@article {pmid38672996,
year = {2024},
author = {Siasios, P and Giosi, E and Ouranos, K and Christoforidi, M and Dimopoulou, I and Leshi, E and Exindari, M and Anastassopoulou, C and Gioula, G},
title = {Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study.},
journal = {Journal of personalized medicine},
volume = {14},
number = {4},
pages = {},
pmid = {38672996},
issn = {2075-4426},
abstract = {Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.},
}

@article {pmid38672978,
year = {2024},
author = {Capozzi, VA and Incognito, GG and Scarpelli, E and Palumbo, M and Randazzo, CL and Pino, A and La Verde, M and Ronsini, C and Riemma, G and Gaiano, M and Romeo, P and Palmara, V and Berretta, R and Cianci, S},
title = {Exploring the Relationship between Ovarian Cancer and Genital Microbiota: A Systematic Review and Meta-Analysis.},
journal = {Journal of personalized medicine},
volume = {14},
number = {4},
pages = {},
pmid = {38672978},
issn = {2075-4426},
abstract = {Ovarian cancer (OC) remains a significant health challenge globally, with high mortality rates despite advancements in treatment. Emerging research suggests a potential link between OC development and genital dysbiosis, implicating alterations in the microbiome composition as a contributing factor. To investigate this correlation, a meta-analysis was conducted following PRISMA and MOOSE guidelines, involving eight studies encompassing 3504 patients. Studies investigating the role of upper and inferior genital tract dysbiosis were included, with particular reference to HPV infection and/or history of pelvic inflammatory disease. The analysis revealed no significant difference in genital dysbiosis prevalence between OC patients and healthy controls. Although previous literature suggests associations between dysbiosis and gynecologic cancers, such as cervical and endometrial cancers, the findings regarding OC are inconclusive. Methodological variations and environmental factors may contribute to these discrepancies, underscoring the need for standardized methodologies and larger-scale studies. Despite the limitations, understanding the microbiome's role in OC development holds promise for informing preventive and therapeutic strategies. A holistic approach to patient care, incorporating microbiome monitoring and personalized interventions, may offer insights into mitigating OC risk and improving treatment outcomes. Further research with robust methodologies is warranted to elucidate the complex interplay between dysbiosis and OC, potentially paving the way for novel preventive and therapeutic approaches.},
}

@article {pmid38672900,
year = {2024},
author = {Saini, RK and Khan, MI and Shang, X and Kumar, V and Kumari, V and Kesarwani, A and Ko, EY},
title = {Dietary Sources, Stabilization, Health Benefits, and Industrial Application of Anthocyanins-A Review.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {38672900},
issn = {2304-8158},
abstract = {Natural phytochemicals are well known to protect against numerous metabolic disorders. Anthocyanins are vacuolar pigments belonging to the parent class of flavonoids. They are well known for their potent antioxidant and gut microbiome-modulating properties, primarily responsible for minimizing the risk of cardiovascular diseases, diabetes, obesity, neurodegenerative diseases, cancer, and several other diseases associated with metabolic syndromes. Berries are the primary source of anthocyanin in the diet. The color and stability of anthocyanins are substantially influenced by external environmental conditions, constraining their applications in foods. Furthermore, the significantly low bioavailability of anthocyanins greatly diminishes the extent of the actual health benefits linked to these bioactive compounds. Multiple strategies have been successfully developed and utilized to enhance the stability and bioavailability of anthocyanins. This review provides a comprehensive view of the recent advancements in chemistry, biosynthesis, dietary sources, stabilization, bioavailability, industrial applications, and health benefits of anthocyanins. Finally, we summarize the prospects and challenges of applications of anthocyanin in foods.},
}

@article {pmid38672848,
year = {2024},
author = {Tenea, GN and Reyes, P and Molina, D},
title = {Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {38672848},
issn = {2304-8158},
support = {7874/2023//Universidad Técnica del Norte/ ; },
abstract = {An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.},
}

