H. pylori BTDIA-resistant clones were selected under increasing BTDIA pressure. Whole genome sequencing showed no mutations in MTAN. Instead, resistant clones had mutations in metK, methionine adenosyltransferase (MAT), feoA, a regulator of the iron transport system, and flhF, a flagellar synthesis regulator. The mutation in metK causes expression of a MAT with increased catalytic activity, leading to elevated cellular S-adenosylmethionine. Metabolite analysis and the mutations associated with resistance suggest multiple inputs associated with BTDIA resistance. Human gut microbiome exposed to MTDIA revealed no growth inhibition under aerobic or anaerobic conditions. Transition state analogues of H. pylori MTAN have potential as agents for treating H. pylori infection without disruption of the human gut microbiome or inducing resistance in the MTAN target.}, }
@article {pmid36919874, year = {2023}, author = {Raksakmanut, R and Thanyasrisung, P and Sritangsirikul, S and Kitsahawong, K and Seminario, AL and Pitiphat, W and Matangkasombut, O}, title = {Prediction of Future Caries in 1-Year-Old Children via the Salivary Microbiome.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345231152802}, doi = {10.1177/00220345231152802}, pmid = {36919874}, issn = {1544-0591}, abstract = {Dental caries is the most common chronic disease in children that causes negative effects on their health, development, and well-being. Early preventive interventions are key to reduce early childhood caries prevalence. An efficient strategy is to provide risk-based targeted prevention; however, this requires an accurate caries risk predictor, which is still lacking for infants before caries onset. We aimed to develop a caries prediction model based on the salivary microbiome of caries-free 1-y-old children. Using a nested case-control design within a prospective cohort study, we selected 30 children based on their caries status at 1-y follow-up (at 2 y old): 10 children who remained caries-free, 10 who developed noncavitated caries, and 10 who developed cavitated caries. Saliva samples collected at baseline before caries onset were analyzed through 16S rRNA gene sequencing. The results of β diversity analysis showed a significant difference in salivary microbiome composition between children who remained caries-free and those who developed cavitated caries at 2 y old (analysis of similarities, Benjamini-Hochberg corrected, P = 0.042). The relative abundance of Prevotella nanceiensis, Leptotrichia sp. HMT 215, Prevotella melaninogenica, and Campylobacter concisus in children who remained caries-free was significantly higher than in children who developed cavitated caries (Wilcoxon rank sum test, P = 0.024, 0.040, 0.049, and 0.049, respectively). These taxa were also identified as biomarkers for children who remained caries-free (linear discriminant analysis effect size, linear discriminant analysis score = 3.69, 3.74, 3.53, and 3.46). A machine learning model based on these 4 species distinguished between 1-y-old children who did and did not develop cavitated caries at 2 y old, with an accuracy of 80%, sensitivity of 80%, and specificity of 80% (area under the curve, 0.8; 95% CI, 44.4 to 97.5). Our findings suggest that these salivary microbial biomarkers could assist in predicting future caries in caries-free 1-y-old children and, upon validation, are promising for development into an adjunctive tool for caries risk prediction for prevention and monitoring.}, }
@article {pmid36919771, year = {2023}, author = {Lei, J and Xu, F and Deng, C and Nie, X and Zhong, L and Wu, Z and Li, J and Wu, X and He, S and Chen, Y}, title = {Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression.}, journal = {Cancer science}, volume = {}, number = {}, pages = {}, doi = {10.1111/cas.15787}, pmid = {36919771}, issn = {1349-7006}, abstract = {Previous studies have shown that gastrointestinal microbiome is associated with the development of esophageal cancer, but the relationship and molecular mechanism between esophageal microbiota and the early development of esophageal cancer remain unclear. Here, we found that Lactobacillus, Escherichia-Shigella, Rikenellaceae-RC9-gut-group, Morganella and Fusobacterium were more abundant in early-stage esophageal cancer (EEC) tissues compared to normal esophageal tissues. The abundance of bacteria such as Prevotella, Fusobacterium, Porphyromonas, Actinobacillus and Neisseria in advanced esophageal cancer (AEC) was higher than that in EEC. Then we further verified that Fusobacterium nucleatum (Fn) was enriched in EEC tissues and that its abundance increased with the progression of esophageal cancer by FISH and RT-PCR. Next, we demonstrated that Fn promoted the proliferation of esophageal squamous cell carcinoma (ESCC) in vitro and in vivo. Finally, we confirmed that Fn promoted ESCC proliferation by upregulating the expression of interleukin (IL)-32/proteinase 3 (PRTN3) and then activating the PI3K/AKT signalling pathway. In conclusion, Fn promoted ESCC early development by upregulating the expression of IL-32/PRTN3 and thereby activating the PI3K/AKT signalling pathway. A better understanding of the molecular mechanism of Fn in early esophageal cancer may contribute to the development of early screening markers to diagnose ESCC and provide new targets for treatment.}, }
@article {pmid36919522, year = {2023}, author = {Merenstein, D and Pot, B and Leyer, G and Ouwehand, AC and Preidis, GA and Elkins, CA and Hill, C and Lewis, ZT and Shane, AL and Zmora, N and Petrova, MI and Collado, MC and Morelli, L and Montoya, GA and Szajewska, H and Tancredi, DJ and Sanders, ME}, title = {Emerging issues in probiotic safety: 2023 perspectives.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2185034}, doi = {10.1080/19490976.2023.2185034}, pmid = {36919522}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; *Probiotics/adverse effects ; Prebiotics ; Anti-Bacterial Agents/adverse effects ; Health Status ; }, abstract = {Probiotics are used for both generally healthy consumers and in clinical settings. However, theoretical and proven adverse events from probiotic consumption exist. New probiotic strains and products, as well as expanding use of probiotics into vulnerable populations, warrants concise, and actionable recommendations on how to work toward their safe and effective use. The International Scientific Association for Probiotics and Prebiotics convened a meeting to discuss and produce evidence-based recommendations on potential acute and long-term risks, risks to vulnerable populations, the importance for probiotic product quality to match the needs of vulnerable populations, and the need for adverse event reporting related to probiotic use. The importance of whole genome sequencing, which enables determination of virulence, toxin, and antibiotic resistance genes, as well as clear assignment of species and strain identity, is emphasized. We present recommendations to guide the scientific and medical community on judging probiotic safety.}, }
@article {pmid36918963, year = {2023}, author = {Faist, H and Trognitz, F and Antonielli, L and Symanczik, S and White, PJ and Sessitsch, A}, title = {Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {18}, pmid = {36918963}, issn = {2524-6372}, abstract = {BACKGROUND: Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure.<br><br>RESULTS: The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desir&#xe9;e, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desir&#xe9;e, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner.<br><br>CONCLUSION: Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.}, }
@article {pmid36918961, year = {2023}, author = {Xu, X and Lubomski, M and Holmes, AJ and Sue, CM and Davis, RL and Muller, S and Yang, JYH}, title = {NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {51}, pmid = {36918961}, issn = {2049-2618}, mesh = {Humans ; Ecotype ; *Parkinson Disease ; Diet ; Nutritional Status ; *Microbiota ; }, abstract = {BACKGROUND: Unrevealing the interplay between diet, the microbiome, and the health state could enable the design of personalized intervention strategies and improve the health and well-being of individuals. A common approach to this is to divide the study population into smaller cohorts based on dietary preferences in the hope of identifying specific microbial signatures. However, classification of patients based solely on diet is unlikely to reflect the microbiome-host health relationship or the taxonomic microbiome makeup.<br><br>RESULTS: We present a novel approach, the Nutrition-Ecotype Mixture of Experts (NEMoE) model, for establishing associations between gut microbiota and health state that accounts for diet-specific cohort variability using a regularized mixture of experts model framework with an integrated parameter sharing strategy to ensure data-driven diet-cohort identification consistency across taxonomic levels. The success of our approach was demonstrated through a series of simulation studies, in which NEMoE showed robustness with regard to parameter selection and varying degrees of data heterogeneity. Further application to real-world microbiome data from a Parkinson's disease cohort revealed that NEMoE is capable of not only improving predictive performance for Parkinson's Disease but also for identifying diet-specific microbial signatures of disease.<br><br>CONCLUSION: In summary, NEMoE can be used to uncover diet-specific relationships between nutritional-ecotype and patient health and to contextualize precision nutrition for different diseases. Video Abstract.}, }