@article {pmid38672817,
year = {2024},
author = {Liu, L and Zhu, S and Zhang, Y and Zhu, Z and Xue, Y and Liu, X},
title = {Hovenia dulcis Fruit Peduncle Polysaccharides Reduce Intestinal Dysbiosis and Hepatic Fatty Acid Metabolism Disorders in Alcohol-Exposed Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
pmid = {38672817},
issn = {2304-8158},
support = {Qiankehejichu-ZK[2022]yiban541, Qiankehejichu-ZK[2022]yiban542//Guizhou Provincial Basic Research Program (Natural Science)/ ; Zunshikehe-HZzi[2021]330, Zunshikehe-HZzi[2022]169//Zunyi Science and Technology projects/ ; mygccrc[2022]010, mygccrc[2022]084, mygccrc[2022]085//Research Foundation for Scientific Scholars of Moutai Institute/ ; },
abstract = {Alcohol abuse can lead to alcoholic liver disease, becoming a major global burden. Hovenia dulcis fruit peduncle polysaccharides (HDPs) have the potential to alleviate alcoholic liver injury and play essential roles in treating alcohol-exposed liver disease; however, the hepatoprotective effects and mechanisms remain elusive. In this study, we investigated the hepatoprotective effects of HDPs and their potential mechanisms in alcohol-exposed mice through liver metabolomics and gut microbiome. The results found that HDPs reduced medium-dose alcohol-caused dyslipidemia (significantly elevated T-CHO, TG, LDL-C), elevated liver glycogen levels, and inhibited intestinal-hepatic inflammation (significantly decreased IL-4, IFN-γ and TNF-α), consequently reversing hepatic pathological changes. When applying gut microbiome analysis, HDPs showed significant decreases in Proteobacteria, significant increases in Firmicutes at the phylum level, increased Lactobacillus abundance, and decreased Enterobacteria abundance, maintaining the composition of gut microbiota. Further hepatic metabolomics analysis revealed that HDPs had a regulatory effect on hepatic fatty acid metabolism, by increasing the major metabolic pathways including arachidonic acid and glycerophospholipid metabolism, and identified two important metabolites-C00157 (phosphatidylcholine, a glycerophospholipid plays a central role in energy production) and C04230 (1-Acyl-sn-glycero-3-phosphocholine, a lysophospholipid involved in the breakdown of phospholipids)-involved in the above metabolism. Overall, HDPs reduced intestinal dysbiosis and hepatic fatty acid metabolism disorders in alcohol-exposed mice, suggesting that HDPs have a beneficial effect on alleviating alcohol-induced hepatic metabolic disorders.},
}

@article {pmid38672797,
year = {2024},
author = {Nayak, G and Dimitriadis, K and Pyrpyris, N and Manti, M and Kamperidis, N and Kamperidis, V and Ziakas, A and Tsioufis, K},
title = {Gut Microbiome and Its Role in Valvular Heart Disease: Not a "Gutted" Relationship.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {38672797},
issn = {2075-1729},
abstract = {The role of the gut microbiome (GM) and oral microbiome (OM) in cardiovascular disease (CVD) has been increasingly being understood in recent years. It is well known that GM is a risk factor for various CVD phenotypes, including hypertension, dyslipidemia, heart failure and atrial fibrillation. However, its role in valvular heart disease (VHD) is less well understood. Research shows that, direct, microbe-mediated and indirect, metabolite-mediated damage as a result of gut dysbiosis and environmental factors results in a subclinical, chronic, systemic inflammatory state, which promotes inflammatory cell infiltration in heart valves and subsequently, via pro-inflammatory molecules, initiates a cascade of reaction, resulting in valve calcification, fibrosis and dysfunction. This relationship between GM and VHD adds a pathophysiological link to the pathogenesis of VHD, which can be aimed therapeutically, in order to prevent or regress any risk for valvular pathologies. Therapeutic interventions include dietary modifications and lifestyle interventions, in order to influence environmental factors that can promote gut dysbiosis. Furthermore, the combination of probiotics and prebiotics, as well as fecal m transplantation and targeted treatment with inducers or inhibitors of microbial enzymes have showed promising results in animal and/or clinical studies, with the potential to reduce the inflammatory state and restore the normal gut flora in patients. This review, thus, is going to discuss the pathophysiological links behind the relationship of GM, CVD and VHD, as well as explore the recent data regarding the effect of GM-altering treatment in CVD, cardiac function and systemic inflammation.},
}

@article {pmid38672739,
year = {2024},
author = {Radu, CM and Radu, CC and Arbănaşi, EM and Hogea, T and Murvai, VR and Chiș, IA and Zaha, DC},
title = {Exploring the Efficacy of Novel Therapeutic Strategies for Periodontitis: A Literature Review.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {38672739},
issn = {2075-1729},
abstract = {Periodontitis, a prevalent oral condition, is facing difficulties in therapeutic approaches, sometimes leading to failure. This literature review was conducted to investigate the diversity of other therapeutic approaches and their potential contributions to the successful management of the disease. This research scrutinized the alterations in microbial diversity and imbalances in crucial microbial species, which contribute significantly to the pathogenesis of periodontitis. Within the limitations of this study, we highlight the importance of understanding the treatment plan's role in periodontitis disease, opening the way for further research and innovative treatment plans to mitigate the impact of periodontitis on oral health. This will aid both healthcare professionals and patients in preventing and effectively treating periodontitis, ultimately improving oral health outcomes and overall systemic health and well-being.},
}

@article {pmid38672631,
year = {2024},
author = {Ward Grados, DF and Ergun, O and Miller, CD and Gaburak, P and Frimpong, NA and Shittu, O and Warlick, CA},
title = {Prostate Tissue Microbiome in Patients with Prostate Cancer: A Systematic Review.},
journal = {Cancers},
volume = {16},
number = {8},
pages = {},
pmid = {38672631},
issn = {2072-6694},
abstract = {Some researchers have speculated that the prostatic microbiome is involved in the development of prostate cancer (PCa) but there is no consensus on certain microbiota in the prostatic tissue of PCa vs. healthy controls. This systematic review aims to investigate and compare the microbiome of PCa and healthy tissue to determine the microbial association with the pathogenesis of PCa. We searched MEDLINE, Embase, and Scopus databases. Articles were screened by two independent and blinded reviewers. Literature that compared the prostatic tissue microbiome of patients with PCa with benign controls was included. We found that PCa may be associated with increased Propionibacterium acnes, the herpesviridae and papillomaviridae families, and Mycoplasma genitalium, but definitive conclusions cannot be drawn from the existing data. Challenges include the difficulty of obtaining uncontaminated tissue samples and securing tissue from healthy controls. As a result, methods are varied with many studies using cancerous and "healthy" tissue from the same prostate. The organisms chosen for each study were also highly variable, making it difficult to compare studies. These issues have led to lower confidence in our results. Overall, further work is warranted to better understand the implications of the prostatic microbiome in the pathogenesis of PCa.},
}

@article {pmid38672546,
year = {2024},
author = {Al-Khazaleh, AK and Chang, D and Münch, GW and Bhuyan, DJ},
title = {The Gut Connection: Exploring the Possibility of Implementing Gut Microbial Metabolites in Lymphoma Treatment.},
journal = {Cancers},
volume = {16},
number = {8},
pages = {},
pmid = {38672546},
issn = {2072-6694},
support = {N/A//Western Sydney University/ ; },
abstract = {Recent research has implicated the gut microbiota in the development of lymphoma. Dysbiosis of the gut microbial community can disrupt the production of gut microbial metabolites, thereby impacting host physiology and potentially contributing to lymphoma. Dysbiosis-driven release of gut microbial metabolites such as lipopolysaccharides can promote chronic inflammation, potentially elevating the risk of lymphoma. In contrast, gut microbial metabolites, such as short-chain fatty acids, have shown promise in preclinical studies by promoting regulatory T-cell function, suppressing inflammation, and potentially preventing lymphoma. Another metabolite, urolithin A, exhibited immunomodulatory and antiproliferative properties against lymphoma cell lines in vitro. While research on the role of gut microbial metabolites in lymphoma is limited, this article emphasizes the need to comprehend their significance, including therapeutic applications, molecular mechanisms of action, and interactions with standard chemotherapies. The article also suggests promising directions for future research in this emerging field of connection between lymphoma and gut microbiome.},
}

@article {pmid38672421,
year = {2024},
author = {Zhang, L and Tang, X and Fan, C and Ren, S and Cheng, Q and Zhou, H and Liu, K and Jia, S and Zhang, Y},
title = {Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
pmid = {38672421},
issn = {2218-273X},
support = {LHZX-2023-02//Sanjiangyuan National Park Collaborative Research Special Fund/ ; 31670394, U21A20186//National Natural Science Foundation of China/ ; 2021-ZJ-Y01//Qinghai innovation platform construction project by Chinese Academy of Sciences/ ; },
mesh = {Animals ; Male ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Infertility, Male/microbiology/metabolism ; *Testosterone/metabolism ; *Lagomorpha/microbiology ; Testis/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.},
}