@article {pmid36918707, year = {2023}, author = {Tran, NTD and Chaidee, A and Surapinit, A and Yingklang, M and Roytrakul, S and Charoenlappanit, S and Pinlaor, P and Hongsrichan, N and Anutrakulchai, S and Cha'on, U and Pinlaor, S}, title = {Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4216}, pmid = {36918707}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Strongyloides stercoralis ; *Strongyloidiasis/parasitology ; Proteome ; Persistent Infection ; Longitudinal Studies ; Ruminococcus ; Chromatography, Liquid ; *COVID-19 ; Communicable Disease Control ; Tandem Mass Spectrometry ; Feces/parasitology ; }, abstract = {We explored the impact of chronic Strongyloides stercoralis infection on the gut microbiome and microbial activity in a longitudinal study. At baseline (time-point T0), 42 fecal samples from matched individuals (21 positive for strongyloidiasis and 21 negative) were subjected to microbiome 16S-rRNA sequencing. Those positive at T0 (untreated then because of COVID19 lockdowns) were retested one year later (T1). Persistent infection in these individuals indicated chronic strongyloidiasis: they were treated with ivermectin and retested four months later (T2). Fecal samples at T1 and T2 were subjected to 16S-rRNA sequencing and LC-MS/MS to determine microbial diversity and proteomes. No significant alteration of indices of gut microbial diversity was found in chronic strongyloidiasis. However, the Ruminococcus torques group was highly over-represented in chronic infection. Metaproteome data revealed enrichment of Ruminococcus torques mucin-degrader enzymes in infection, possibly influencing the ability of the host to expel parasites. Metaproteomics indicated an increase in carbohydrate metabolism and Bacteroidaceae accounted for this change in chronic infection. STITCH interaction networks explored highly expressed microbial proteins before treatment and short-chain fatty acids involved in the synthesis of acetate. In conclusion, our data indicate that chronic S. stercoralis infection increases Ruminococcus torques group and alters the microbial proteome.}, }
@article {pmid36918627, year = {2023}, author = {Russell, MW and Muste, JC and Kuo, BL and Wu, AK and Singh, RP}, title = {Clinical trials targeting the gut-microbiome to effect ocular health: a systematic review.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {36918627}, issn = {1476-5454}, abstract = {Clinical trials targeting the gut microbiome to mitigate ocular disease are now on the horizon. A review of clinical data thus far is essential to determine future directions in this novel promising field. This review examines recent clinical trials that support the plausibility of a gut-eye axis, and may form the basis of novel clinical interventions. PubMed was queried for English language clinical studies examining the relationships between gut microbiota and ocular pathology. 25 studies were extracted from 828 candidate publications, which suggest that gut imbalance is associated with ocular pathology. Of these, only four interventional studies exist which suggest probiotic supplementation or fecal microbiota transplant can reduce symptoms of chalazion or uveitis. The gut-eye axis appears to hold clinical relevance, but current data is limited in sample size and design. Further investigation via longitudinal clinical trials may be warranted.}, }
@article {pmid36918616, year = {2023}, author = {Kalu, EI and Reyes-Prieto, A and Barbeau, MA}, title = {Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {21}, pmid = {36918616}, issn = {2730-6151}, abstract = {Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.}, }
@article {pmid36918294, year = {2023}, author = {Bai, Y and Huang, W and Jiang, X and Xu, W and Li, Y and Wang, Y and Huang, S and Wu, K and Hu, L and Chen, C}, title = {Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {}, number = {}, pages = {e9504}, doi = {10.1002/rcm.9504}, pmid = {36918294}, issn = {1097-0231}, abstract = {RATIONAL: Cardiac surgery-associated acute kidney injury (CSA-AKI) is a prevalent complication of cardiac surgery, which may be associated with a great risk of developing chronic kidney disease and mortality. This study aimed to investigate the possible links between gut microbiota metabolism and CSA-AKI.<br><br>METHODS: A prospective cohort of patients who underwent cardiac surgery was continuously recruited, who were further divided into CSA-AKI group and Non-AKI group based on the clinical outcomes. Their faecal and plasma samples were collected before the surgery and were separately analysed by non-targeted and targeted metabolomics. The differential metabolites related to CSA-AKI were screened out using statistical methods, and altered metabolic pathways were determined by examining the Kyoto Encyclopedia of Genes and Genomes database.<br><br>RESULTS: Nearly 1000 faecal metabolites were detected through high-resolution mass spectrometry (MS) and bioinformatics at high and mid confidence levels, and 49 differential metabolites at high confidence level may perform essential biological functions and provide potential diagnostic indicators. Compared with the Non-AKI group, the patients in the CSA-AKI group displayed dramatic changes in gut microbiota metabolism, including amino acid metabolism, nicotinate and nicotinamide metabolism, purine metabolism, and ABC transporters. Meanwhile, 188 plasma metabolites were identified and quantified by tandem MS, and 34 differential plasma metabolites were screened out between the two groups using univariate statistical analysis. These differential plasma metabolites were primarily enriched in the following metabolic pathways: sulphur metabolism, amino acid biosynthesis, tryptophan metabolism, and ABC transporters. Furthermore, the content of indole metabolites in the faecal and plasma samples of the CSA-AKI group was higher than that of the Non-AKI group.<br><br>CONCLUSIONS: Patients with CSA-AKI may have dysbiosis of their intestinal microbiota and metabolic abnormalities in their gut system before cardiac surgery. Thus, some metabolites and related metabolic pathways may be potential biomarkers and new therapeutic targets for the disease.}, }
@article {pmid36918234, year = {2023}, author = {Otten, AT and Peters, V and Barth, I and Stevens, CL and Bourgonje, AR and Frijlink, HW and Harmsen, HJM and Rehman, A and Campmans-Kuijpers, MJE and Dijkstra, G}, title = {Effects of ileocolonic delivered vitamin B2, B3 and C (ColoVit) or the Groningen anti-inflammatory diet on disease course and microbiome of patients with Crohn's disease (VITA-GrAID study): a protocol for a randomised and partially blinded trial.}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e069654}, pmid = {36918234}, issn = {2044-6055}, mesh = {Humans ; *Crohn Disease/drug therapy ; Diet ; *Microbiota ; Anti-Inflammatory Agents ; Vitamins ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Diet plays a pivotal role in the onset and progression of Crohn's disease (CD). Nutritional interventions revealed effects on intestinal inflammation and gut microbial composition. However, data from well-designed and controlled dietary trials are lacking. Therefore, evidence-based dietary recommendations are still unavailable to patients and physicians. Here, we aim to investigate the effects of an evidence-based anti-inflammatory diet, and an ileocolonic-targeted capsule containing vitamin B2, B3 and C (ColoVit) on patients with CD and their healthy household members.<br><br>METHODS AND ANALYSIS: In this multicentre, randomised, placebo-controlled, partially blinded nutritional intervention trial, we aim to recruit 255&#x2009;CD patients with Harvey-Bradshaw Index <8&#x2009;and a faecal calprotectin (FCal) cut-off of &#x2265;100&#x2009;&#xb5;g/g at baseline. Participants will be randomised into two experimental intervention groups and one placebo group. In the experimental groups, participants will either adhere to the Groningen anti-inflammatory diet (GrAID) or ingest an ileocolonic-delivered oral vitamin B2/B3/C capsule (ColoVit). The study consists of a 12-week controlled interventional phase, which proceeds to a 9-month observational follow-up phase in which patients allocated to the GrAID group will be requested to continue the intervention on their own accord. Household members of participating patients will be asked to participate in the trial as healthy subjects and are allocated to the same group as their peer. The primary study outcome for patients is the change in FCal level from baseline. The primary outcome for household members is the change in gut microbial composition, which is set as secondary outcome for patients.<br><br>ETHICS AND DISSEMINATION: The protocol has been approved by the Institutional Review Board of the Stichting Beoordeling Ethiek Biomedisch Onderzoek in Assen, the Netherlands. Written informed consent will be obtained from all participants. Results will be disseminated through peer-reviewed journals and conference presentations.<br><br>TRIAL REGISTRATION NUMBER: NCT04913467.}, }