Animals
Male
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Infertility, Male/microbiology/metabolism
*Testosterone/metabolism
*Lagomorpha/microbiology
Testis/microbiology/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid38672407,
year = {2024},
author = {Schiano-Lomoriello, D and Abicca, I and Contento, L and Gabrielli, F and Alfonsi, C and Di Pietro, F and Papa, FT and Ballesteros-Sánchez, A and Sánchez-González, JM and Rocha-De-Lossada, C and Mazzotta, C and Giannaccare, G and Bonzano, C and Borroni, D},
title = {Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
pmid = {38672407},
issn = {2218-273X},
mesh = {*Keratitis/microbiology ; Humans ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.},
}

*Keratitis/microbiology
Humans
*Biodiversity
Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid38672337,
year = {2024},
author = {Shao, Y and Xu, J and Wang, M and Ren, Y and Wei, M and Tian, B and Luo, J and Loor, JJ and Shi, H},
title = {Preliminary Results on the Effects of Soybean Isoflavones on Growth Performance and Ruminal Microbiota in Fattening Goats.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {8},
pages = {},
pmid = {38672337},
issn = {2076-2615},
support = {32272828//National Natural Science Foundation of China/ ; ZDYF-NYGG-110//Key Research and Development Projects of Weinan City/ ; 2208-610528-04-02-755608//Shaanxi Province Announced and Commanded Project/ ; },
abstract = {Soybean isoflavones (SIFs), a group of secondary metabolites, have antioxidant, anti-inflammatory, and hormone-like activities. Supplementation with SIFs in the diet was reported to promote lactation performance in ruminants. The present study was performed to further decipher the effect of various concentrations of SIFs on growth and slaughter performance, serum parameters, meat quality, and ruminal microbiota in fattening goats. After a two-week acclimation, a total of 27 5-month-old Guanzhong male goats (18.29 ± 0.44 kg) were randomly assigned to control (NC), 100 mg/d SIF (SIF1), or 200 mg/d SIF (SIF2) groups. The experimental period lasted 56 days. The weight of the large intestine was greater (p < 0.05) in the SIF1 and SIF2 groups compared with the NC group. Meat quality parameters indicated that SIF1 supplementation led to lower (p < 0.05) cooking loss and shear force (0.05 < p < 0.10). The 16S rRNA sequencing analysis demonstrated that SIF1 supplementation led to lower (p < 0.05) proportions of Papillibacter and Prevotellaceae_UCG-004 but greater (p < 0.05) CAG-352 abundance in the rumen; these responses might have contributed to the improvement in production performance. In conclusion, meat quality and ruminal microbiome could be manipulated in a positive way by oral supplementation with 100 mg/d of SIFs in fattening goats. Thus, this study provides new insights and practical evidence for the introduction of SIFs as a novel additive in goat husbandry.},
}

@article {pmid38672336,
year = {2024},
author = {Atuahene, D and Zuniga-Chaves, I and Martello, E and Stefanon, B and Suen, G and Balouei, F and Meineri, G},
title = {The Canine Gut Health: The Impact of a New Feed Supplement on Microbiota Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {8},
pages = {},
pmid = {38672336},
issn = {2076-2615},
abstract = {This study aimed to determine the impact of a novel formulation of a supplement composed of the natural ingredients, bromelain, quercetin, and Lentinula edodes, on the gut microbiota of healthy adult dogs. Adult healthy female dogs were administered either a placebo (CTR, n = 15) or the supplement (TRT, n = 15) over 28 days. Stool samples were collected for 16S rRNA sequencing before supplement administration (T0), at completion of supplement administration (T28), and one week after the end of supplement administration (T35) to characterize changes in the gut microbial communities. QIIME was used to determine both alpha- and beta-diversity, and ANCOM-BC was used to identify differences in taxonomic abundances before and after supplementation. We found a significant decrease in overall diversity in the CTR group but no significant differences in overall diversity in the TRT group over time. Furthermore, we found differences in the abundance of several taxa in both the CTR and TRT groups, but differences in the abundance of beneficial bacteria were more pronounced in the TRT group. Specifically, we found increases in the abundance of sequences belonging to the genera Bifidobacterium, Lactobacillus, and Pediococcus at T28 in the TRT group with significant increases in Bifidobacterium and Lactobacillus persisting at T35 when compared to T0. Importantly, members of these genera are considered important for their anti-inflammatory properties, vital for fostering a balanced and robust gut microbiota in dogs. The results of our study show the potential of our supplement to selectively enhance specific beneficial bacterial taxa, offering a targeted approach to modulating the gut microbiome without causing disruptions to the overall equilibrium.},
}

@article {pmid38672291,
year = {2024},
author = {Gonçalves, JPR and Melo, ADB and Yang, Q and de Oliveira, MJK and Marçal, DA and Ortiz, MT and Righetti Arnaut, P and França, I and Alves da Cunha Valini, G and Silva, CA and Korth, N and Pavlovikj, N and Campos, PHRF and Brand, HG and Htoo, JK and Gomes-Neto, JC and Benson, AK and Hauschild, L},
title = {Increased Dietary Trp, Thr, and Met Supplementation Improves Performance, Health, and Protein Metabolism of Weaned Piglets under Mixed Management and Poor Housing Conditions.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {8},
pages = {},
pmid = {38672291},
issn = {2076-2615},
support = {2018/15559-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {A sanitary challenge was carried out to induce suboptimal herd health while investigating the effect of amino acids supplementation on piglet responses. Weaned piglets of high sanitary status (6.33 ± 0.91 kg of BW) were distributed in a 2 × 2 factorial arrangement into two similar facilities with contrasting sanitary conditions and two different diets. Our results suggest that increased Trp, Thr, and Met dietary supplementation could support the immune systems of piglets under a sanitary challenge. In this manner, AA+ supplementation improved the performance and metabolism of piglets under mixed management and poor sanitary conditions. No major temporal microbiome changes were associated with differences in performance regardless of sanitary conditions or diets. Since piglets often become mixed in multiple-site production systems and facility hygiene is also often neglected, this study suggests that increased Trp, Thr, and Met (AA+) dietary supplementation could contribute to mitigating the side effects of these harmful risk factors in modern pig farms.},
}

@article {pmid38672250,
year = {2024},
author = {Mickiewicz-Góra, D and Sznurkowska, K and Drozd, A and Borkowska, A and Zagierski, M and Troch, J and Skonieczna-Żydecka, K and Szlagatys-Sidorkiewicz, A},
title = {No Impact of Enteral Nutrition on Fecal Short-Chain Fatty Acids in Children with Cerebral Palsy.},
journal = {Biomedicines},
volume = {12},
number = {4},
pages = {},
pmid = {38672250},
issn = {2227-9059},
support = {01-0329/08/153//Medical University of Gdańsk/ ; },
abstract = {Bacteria can impact the host organism through their metabolites, with short-chain fatty acids (SCFAs) being the most important, including acetate (C2), propionate (C3), butyrate (C4), valerate (C5n), and isovalerate (C5i). This study aimed to identify the impact of enteral nutrition on SCFAs in children with cerebral palsy and to test the hypothesis that the type of nutrition in cerebral palsy affects gut SCFA levels. Cerebral palsy is a heterogeneous syndrome resulting from non-progressive damage to the central nervous system. The study group included 30 children diagnosed with cerebral palsy, receiving enteral nutrition (Cerebral Palsy Enteral Nutrition (CPEN)) via gastrostomy. The first reference group (Cerebral Palsy Controls (CPCs)) consisted of 24 children diagnosed with cerebral palsy and fed orally on a regular diet. The second reference group (Healthy Controls (HCs)) consisted of 24 healthy children with no chronic disease and fed on a regular diet. Isolation and measurement of SCFAs were conducted using gas chromatography. Differences were observed in the median contents of isobutyric acid, valeric acid, and isovaleric acid between the CPC group, which had significantly higher levels of those acids than the HC group. No differences were found between the CPEN and CPC groups nor between the CPEN and HC groups. We conclude that enteral nutrition in cerebral palsy has no influence on the levels of SCFAs.},
}