@article {pmid36918089, year = {2023}, author = {Kapoor, B and Gulati, M and Gupta, R and Singla, RK}, title = {Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome?.}, journal = {Autoimmunity reviews}, volume = {22}, number = {5}, pages = {103313}, doi = {10.1016/j.autrev.2023.103313}, pmid = {36918089}, issn = {1873-0183}, abstract = {Dysregulated immune system with a failure to recognize self from non-self-antigens is one of the common pathogeneses seen in autoimmune diseases. The complex interplay of genetic and environmental factors is important for the occurrence and development of the disease. Among the environmental factors, disturbed gut microbiota (gut dysbiosis) has recently attracted particular attention, especially with advancement in human microbiome research. Although the alterations in microbiota have been seen in various autoimmune diseases, including those of nervous system, there is paucity of information on neuromuscular system diseases. Myasthenia gravis (MG) is one such rare autoimmune disease of neuromuscular junction, and is caused by generation of pathogenic autoantibodies to components of the postsynaptic muscle endplate. In the recent years, accumulating evidences have endorsed the key role of host microbiota, particularly those of gut, in the pathogenesis of MG. Differential microbiota composition, characterized by increased abundance of Fusobacteria, Bacteroidetes, and Proteobacteria, and decreased abundance of Actinobacteria and Firmicutes, has been seen in MG patients in comparison to healthy subjects. Disturbance of microbiota composition, particularly reduced ratio of Firmicutes/Bacteroidetes, alter the gut permeability, subsequently triggering the immunological response. Resultant reduction in levels of short chain fatty acids (SCFAs) is another factor contributing to the immunological response in MG patients. Modulation of gut microbiota via intervention of probiotics, prebiotics, synbiotics, postbiotics (metabiotics), and fecal microbiota transplantation (FMT) is considered to be the futuristic approach for the management of MG. This review summarizes the role of gut microbiota and their metabolites (postbiotics) in the progression of MG. Also, various bacteriotherapeutic approaches involving gut microbiota are discussed for the prevention of MG progression.}, }
@article {pmid36917755, year = {2023}, author = {Mitchell, CM}, title = {Is the vaginal microbiome a marker or an effector of vaginal health?.}, journal = {Menopause (New York, N.Y.)}, volume = {}, number = {}, pages = {}, pmid = {36917755}, issn = {1530-0374}, }
@article {pmid36917674, year = {2023}, author = {Spindler, MP and Mogno, I and Suri, P and Britton, GJ and Faith, JJ}, title = {Species-specific CD4[+] T cells enable prediction of mucosal immune phenotypes from microbiota composition.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {12}, pages = {e2215914120}, doi = {10.1073/pnas.2215914120}, pmid = {36917674}, issn = {1091-6490}, abstract = {How bacterial strains within a complex human microbiota collectively shape intestinal T cell homeostasis is not well understood. Methods that quickly identify effector strains or species that drive specific mucosal T cell phenotypes are needed to define general principles for how the microbiota modulates host immunity. We colonize germ-free mice with defined communities of cultured strains and profile antigen-specific responses directed toward individual strains ex vivo. We find that lamina propria T cells are specific to bacterial strains at the species level and can discriminate between strains of the same species. Ex vivo restimulations consistently identify the strains within complex communities that induce Th17 responses in vivo, providing the potential to shape baseline immune tone via community composition. Using an adoptive transfer model of colitis, we find that lamina propria T cells respond to different bacterial strains in conditions of inflammation versus homeostasis. Collectively, our approach represents a unique method for efficiently predicting the relative impact of individual bacterial strains within a complex community and for parsing microbiota-dependent phenotypes into component fractions.}, }
@article {pmid36917465, year = {2023}, author = {Azevedo, MJ and Campos, P and Araujo, R and Magalhães, I and Pereira, ML and Azevedo, A and Zaura, E and Ramalho, C and Sampaio-Maia, B}, title = {The potential impact of delivery mode and breastfeeding on oral Candida species carriage in a population of young adults.}, journal = {Quintessence international (Berlin, Germany : 1985)}, volume = {0}, number = {0}, pages = {0}, doi = {10.3290/j.qi.b3957701}, pmid = {36917465}, issn = {1936-7163}, abstract = {OBJECTIVES: In early life, children are exposed to microorganisms from maternal and environmental sources, which influence the development of their microbiome throughout life. Several studies have demonstrated the influence of the delivery mode and breastfeeding on the oral microbiome of children, mostly regarding bacterial colonization. However, their influence on the oral fungal carriage is still underexplored. This study aimed to assess the association of the delivery and feeding mode with the oral carriage of yeasts in adulthood.<br><br>METHOD AND MATERIALS: Fungal oral carriage was evaluated by collecting unstimulated saliva in 185 healthy dental students (mean age of 21.51&#xb1;1.55 years old; 81.6% females). Yeast identification was performed by culture in ChromAgar Candida medium and sequencing of the 18S genes and ITS regions for determination of the species. Demographic and clinical data of each participant was recorded through questionnaires and oral examinations were performed in a subgroup of participants (n=49).<br><br>RESULTS: Candida species were isolated in 37.5% of all participants. The prevalence of yeasts in the oral cavity was significantly higher in those who were born by vaginal delivery compared to those born by caesarean-section (p=0.035), whereas no statistically significant differences were observed regarding breastfeeding (p=0.398). Low salivary flow rate and frequency of dental visits also were associated with oral yeast carriage (p<0.05).<br><br>CONCLUSION: Our study suggests a possible impact of the type of delivery on fungal colonization, which is sustained throughout life due to oral health-related factors.}, }
@article {pmid36917415, year = {2023}, author = {Poto, R and Ianiro, G and de Paulis, A and Spadaro, G and Marone, G and Gasbarrini, A and Varricchi, G}, title = {Correction to: Is there a role for microbiome‑based approach in common variable immunodeficiency?.}, journal = {Clinical and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10238-023-01032-1}, pmid = {36917415}, issn = {1591-9528}, }
@article {pmid36917032, year = {2023}, author = {Faden, H}, title = {Development of the Anaerobic Microbiome in the Infant Gut.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000003905}, pmid = {36917032}, issn = {1532-0987}, abstract = {Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.}, }
@article {pmid36916990, year = {2023}, author = {Zhang, Y and Cao, B and Pan, Y and Tao, S and Zhang, N}, title = {Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0383122}, doi = {10.1128/spectrum.03831-22}, pmid = {36916990}, issn = {2165-0497}, abstract = {Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.}, }
@article {pmid36916973, year = {2023}, author = {Sah, GP and Kovalick, G and Chopyk, J and Kuo, P and Huang, L and Ghatbale, P and Das, P and Realegeno, S and Knight, R and Gilbert, JA and Pride, DT}, title = {Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0450922}, doi = {10.1128/spectrum.04509-22}, pmid = {36916973}, issn = {2165-0497}, abstract = {The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.}, }