@article {pmid38672158,
year = {2024},
author = {Itoh, K and Matsueda, S},
title = {Exploring the Potential of Humoral Immune Response to Commensal Bifidobacterium as a Biomarker for Human Health, including Both Malignant and Non-Malignant Diseases: A Perspective on Detection Strategies and Future Directions.},
journal = {Biomedicines},
volume = {12},
number = {4},
pages = {},
pmid = {38672158},
issn = {2227-9059},
abstract = {In this comprehensive review, we explore the pivotal role of commensal Bifidobacterium (c-BIF) as potent non-self-antigens through antigenic mimicry, along with exploring the potential of humoral immune responses for both malignant and non-malignant disease. c-BIF, a predominant component of the human gut microbiome encompassing around 90% of the human genome, has emerged as a pivotal player in human biology. Over recent decades, there has been extensive research elucidating the intricate connections between c-BIF and various facets of human health, with particular emphasis on their groundbreaking impact on anti-cancer effects and the management of non-malignant diseases. The multifaceted role of c-BIF is explored, ranging from enhancing anti-tumor immunity to improving the efficacy of anti-cancer and anti-infectious disease strategies, and serving as predictive biomarkers for various diseases. Recent studies highlight not only c-BIF's promotion of anti-tumor immunity but also their role in enhancing the efficacy of immune checkpoint inhibitors. The review emphasizes the promising avenue of manipulating the gut microbiota, particularly c-BIF, for modulating cancer immunotherapy with targeted effects on tumor cells while minimizing harm to normal tissue. In the context of infectious and inflammatory diseases, the crucial role of c-BIFs in the management of COVID-19 symptoms is examined, emphasizing their impact on the severity of and immune response to COVID-19. Furthermore, c-BIF exhibits preventive and therapeutic effects on Human Papillomaviruses (HPV) and shows promise in improving inflammatory bowel diseases. The potential application of c-BIF as a biomarker for immunotherapy is explored, with a specific emphasis on its predictive and prognostic value in cancer. Suggestions are made regarding the use of humoral immune responses to cytotoxic T lymphocyte (CTL) epitope peptides that share motifs with c-BIF, proposing them as potential markers for predicting overall survival in diverse cancer patients. In conclusion, c-BIF emerges as a crucial and multifaceted determinant of human health, across anti-tumor immunity to infectious and inflammatory disease management. The manipulation of c-BIF and gut microbiota presents a promising avenue for advancing therapeutic strategies, particularly in the realm of cancer immunotherapy. Additionally, this review highlights the significance of c-BIF as potent non-self-antigens via antigenic mimicry, emphasizing the importance of robust humoral immune responses against c-BIF for preventing various diseases, including inflammatory conditions. Elevated levels of circulating antibodies against c-BIF in healthy individuals may serve as potential indicators of lower risks for malignant and non-malignant diseases.},
}

@article {pmid38672155,
year = {2024},
author = {Shin, J and Baek, GH and Cha, B and Park, SH and Lee, JH and Kim, JS and Kwon, KS},
title = {Complementary Therapeutic Effect of Fecal Microbiota Transplantation in Ulcerative Colitis after the Response to Anti-Tumor Necrosis Factor Alpha Agent Was Lost: A Case Report.},
journal = {Biomedicines},
volume = {12},
number = {4},
pages = {},
pmid = {38672155},
issn = {2227-9059},
support = {2021R1G1A1095241//National Research Foundation of Korea/ ; },
abstract = {In patients with ulcerative colitis (UC), the development of an antidrug antibody (ADA) to anti-tumor necrosis factor (TNF)α agent is a crucial problem which aggravates the clinical course of the disease, being cited as one of the most common causes for discontinuing anti-TNFα treatment. This is due to ADA eventually causing secondary LOR, leading to discontinuation of anti-TNFα treatment. Recently, research on the microbiome and relationship between worsening UC and dysbiosis has been conducted. Further, investigations on the association between the microbiome and secondary LOR are increasing. Here, we present the therapeutic effect of fecal microbiota transplantation (FMT) on a 42-year-old man with secondary LOR and high ADA levels. FMT has recently been used for the treatment of, and for overcoming, drug resistance through microbiome modification. Stool samples were collected from the patient before and 4 weeks after FMT. Symptoms, including hematochezia and Mayo endoscopy sub-scores, improved after FMT, while ADA levels decreased by one-third to less than half the value (29 ng/mL) compared to before FMT (79 ng/mL). Additionally, the trough level of infliximab became measurable, which reflects the improvement in the area under the concentration (AUC). Butyricicoccus, Faecalibacterium, Bifidobacterium, Ligilactobacillus, Alistipes, and Odoribacter, which regulate immune responses and alleviate inflammation, also increased after FMT. We report a case in which microbiome modification by FMT increased the AUC of anti-TNFα in a patient who developed secondary LOR during anti-TNFα treatment, thereby improving symptoms and mucosal inflammation.},
}

@article {pmid38672096,
year = {2024},
author = {Garvey, M},
title = {Intestinal Dysbiosis: Microbial Imbalance Impacts on Colorectal Cancer Initiation, Progression and Disease Mitigation.},
journal = {Biomedicines},
volume = {12},
number = {4},
pages = {},
pmid = {38672096},
issn = {2227-9059},
abstract = {The human gastrointestinal tract houses a diverse range of microbial species that play an integral part in many biological functions. Several preclinical studies using germ-free mice models have demonstrated that the gut microbiome profoundly influences carcinogenesis and progression. Colorectal cancer appears to be associated with microbial dysbiosis involving certain bacterial species, including F. nucleatum, pks+ E. coli, and B. fragilis, with virome commensals also disrupted in patients. A dysbiosis toward these pro-carcinogenic species increases significantly in CRC patients, with reduced numbers of the preventative species Clostridium butyicum, Roseburia, and Bifidobacterium evident. There is also a correlation between Clostridium infection and CRC. F. nucleatum, in particular, is strongly associated with CRC where it is associated with therapeutic resistance and poor outcomes in patients. The carcinogenic mode of action of pathogenic bacteria in CRC is a result of genotoxicity, epigenetic alterations, ROS generation, and pro-inflammatory activity. The aim of this review is to discuss the microbial species and their impact on colorectal cancer in terms of disease initiation, progression, and metastasis. The potential of anticancer peptides as anticancer agents or adjuvants is also discussed, as novel treatment options are required to combat the high levels of resistance to current pharmaceutical options.},
}

@article {pmid38672071,
year = {2024},
author = {Ancuţa, DL and Alexandru, DM and Crivineanu, M and Coman, C},
title = {Induction of Experimental Peri-Implantitis with Strains Selected from the Human Oral Microbiome.},
journal = {Biomedicines},
volume = {12},
number = {4},
pages = {},
pmid = {38672071},
issn = {2227-9059},
abstract = {Peri-implantitis (PI), the most widespread condition in the oral cavity, affects patients globally; thus, advanced research in both in vitro and in vivo studies is required. This study aimed to develop peri-implantitis in the rat model by oral contamination with bacteria responsible for PI in humans. The study was carried out in three stages: the extraction of the maxillary first molar to reproduce the human edentation, the mounting of the implant, and finally, the contamination of the device by gavage with Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum and Streptococcus oralis. The hematological examinations showed statistically significant increases for WBCs (white blood cells), Hb (hemoglobin), RBCs (red blood cells), MCH (mean corpuscular hemoglobin), MCHC (mean corpuscular hemoglobin concentration), and PLTs (platelets), but especially for the level of neutrophils and lymphocytes, and the systemic immunoinflammatory index completed the picture related to the inflammatory response triggered as a result of the activity of microorganisms pathogens on oral tissues. By examining the liver and kidney profile, we hypothesized that peri-implantitis is associated with systemic diseases, and the histopathological examination showed peri-implantitis lesions characterized by a marked inflammatory infiltrate with numerous neutrophils and lymphocytes. By corroborating all the results, we successfully developed a rat peri-implantitis model using a mixed bacterial infection through the oral gavage technique.},
}

@article {pmid38671932,
year = {2024},
author = {Senavirathna, T and Shafaei, A and Lareu, R and Balmer, L},
title = {Unlocking the Therapeutic Potential of Ellagic Acid for Non-Alcoholic Fatty Liver Disease and Non-Alcoholic Steatohepatitis.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38671932},
issn = {2076-3921},
abstract = {Obesity is in epidemic proportions in many parts of the world, contributing to increasing rates of non-alcoholic fatty liver disease (NAFLD). NAFLD represents a range of conditions from the initial stage of fatty liver to non-alcoholic steatohepatitis (NASH), which can progress to severe fibrosis, through to hepatocellular carcinoma. There currently exists no treatment for the long-term management of NAFLD/NASH, however, dietary interventions have been investigated for the treatment of NASH, including several polyphenolic compounds. Ellagic acid is one such polyphenolic compound. Nutraceutical food abundant in ellagic acid undergoes initial hydrolysis to free ellagic acid within the stomach and small intestine. The proposed mechanism of action of ellagic acid extends beyond its initial therapeutic potential, as it is further broken down by the gut microbiome into urolithin. Both ellagic acid and urolithin have been found to alleviate oxidative stress, inflammation, and fibrosis, which are associated with NAFLD/NASH. While progress has been made in understanding the pharmacological and biological activity of ellagic acid and its involvement in NAFLD/NASH, it has yet to be fully elucidated. Thus, the aim of this review is to summarise the currently available literature elucidating the therapeutic potential of ellagic acid and its microbial-derived metabolite urolithin in NAFLD/NASH.},
}