@article {pmid36916965, year = {2023}, author = {Zhao, C and Men, X and Dang, Y and Zhou, Y and Ren, Y}, title = {Probiotics Mediate Intestinal Microbiome and Microbiota-Derived Metabolites Regulating the Growth and Immunity of Rainbow Trout (Oncorhynchus mykiss).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0398022}, doi = {10.1128/spectrum.03980-22}, pmid = {36916965}, issn = {2165-0497}, abstract = {Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, we used rainbow trout (Oncorhynchus mykiss) as a model to investigate the internal mechanisms of host-microbiome interactions influenced by two probiotic bacteria, Bacillus velezensis and Lactobacillus sakei. We carried out experiments, including intestinal histology, serum physiology, and transcriptome and combined intestinal microbiome and metabolite profiling. Our results showed that both probiotics had a positive effect on growth, immunity, serum enzyme activity, the gut microbiome, and resistance to Aeromonas salmonicida in rainbow trout. Moreover, the intestinal microbial structure was reshaped with increased relative abundance of potential beneficial bacteria, such as Ruminococcus, Lachnospiraceae ucg-004, Leptotrichia, Bacillus coagulans, Porphyromonadaceae, Anaerococcus, and Photobacterium in the B. velezensis group and Paenibacillaceae and Eubacterium hallii in the L. sakei group. Metabolomic profiling and transcriptome analysis revealed upregulated metabolites as biomarkers, i.e., sucrose and l-malic acid in the B. velezensis group, and N-acetyl-l-phenylalanine, N-acetylneuraminic acid, and hydroxyproline in the L. sakei group. Additionally, a multiomics combined analysis illustrated significant positive correlations between the relative abundance of microflora, metabolites, and gene expression associated with immunity and growth. This study highlights the significant role of probiotics as effectors of intestinal microbial activity and shows that different probiotics can have a species-specific effect on the physiological regulation of the host. These findings contribute to a better understanding of the complex host-microbiome interactions in rainbow trout and may have implications for the use of probiotics in aquaculture. IMPORTANCE Probiotics are kinds of beneficial live microbes that impart beneficial effects on the host. Recent studies have proven that when given supplementation with probiotics, farmed fish showed improved disease prevention and growth promotion. However, the underlying metabolic functions regarding their involvement in regulating growth phenotypes, nutrient utilization, and immune response are not yet well understood in the aquaculture field. Given the active interactions between the gut microbiota and fish immune and growth performance, we conducted the supplementation experiments with the probiotics Bacillus velezensis and Lactobacillus sakei. The results showed that probiotics mediated intestinal microbiome- and microbiota-derived metabolites regulating the growth and immunity of fish, and different probiotics participated in the species-specific physiological regulation of the host. This study contributed to a better understanding of the functional interactions associated with host health and gut microbiota species.}, }
@article {pmid36916950, year = {2023}, author = {Wen, Z and Yang, M and Han, H and Fazal, A and Liao, Y and Ren, R and Yin, T and Qi, J and Sun, S and Lu, G and Hu, S and Yang, Y}, title = {Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0331022}, doi = {10.1128/spectrum.03310-22}, pmid = {36916950}, issn = {2165-0497}, abstract = {Strongly acidic soils are characterized by high aluminum (Al) toxicity and low phosphorus (P) availability, which suppress legume plant growth and nodule development. Arbuscular mycorrhizal fungi (AMF) stimulate rhizobia and enhance plant P uptake. However, it is unclear how this symbiotic soybean-AMF-rhizobial trio promotes soybean growth in acidic soils. We examined the effects of AMF and rhizobium addition on the growth of two soybean genotypes, namely, Al-tolerant and Al-sensitive soybeans as well as their associated bacterial and fungal communities in an acidic soil. With and without rhizobial addition, AMF significantly increased the fresh shoot and root biomass of Al-tolerant soybean by 47%/87% and 37%/24%, respectively. This increase in plant biomass corresponded to the enrichment of four plant growth-promoting rhizobacteria (PGPR) in the rhizospheric soil, namely, Chitinophagaceae bacterium 4GSH07, Paraburkholderia soli, Sinomonas atrocyanea, and Aquincola tertiaricarbonis. For Al-sensitive soybean, AMF addition increased the fresh shoot and root biomass by 112%/64% and 30%/217%, respectively, with/without rhizobial addition. Interestingly, this significant increase coincided with a decrease in the pathogenic fungus Nigrospora oryzae as well as an increase in S. atrocyanea, A. tertiaricarbonis, and Talaromyces verruculosus (a P-solubilizing fungus) in the rhizospheric soil. Lastly, the compartment niche along the soil-plant continuum shaped microbiome assembly, with pathogenic/saprotrophic microbes accumulating in the rhizospheric soil and PGPR related to nitrogen fixation or stress resistance (e.g., Rhizobium leguminosarum and Sphingomonas azotifigens) accumulating in the endospheric layer. IMPORTANCE Taken together, this study examined the effects of arbuscular mycorrhizal fungi (AMF) and rhizobial combinations on the growth of Al-tolerant and Al-sensitive soybeans as well as their associated microbial communities in acidic soils and concluded that AMF enhances soybean growth and Al stress tolerance by recruiting PGPR and altering the root-associated microbiome assembly in a host-dependent manner. In the future, these findings will help us better understand the impacts of AMF on rhizosphere microbiome assembly and will contribute to the development of soybean breeding techniques for the comprehensive use of PGPR in sustainable agriculture.}, }
@article {pmid36916927, year = {2023}, author = {Du, Q and Xu, Q and Pan, F and Shi, Y and Yu, F and Zhang, T and Jiang, J and Liu, W and Pan, X and Han, D and Zhang, H}, title = {Association between Intestinal Colonization and Extraintestinal Infection with Carbapenem-Resistant Klebsiella pneumoniae in Children.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0408822}, doi = {10.1128/spectrum.04088-22}, pmid = {36916927}, issn = {2165-0497}, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a critical public health threat. However, the association between intestinal colonization and parenteral infection among pediatric patients has not been elucidated. We collected 8 fecal CRKP strains and 10 corresponding CRKP strains responsible for extraintestinal infection from eight patients who did not manifest infection upon admission to the hospital. Paired isolates showed identical resistance to antimicrobials and identical virulence in vitro and in vivo. wzi capsule typing, multilocus sequence typing, and whole-genome sequencing (WGS) indicated high similarity between paired colonizing and infecting isolates. Mutations between colonizing and infecting isolate pairs found by WGS had a distinctive molecular signature of a high proportion of complex structural variants. The mutated genes were involved in pathways associated with infection-related physiological and pathogenic functions, including antibiotic resistance, virulence, and response to the extracellular environment. The latter is important for bacterial infection of environmental niches. Various mutations related to antibiotic resistance, virulence, and colonization that were not associated with any particular mutational hot spot correlated with an increased risk of extraintestinal infection. Notably, novel subclone carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) KL19-ST15 exhibited hypervirulence in experimental assays that reflected the severe clinical symptoms of two patients infected with the clonal strains. Taken together, our findings indicate the association between CRKP intestinal colonization and extraintestinal infection, suggesting that active screening for colonization on admission could decrease infection risk in children. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes an increasing number of nosocomial infections, which can be life-threatening, as carbapenems are last-resort antibiotics. K. pneumoniae is part of the healthy human microbiome, and this provides a potential advantage for infection. This study demonstrated that CRKP intestinal colonization is strongly linked to extraintestinal infection, based on the evidence given by whole-genome sequencing data and phenotypic assays of antimicrobial resistance and virulence. Apart from these findings, our in-depth analysis of point mutations and chromosome structural variants in patient-specific infecting isolates compared with colonizing isolates may contribute insights into bacterial adaptation underlying CRKP infection. In addition, a novel subclone of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) was observed in the study. This finding highlights the importance of CRKP active surveillance among children, targeting in particular the novel high-risk CR-hvKP clone.}, }
@article {pmid36916922, year = {2023}, author = {Webb, EM and Holman, DB and Schmidt, KN and Crouse, MS and Dahlen, CR and Cushman, RA and Snider, AP and McCarthy, KL and Amat, S}, title = {A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0518022}, doi = {10.1128/spectrum.05180-22}, pmid = {36916922}, issn = {2165-0497}, abstract = {In this study, we evaluated the seminal and fecal microbiota in yearling beef bulls fed a common diet to achieve moderate (1.13 kg/day) or high (1.80 kg/day) rates of weight gain. Semen samples were collected on days 0 and 112 of dietary intervention (n = 19/group) as well as postbreeding (n = 6/group) using electroejaculation, and the microbiota was assessed using 16S rRNA gene sequencing, quantitative PCR (qPCR), and culturing. The fecal microbiota was also evaluated, and its similarity with seminal microbiota was assessed. A subset of seminal bacterial isolates (n = 33) was screened for resistance against 28 antibiotics. A complex and dynamic microbiota was detected in bovine semen, and the community structure was affected by sampling time (R[2] = 0.16, P < 0.001). Microbial richness increased significantly from day 0 to day 112, and diversity increased after breeding (P > 0.05). Seminal microbiota remained unaffected by the differential rates of gain, and its overall composition was distinct from fecal microbiota, with only 6% of the taxa shared between them. A total of 364 isolates from 49 different genera were recovered under aerobic and anaerobic culturing. Among these seminal isolates were pathogenic species and those resistant to several antibiotics. Overall, our results suggest that bovine semen harbors a rich and complex microbiota which changes over time and during the breeding season but appears to be resilient to differential gains achieved via a common diet. Seminal microbiota is distinct from the fecal microbiota and harbors potentially pathogenic and antibiotic-resistant bacterial species. IMPORTANCE Increasing evidence from human and other animal species supports the existence of a commensal microbiota in semen and that this seminal microbiota may influence not only sperm quality and fertility but also female reproduction. Seminal microbiota in bulls and its evolution and factors shaping this community, however, remain largely underexplored. In this study, we characterized the seminal microbiota of yearling beef bulls and its response to the bull age, different weight gains, and mating activity. We compared bacterial composition between seminal and fecal microbiota and evaluated the diversity of culturable seminal bacteria and their antimicrobial resistance. Our results obtained from sequencing, culturing, and antibiotic susceptibility testing provide novel information on the taxonomic composition, evolution, and factors shaping the seminal microbiota of yearling beef bulls. This information will serve as an important basis for further understanding of the seminal microbiome and its involvement in reproductive health and fertility in cattle.}, }
@article {pmid36916778, year = {2023}, author = {Panzer, AR and Sitarik, AR and Fadrosh, D and Havstad, SL and Jones, K and Davidson, B and Finazzo, S and Wegienka, GR and Woodcroft, K and Lukacs, NW and Levin, AM and Ownby, DR and Johnson, CC and Lynch, SV and Zoratti, EM}, title = {The impact of prenatal dog keeping on infant gut microbiota development.}, journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cea.14303}, pmid = {36916778}, issn = {1365-2222}, abstract = {INTRODUCTION: Prenatal and early-life dog exposure has been linked to reduced childhood allergy and asthma. A potential mechanism includes altered early immune development in response to changes in the gut microbiome among dog-exposed infants. We thus sought to determine whether infants born into homes with indoor dog(s) exhibit altered gut microbiome development.<br><br>METHODS: Pregnant women living in homes with dogs or in pet-free homes were recruited in southeast Michigan. Infant stool samples were collected at intervals between 1&#xa0;week and 18&#x2009;months after birth and microbiome was assessed using 16S ribosomal sequencing. Perinatal maternal vaginal/rectal swabs and stool samples were sequenced from a limited number of mothers. Mixed effect adjusted models were used to assess stool microbial community trajectories comparing infants from dog-keeping versus pet-free homes with adjustment for relevant covariates.<br><br>RESULTS: Infant gut microbial composition among vaginally born babies became less similar to the maternal vaginal/rectal microbiota and more similar to the maternal gut microbiota with age-related accumulation of bacterial species with advancing age. Stool samples from dog-exposed infants were microbially more diverse (p&#xa0;=&#x2009;.041) through age 18&#x2009;months with enhanced diversity most apparent between 3 and 6&#xa0;months of age. Statistically significant effects of dog exposure on &#x3b2;-diversity metrics were restricted to formula-fed children. Across the sample collection period, dog exposure was associated with Fusobacterium genera enrichment, as well as enrichment of Collinsella, Ruminococcus, Clostridaceae and Lachnospiraceae OTUs.<br><br>CONCLUSION: Prenatal/early-life dog exposure is associated with an altered gut microbiome during infancy and supports a potential mechanism explaining lessened atopy and asthma risk. Further research directly linking specific dog-attributable changes in the infant gut microbiome to the risk of allergic disorders is needed.}, }
@article {pmid36916773, year = {2023}, author = {Li, Y and Ten, MMZ and Tham, CAT and Lim, YX and Lu, Y and Li, D}, title = {Brassica rapa subsp. Chinensis juice enhances Bacillus subtilis selectively in leafy green production.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13154}, pmid = {36916773}, issn = {1758-2229}, abstract = {Bacillus subtilis (BS) is a well-known beneficial microorganism for plants but is not competitive in the plant rhizosphere microbiome. We report the selective support of Brassica rapa subsp. Chinensis (Xiao Bai Cai) juice (XBCJ) on BS both in hydroponic nutrient solution and the plant rhizosphere of lettuce. After 2 weeks of being inoculated in the lettuce rhizosphere, the Bacillus population was enumerated at 3.30 ± 0.07 log CFU/unit in the BS group and at 5.20 ± 0.39 log CFU/unit in the BS + XBCJ group (p < 0.05). Accordingly, lettuce crops from the BS + XBCJ group were significantly higher than the control group for all of the tested biomass-related parameters (p < 0.05). The treatment did not significantly affect the texture, colour, moisture contents, total phenolic contents, or antioxidant activities of the lettuce crops (p > 0.05). Non-target ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) suggested that phenolic compounds could be the key class of phytochemicals being responsible for the selectivity. High-throughput RNA-based 16S rRNA gene sequencing and analysis were performed to depict the influence of BS and XBCJ over the global microbiome compositions of plant rhizosphere.}, }
@article {pmid36916558, year = {2023}, author = {Aditya, A and Tabashsum, Z and Alvarado Martinez, Z and Wei Tung, C and Suh, G and Nguyen, P and Biswas, D}, title = {Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems.}, journal = {Journal of food protection}, volume = {86}, number = {3}, pages = {100051}, doi = {10.1016/j.jfp.2023.100051}, pmid = {36916558}, issn = {1944-9097}, mesh = {Humans ; *Escherichia coli ; Farms ; *Ecosystem ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Feces/microbiology ; Bacteria ; Soil ; Dairying ; }, abstract = {Ruminants are the largest reservoir for all types of Escherichia coli, including the pathogenic ones, which can potentially be transmitted to humans via the food chain and environment. A longitudinal study was performed to estimate the prevalence and antibiotic-resistant pattern of pathogenic E. coli (pE.coli) strains in dairy farm environments. A total of 846 environmental samples (water, lagoon slurry, bedding, feed, feces, soil, and compost) were collected in summer over two years from five dairy farms in Maryland, USA. An additional 40 soil samples were collected in winter and summer seasons for evaluating microbiome composition. Collected environmental samples were screened for the presence of pE.coli, which was isolated using a selective culture medium, for later confirmation and virotyping using PCR with specific primers. The overall prevalence of pE.coli in dairy farms was 8.93% (71/846), with the most common virotype identified in isolates being ETEC, followed by STEC. The highest pE.coli prevalence were recorded in lagoon slurry (21.57%) while the lowest was in compost heap (2.99%). Among isolates, 95.87% of the virotypes were resistant to 9 classes of antibiotics whereas only 4.12% were sensitive. The highest proportion (68.04%) of resistance was found for quinolones (e.g., ciprofloxacin). The resulting metagenomic analysis at the phylum and genus levels of the grazing land soil suggests that climatic conditions actively influence the abundance of bacteria. Proteobacteria, which contains many Gram-negative foodborne pathogens (including pE.coli), was the most predominant phylum, accounting for 26.70% and 24.93% of soil bacteria in summer and winter, respectively. In addition to relative abundance, there was no significant difference in species diversity between seasons when calculated via Simpson (D) and Shannon (H) index. This study suggests that antibiotic-resistant E. coli virotypes are present in the dairy farm environment, and proper steps are warranted to control its transmission irrespective of seasonality.}, }
@article {pmid36916422, year = {2023}, author = {Wang, AJ and Song, D and Hong, YM and Liu, NN}, title = {Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age.}, journal = {Molecular omics}, volume = {}, number = {}, pages = {}, doi = {10.1039/d2mo00288d}, pmid = {36916422}, issn = {2515-4184}, abstract = {Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.}, }
@article {pmid36916216, year = {2023}, author = {Georgiou, AC and van der Waal, SV and Buijs, MJ and Crielaard, W and Zaura, E and Brandt, BW}, title = {Host microbiome interactions in apical periodontitis: the endodontic microbiome in relation to circulatory immunologic markers.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.13912}, pmid = {36916216}, issn = {1365-2591}, abstract = {AIM: To explore microbial differences in the endodontic infection of teeth with primary and secondary apical periodontitis, with or without symptomatology. Additionally, to investigate if these differences are depicted in immunologic markers in blood.<br><br>METHODOLOGY: Twenty-nine teeth with primary or secondary apical periodontitis were extracted and cryo-pulverized. Blood was drawn from the subjects at three different timepoints before and three timepoints after the extraction in a time period of four months. The V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina MiSeq. The microbiome profiles were ordinated using Principal Component Analysis and tested for differences between groups with permutational multivariate analysis of variance using the Bray-Curtis distance. If significantly different, the microbial profiles were further analyzed using the LDA effect size (LEfSe) biomarker discovery tool. A broad panel of inflammatory mediators in blood was examined longitudinally in all subjects during the six visits with mixed models. The Spearman correlation between these mediators and the zOTUs was calculated, significant correlations (p<0.05) were used as input for significant analysis of microarrays (SAM) using MeV.<br><br>RESULTS: After subsampling, the 467 zOTUs were classified into 9 phyla and 99 genera or higher-level taxa. The predominant genus in the entire sample set was Fusobacterium with a relative abundance of 12.3%, followed by Prevotella (9.9%), Actinomyces (7.7%), and Streptococcus (6.7%). The microbiomes of the endodontic infections were significantly associated with endodontic status (primary/secondary infection) (p=0.015) as well as with the presence or absence of pain (p=0.011). There was also a difference in the concentration of inflammatory mediators, namely CRP, IL-8, IL-10, IL-12p70, RANKL and TNF-&#x3b1;, depending on the existence of pain. In addition, the presence of specific bacteria (zOTUs) was correlated, positively or negatively, with the expression of several circulating inflammatory markers.<br><br>CONCLUSIONS: The microbial profiles and the concentration-time relationship of systemic inflammatory mediators of primary endodontic infection differed from those of secondary, and of symptomatic from those of asymptomatic cases. The fingerprint of associations between the immunological and microbiological profiles differed between of asymptomatic and symptomatic patients.}, }
@article {pmid36915683, year = {2023}, author = {Aoi, W and Inoue, R and Mizushima, K and Honda, A and Björnholm, M and Takagi, T and Naito, Y}, title = {Exercise-acclimated microbiota improves skeletal muscle metabolism via circulating bile acid deconjugation.}, journal = {iScience}, volume = {26}, number = {3}, pages = {106251}, pmid = {36915683}, issn = {2589-0042}, abstract = {Habitual exercise alters the intestinal microbiota composition, which may mediate its systemic benefits. We examined whether transplanting fecal microbiota from trained mice improved skeletal muscle metabolism in high-fat diet (HFD)-fed mice. Fecal samples from sedentary and exercise-trained mice were gavage-fed to germ-free mice. After receiving fecal samples from trained donor mice for 1 week, recipient mice had elevated levels of AMP-activated protein kinase (AMPK) and insulin growth factor-1 in skeletal muscle. In plasma, bile acid (BA) deconjugation was found to be promoted in recipients transplanted with feces from trained donor mice; free-form BAs also induced more AMPK signaling and glucose uptake than tauro-conjugated BAs. The transplantation of exercise-acclimated fecal microbiota improved glucose tolerance after 8 weeks of HFD administration. Intestinal microbiota may mediate exercise-induced metabolic improvements in mice by modifying circulating BAs. Our findings provide insights into the prevention and treatment of metabolic diseases.}, }
@article {pmid36915549, year = {2023}, author = {Qin, J and Ji, B and Ma, Y and Liu, X and Wang, T and Liu, G and Li, B and Wang, G and Gao, P}, title = {Diversity and potential function of pig gut DNA viruses.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14020}, pmid = {36915549}, issn = {2405-8440}, abstract = {Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.}, }
@article {pmid36915209, year = {2023}, author = {Du, LF and Zhang, MZ and Yuan, TT and Ni, XB and Wei, W and Cui, XM and Wang, N and Xiong, T and Zhang, J and Pan, YS and Zhu, DY and Li, LJ and Xia, LY and Wang, TH and Wei, R and Liu, HB and Sun, Y and Zhao, L and Lam, TT and Cao, WC and Jia, N}, title = {New insights into the impact of microbiome on horizontal and vertical transmission of a tick-borne pathogen.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {50}, pmid = {36915209}, issn = {2049-2618}, abstract = {BACKGROUND: The impact of host skin microbiome on horizontal transmission of tick-borne pathogens , and of pathogen associated transstadial and transovarial changes in tick microbiome are largely unknown, but are important to control increasingly emerging tick-borne diseases worldwide.<br><br>METHODS: Focusing on a rickettsiosis pathogen, Rickettsia raoultii, we used R. raoultii-positive and R. raoultii-negative Dermacentor spp. tick colonies to study the involvement of skin microbiota in cutaneous infection with rickettsiae&#xa0;in laboratory mice, and the function of the&#xa0;tick microbiome on maintenance&#xa0;of rickettsiae through all tick&#xa0;developmental stages (eggs, larvae, nymphs, adults) over two generations.<br><br>RESULTS: We observed changes in the&#xa0;skin bacteria community, such as Chlamydia, not only associated with&#xa0;rickettsial colonization but also with tick feeding on skin. The diversity of skin microbiome differed between paired tick-bitten and un-bitten sites. For vertical transmission, significant differences in the tick microbiota between pathogenic rickettsia-positive and -negative tick chorts was observed across all developmental stages at least over two generations, which appeared to be a common pattern not only for R. raoultii but also for another pathogenic species, Candidatus Rickettsia tarasevichiae. More importantly, bacterial differences were complemented by functional shifts primed for genetic information processing during blood feeding. Specifically, the differences in tick microbiome gene repertoire between pathogenic Rickettsia-positive and -negative progenies were enriched in pathways associated with metabolism and hormone signals during vertical transmission.<br><br>CONCLUSIONS: We demonstrate that host skin microbiome might be a new factor determining the transmission of rickettsial pathogens through ticks. While pathogenic rickettsiae infect vertebrate hosts during blood-feeding by the tick, they may also manipulate the maturation of the tick through changing the functional potential of its&#xa0;microbiota over the tick's life stages. The findings here might spur the development of new-generation control methods for ticks and tick-borne pathogens. Video Abstract.}, }
@article {pmid36914893, year = {2023}, author = {Stein-Thoeringer, CK and Saini, NY and Zamir, E and Blumenberg, V and Schubert, ML and Mor, U and Fante, MA and Schmidt, S and Hayase, E and Hayase, T and Rohrbach, R and Chang, CC and McDaniel, L and Flores, I and Gaiser, R and Edinger, M and Wolff, D and Heidenreich, M and Strati, P and Nair, R and Chihara, D and Fayad, LE and Ahmed, S and Iyer, SP and Steiner, RE and Jain, P and Nastoupil, LJ and Westin, J and Arora, R and Wang, ML and Turner, J and Menges, M and Hidalgo-Vargas, M and Reid, K and Dreger, P and Schmitt, A and Müller-Tidow, C and Locke, FL and Davila, ML and Champlin, RE and Flowers, CR and Shpall, EJ and Poeck, H and Neelapu, SS and Schmitt, M and Subklewe, M and Jain, MD and Jenq, RR and Elinav, E}, title = {A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {36914893}, issn = {1546-170X}, abstract = {Increasing evidence suggests that the gut microbiome may modulate the efficacy of cancer immunotherapy. In a B cell lymphoma patient cohort from five centers in Germany and the United States (Germany, n = 66; United States, n = 106; total, n = 172), we demonstrate that wide-spectrum antibiotics treatment ('high-risk antibiotics') prior to CD19-targeted chimeric antigen receptor (CAR)-T cell therapy is associated with adverse outcomes, but this effect is likely to be confounded by an increased pretreatment tumor burden and systemic inflammation in patients pretreated with high-risk antibiotics. To resolve this confounding effect and gain insights into antibiotics-masked microbiome signals impacting CAR-T efficacy, we focused on the high-risk antibiotics non-exposed patient population. Indeed, in these patients, significant correlations were noted between pre-CAR-T infusion Bifidobacterium longum and microbiome-encoded peptidoglycan biosynthesis, and CAR-T treatment-associated 6-month survival or lymphoma progression. Furthermore, predictive pre-CAR-T treatment microbiome-based machine learning algorithms trained on the high-risk antibiotics non-exposed German cohort and validated by the respective US cohort robustly segregated long-term responders from non-responders. Bacteroides, Ruminococcus, Eubacterium and Akkermansia were most important in determining CAR-T responsiveness, with Akkermansia also being associated with pre-infusion peripheral T cell levels in these patients. Collectively, we identify conserved microbiome features across clinical and geographical variations, which may enable cross-cohort microbiome-based predictions of outcomes in CAR-T cell immunotherapy.}, }
@article {pmid36914821, year = {2023}, author = {Lahat, A and Shachar, E and Avidan, B and Shatz, Z and Glicksberg, BS and Klang, E}, title = {Evaluating the use of large language model in identifying top research questions in gastroenterology.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4164}, pmid = {36914821}, issn = {2045-2322}, abstract = {The field of gastroenterology (GI) is constantly evolving. It is essential to pinpoint the most pressing and important research questions. To evaluate the potential of chatGPT for identifying research priorities in GI and provide a starting point for further investigation. We queried chatGPT on four key topics in GI: inflammatory bowel disease, microbiome, Artificial Intelligence in GI, and advanced endoscopy in GI. A panel of experienced gastroenterologists separately reviewed and rated the generated research questions on a scale of 1-5, with 5 being the most important and relevant to current research in GI. chatGPT generated relevant and clear research questions. Yet, the questions were not considered original by the panel of gastroenterologists. On average, the questions were rated 3.6 ± 1.4, with inter-rater reliability ranging from 0.80 to 0.98 (p < 0.001). The mean grades for relevance, clarity, specificity, and originality were 4.9 ± 0.1, 4.6 ± 0.4, 3.1 ± 0.2, 1.5 ± 0.4, respectively. Our study suggests that Large Language Models (LLMs) may be a useful tool for identifying research priorities in the field of GI, but more work is needed to improve the novelty of the generated research questions.}, }
@article {pmid36914812, year = {2023}, author = {Huang, Y and Wu, J and Zhang, H and Li, Y and Wen, L and Tan, X and Cheng, K and Liu, Y and Pu, J and Liu, L and Wang, H and Li, W and Perry, SW and Wong, ML and Licinio, J and Zheng, P and Xie, P}, title = {The gut microbiome modulates the transformation of microglial subtypes.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {36914812}, issn = {1476-5578}, abstract = {Clinical and animal studies have shown that gut microbiome disturbances can affect neural function and behaviors via the microbiota-gut-brain axis, and may be implicated in the pathogenesis of several brain diseases. However, exactly how the gut microbiome modulates nervous system activity remains obscure. Here, using a single-cell nucleus sequencing approach, we sought to characterize the cell type-specific transcriptomic changes in the prefrontal cortex and hippocampus derived from germ-free (GF), specific pathogen free, and colonized-GF mice. We found that the absence of gut microbiota resulted in cell-specific transcriptomic changes. Furthermore, microglia transcriptomes were preferentially influenced, which could be effectively reversed by microbial colonization. Significantly, the gut microbiome modulated the mutual transformation of microglial subpopulations in the two regions. Cross-species analysis showed that the transcriptome changes of these microglial subpopulations were mainly associated with Alzheimer's disease (AD) and major depressive disorder (MDD), which were further supported by animal behavioral tests. Our findings demonstrate that gut microbiota mainly modulate the mutual transformation of microglial subtypes, which may lead to new insights into the pathogenesis of AD and MDD.}, }
@article {pmid36914755, year = {2023}, author = {Foley, MH and Walker, ME and Stewart, AK and O'Flaherty, S and Gentry, EC and Patel, S and Beaty, VV and Allen, G and Pan, M and Simpson, JB and Perkins, C and Vanhoy, ME and Dougherty, MK and McGill, SK and Gulati, AS and Dorrestein, PC and Baker, ES and Redinbo, MR and Barrangou, R and Theriot, CM}, title = {Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {36914755}, issn = {2058-5276}, support = {P42 ES027704/ES/NIEHS NIH HHS/United States ; }, abstract = {Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.}, }
@article {pmid36914691, year = {2023}, author = {Mahmud, ASM and Seers, CA and Shaikh, AA and Taznin, T and Uzzaman, MS and Osman, E and Habib, MA and Akter, S and Banu, TA and Sarkar, MMH and Goswami, B and Jahan, I and Okeoma, CM and Khan, MS and Reynolds, EC}, title = {A multicentre study reveals dysbiosis in the microbial co-infection and antimicrobial resistance gene profile in the nasopharynx of COVID-19 patients.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4122}, pmid = {36914691}, issn = {2045-2322}, support = {R01DA042348/NH/NIH HHS/United States ; R01DA050169/NH/NIH HHS/United States ; R21/R33DA053643/NH/NIH HHS/United States ; }, abstract = {The impact of SARS-CoV-2 infection on the nasopharyngeal microbiome has not been well characterised. We sequenced genetic material extracted from nasopharyngeal swabs of SARS-CoV-2-positive individuals who were asymptomatic (n = 14), had mild (n = 64) or severe symptoms (n = 11), as well as from SARS-CoV-2-negative individuals who had never-been infected (n = 5) or had recovered from infection (n = 7). Using robust filters, we identified 1345 taxa with approximately 0.1% or greater read abundance. Overall, the severe cohort microbiome was least diverse. Bacterial pathogens were found in all cohorts, but fungal species identifications were rare. Few taxa were common between cohorts suggesting a limited human nasopharynx core microbiome. Genes encoding resistance mechanisms to 10 antimicrobial classes (> 25% sequence coverages, 315 genes, 63 non-redundant) were identified, with β-lactam resistance genes near ubiquitous. Patients infected with SARS-CoV-2 (asymptomatic and mild) had a greater incidence of antibiotic resistance genes and a greater microbial burden than the SARS-CoV-2-negative individuals. This should be considered when deciding how to treat COVID-19 related bacterial infections.}, }
@article {pmid36914667, year = {2023}, author = {Kim, RH and Tagele, SB and Jeong, M and Jung, DR and Lee, D and Park, T and Tino, BF and Lim, K and Kim, MA and Park, YJ and Shin, JH}, title = {Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4140}, pmid = {36914667}, issn = {2045-2322}, abstract = {Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot [-1]) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4[+], and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.}, }
@article {pmid36914646, year = {2023}, author = {Ngugi, DK and Acinas, SG and Sánchez, P and Gasol, JM and Agusti, S and Karl, DM and Duarte, CM}, title = {Abiotic selection of microbial genome size in the global ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1384}, pmid = {36914646}, issn = {2041-1723}, abstract = {Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.}, }
@article {pmid36914549, year = {2023}, author = {Dai, Y and Sun, Z and Zheng, Y and Ge, J}, title = {Recent advances in the gut microbiome and microbial metabolites alterations of coronary artery disease.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2023.03.009}, pmid = {36914549}, issn = {2095-9281}, }
@article {pmid36914394, year = {2022}, author = {Liu, Y and Xu, MM and Zhang, Y and Liu, SQ and Yuan, MQ and Jia, ZJ}, title = {Application Value and Research Progress of Human Microbiome in Sexual Assault Cases.}, journal = {Fa yi xue za zhi}, volume = {38}, number = {6}, pages = {774-782}, doi = {10.12116/j.issn.1004-5619.2021.511101}, pmid = {36914394}, issn = {1004-5619}, abstract = {In recent years, sexual assault cases have been on the rise, seriously infringing the legitimate rights and interests of women and children, causing widespread concern in society. DNA evidence has become the key evidence to prove the facts in sexual assault cases, but lack of DNA evidence or only DNA evidence in some sexual assault cases leads to unclear facts and insufficient evidence. With the emergence of high-throughput sequencing technology and the development of bioinformatics and artificial intelligence, new progress has been made in the study of human microbiome. Researchers have begun to use human microbiome for difficult sexual assault cases indentification. This paper reviews the characteristics of human microbiome, and its application value in the inferences of the body fluid stain origin, the sexual assault method, the crime time, etc. In addition, the challenges faced by the application of the human microbiome in practical case handling, the solutions and future development potential are analyzed and prospected.}, }
@article {pmid36914054, year = {2023}, author = {Meng, Y and Mao, Y and Tang, Z and Qiu, X and Bajinka, O and Tan, Y and Song, Z}, title = {Crosstalk between the lung microbiome and lung cancer.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106062}, doi = {10.1016/j.micpath.2023.106062}, pmid = {36914054}, issn = {1096-1208}, abstract = {The human microbiome is a complex ecosystem that mediates interaction between the human host and the environment. All of the human body is colonized by microorganisms. The lung as an organ used to be considered sterile. Recently, however, there has been a growing number of reports with evidence that the lungs are also in a state of carrying bacteria. The pulmonary microbiome is associated with many lung diseases and is increasingly reported in current studies. These include; chronic obstructive pulmonary disease (COPD), asthma, acute chronic respiratory infections, and cancers. These lung diseases are associated with reduced diversity and dysbiosis. It directly or indirectly affects the occurrence and development of lung cancer. Very few microbes directly cause cancer, while many are complicit in cancer growth, usually working through the host's immune system. This review focuses on the correlation between lung microbiota and lung cancer, and investigates the mechanism of action of lung microorganisms on lung cancer, which will provide new and reliable treatments and diagnosis of lung cancer in the future.}, }
@article {pmid36914014, year = {2023}, author = {Murray, E and Butcher, J and May Kearns, M and Lamba, S and Liang, J and Stintzi, A and Ismail, N}, title = {Effects of pair-housing pubertal and adult male and female mice on LPS-induced age-dependent immune responses: A potential role for the gut microbiota.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2023.03.009}, pmid = {36914014}, issn = {1090-2139}, abstract = {Puberty is a critical period of development that is marked by the maturation of the stress and immune systems. There are marked age and sex differences in peripheral and central inflammatory responses to an immune challenge between pubertal and adult mice. Given the strong link between the gut microbiome and immune system, it is possible that the age and sex differences in immune responses are mediated by age and sex differences in gut microbial composition. The current study investigated whether cohousing adult and pubertal CD1 mice through three weeks of pair-housing, with the potential for microbiome exchange via coprophagy and other close contact, could mitigate age-dependent immune responses. Cytokine concentrations in the blood and cytokine mRNA expression in the brain were assessed following exposure to the immune challenge lipopolysaccharide (LPS). The results show that all mice displayed increased cytokine concentrations in serum and central cytokine mRNA expression in the hippocampus, hypothalamus and prefrontal cortex (PFC) at eight hours following LPS treatment. Pubertal male and female mice, that were pair-housed with a pubertal counterpart, displayed lower cytokine concentrations in serum and lower cytokine mRNA expression in the brain compared to adult mice that were pair-housed with an adult counterpart. However, when adult and pubertal mice were pair-housed, the age differences in both peripheral cytokine concentrations and central cytokine mRNA expression were mitigated. We also found that pair-housing adult and pubertal mice eliminated the age difference in gut bacterial diversity. These results suggest that microbial composition could be involved in modulating these age-associated immune responses and thus may represent a potential therapeutic target.}, }
@article {pmid36913975, year = {2023}, author = {Akbalut, C and Arisz, R and Baaten, C and Baildildinova, G and Barakzie, A and Bauersachs, R and Ten Berg, JM and van den Broek, W and de Boer, HC and Broker, V and Buka, R and Ten Cate, H and Cate, AT and De Luca, C and De Simone, I and Dignat-George, F and Freson, K and Gazzaniga, G and van Gorp, E and Habibi, A and Henskens, YMC and Iding, AFJ and Khan, A and Koenderink, G and Konkoth, A and Lacroix, R and Lahiri, T and Lam, W and Lamerton, R and Lorusso, R and Luo, Q and Maas, C and McCarty, OJT and van der Meijden, P and Meijers, J and Mohapatra, A and Nevo, N and Pallares Robles, A and Poncelet, P and Reinhardt, C and Ruf, W and Saraswat, R and Schonichen, C and Schutgens, REG and Simioni, P and Spada, S and Spronk, HMH and Tazhibayeva, K and Thachil, J and Vacik-Diaz, R and Veninga, A and Verhamme, P and Visser, C and Watson, SP and Wenzel, P and Willems, R and Willers, A and Zhang, P and Zifkos, K and van Zonneveld, AJ}, title = {Blood coagulation and beyond: Position paper from the Fourth Maastricht Consensus Conference on Thrombosis.}, journal = {Thrombosis and haemostasis}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2052-9175}, pmid = {36913975}, issn = {2567-689X}, abstract = {The 4th Maastricht Consensus Conference on Thrombosis (MCCT), included the following themes: Theme 1: The "coagulome" as a critical driver of cardiovascular disease Blood coagulation proteins also play divergent roles in biology and pathophysiology, related to specific organs, including brain, heart, bone marrow and kidney. Four investigators shared their views on these organ-specific topics. Theme 2: Novel mechanisms of thrombosis Mechanisms linking factor XII to fibrin, including their structural and physical properties, contribute to thrombosis, which is also affected by variation in microbiome status. Virus infections associated-coagulopathies perturb the hemostatic balance resulting in thrombosis and/or bleeding. Theme 3: How to limit bleeding risks: insights from translational studies This theme included state of the art methodology for exploring the contribution of genetic determinants of a bleeding diathesis; determination of polymorphisms in genes that control the rate of metabolism by the liver of P2Y12 inhibitors, to improve safety of antithrombotic therapy. Novel reversal agents for direct oral anticoagulants are discussed. Theme 4: Hemostasis in extracorporeal systems: how to utilize ex vivo models? Perfusion flow chamber and nanotechnology developments are developed for studying bleeding and thrombosis tendencies. Vascularised organoids are utilized for disease modeling and drug development studies. Strategies for tackling extracorporeal membrane oxygenation (ECMO) associated coagulopathy are discussed. Theme 5: Clinical dilemmas in thrombosis and antithrombotic management Plenary presentations addressed controversial areas, ie thrombophilia testing, thrombosis risk assessment in hemophilia, novel antiplatelet strategies and clinically tested factor XI(a) inhibitors,both possibly with reduced bleeding risk. Finally, Covid-19 associated coagulopathy is revisited.}, }
@article {pmid36913756, year = {2023}, author = {Ye, J and Yang, H and Hu, W and Tang, K and Liu, A and Bi, S}, title = {Changed cecal microbiota involved in growth depression of broiler chickens induced by immune stress.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102598}, doi = {10.1016/j.psj.2023.102598}, pmid = {36913756}, issn = {1525-3171}, abstract = {A previous study identified genes and metabolites associated with amino acid metabolism, glycerophospholipid metabolism, and inflammatory response in the liver of broilers with immune stress. The present research was designed to investigate the effect of immune stress on the cecal microbiome in broilers. In addition, the correlation between altered microbiota and liver gene expression, the correlation between altered microbiota and serum metabolites were compared using the Spearman correlation coefficients. Eighty broiler chicks were randomly assigned to 2 groups with 4 replicate pens per group and 10 birds per pen. The model broilers were intraperitoneally injected of 250 µg/kg LPS at 12, 14, 33, and 35 d of age to induce immunological stress. Cecal contents were taken after the experiment and kept at -80°C for 16S rDNA gene sequencing. Then the Pearson's correlation between gut microbiome and liver transcriptome, between gut microbiome and serum metabolites were calculated using R software. The results showed that immune stress significantly changed microbiota composition at different taxonomic levels. KEGG pathways analysis suggested that these gut microbiota were mainly involved in biosynthesis of ansamycins, glycan degradation, D-glutamine and D-glutamate metabolism, valine, leucine, and isoleucine biosynthesis and biosynthesis of vancomycin group antibiotics. Moreover, immune stress increased the activities of metabolism of cofactors and vitamins, as well as decreased the ability of energy metabolism and digestive system. Pearson's correlation analysis identified several bacteria were positively correlated with the gene expression while a few of bacteria were negatively correlated with the gene expression. The results identified potential microbiota involvement in growth depression mediated by immune stress and provided strategies such as supplement of probiotic for alleviating immune stress in broiler chickens.}, }
@article {pmid36913464, year = {2023}, author = {Wang, L and Shu, XO and Cai, H and Yang, Y and Xu, W and Wu, J and Cai, Q and Zheng, W and Yu, D}, title = {Tea Consumption and Gut Microbiome in Older Chinese Adults.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {293-300}, doi = {10.1016/j.tjnut.2022.12.002}, pmid = {36913464}, issn = {1541-6100}, abstract = {BACKGROUND: Animal and small-cohort human studies have shown that tea consumption affects the gut microbiome, but evidence from large cohort studies is lacking.<br><br>OBJECTIVES: We examined associations between tea consumption and gut microbiome composition among older Chinese adults.<br><br>METHODS: The study included 1179 men and 1078 women from the Shanghai Men's and Women's Health Studies, who reported tea drinking status, type, amount, and duration at baseline and follow-up surveys (1996-2017) and were free of cancer, cardiovascular disease, and diabetes at stool collection (2015-2018). Fecal microbiome was p