@article {pmid38671919,
year = {2024},
author = {Santilli, A and Shapiro, D and Han, Y and Sangwan, N and Cresci, GAM},
title = {Tributyrin Supplementation Rescues Chronic-Binge Ethanol-Induced Oxidative Stress in the Gut-Lung Axis in Mice.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38671919},
issn = {2076-3921},
support = {R01AA028043/AA/NIAAA NIH HHS/United States ; S10OD02520/GF/NIH HHS/United States ; },
abstract = {Excessive alcohol consumption increases the severity and worsens outcomes of pulmonary infections, often due to oxidative stress and tissue damage. While the mechanism behind this relationship is multifaceted, recent evidence suggests ethanol-induced changes to the gut microbiome impact the gut-lung axis. To assess this, a chronic-binge ethanol feeding mouse model was used to determine how ethanol altered the gut microbiome, small intestinal epithelial barrier, and immune responses, as well as neutrophil abundance and oxidative stress in the lungs, and how supporting gut health with tributyrin supplementation during chronic-binge ethanol exposure affected these responses. We found that ethanol consumption altered gut bacterial taxa and metabolic processes, distorted small intestinal immune responses, and induced both bacteria and endotoxin translocation into the lymphatic and circulatory systems. These changes were associated with increased neutrophil (Ly6G) presence and markers of oxidative stress, lipocalin-2 and myeloperoxidase, in the lungs. Importantly, tributyrin supplementation during ethanol exposure rescued gut bacterial function (p < 0.05), small intestinal barrier integrity, and immune responses, as well as reducing both Ly6G mRNA (p < 0.05) and lipocalin-2 mRNA (p < 0.01) in the lungs. These data suggest ethanol-associated disruption of gut homeostasis influenced the health of the lungs, and that therapeutics supporting gut health may also support lung health.},
}

@article {pmid38671402,
year = {2024},
author = {Zhou, Q and Wang, Y and Yue, L and Ye, A and Xie, X and Zhang, M and Tian, Y and Liu, Y and Turatsinze, AN and Constantine, U and Zhao, X and Zhang, Y and Wang, R},
title = {Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {340},
pmid = {38671402},
issn = {1471-2229},
mesh = {*Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Astragalus Plant/microbiology ; Plant Exudates/metabolism ; Fungi/genetics/physiology ; Crop Production/methods ; Bacteria/genetics/metabolism ; },
abstract = {Astragalus mongholicus is a medicinal plant that is known to decrease in quality in response to continuous cropping. However, the differences in the root-associated microbiome and root exudates in the rhizosphere soil that may lead to these decreases are barely under studies. We investigated the plant biomass production, root-associated microbiota, and root exudates of A. mongholicus grown in two different fields: virgin soil (Field I) and in a long-term continuous cropping field (Field II). Virgin soil is soil that has never been cultivated for A. mongholicus. Plant physiological measurements showed reduced fresh and dry weight of A. mongholicus under continuous cropping conditions (i.e. Field II). High-throughput sequencing of the fungal and bacterial communities revealed differences in fungal diversity between samples from the two fields, including enrichment of potentially pathogenic fungi in the roots of A. mongholicus grown in Field II. Metabolomic analysis yielded 20 compounds in A. mongholicus root exudates that differed in relative abundance between rhizosphere samples from the two fields. Four of these metabolites (2-aminophenol, quinic acid, tartaric acid, and maleamate) inhibited the growth of A. mongholicus, the soil-borne pathogen Fusarium oxysporum, or both. This comprehensive analysis enhances our understanding of the A. mongholicus microbiome, root exudates, and interactions between the two in response to continuous cropping. These results offer new information for future design of effective, economical approaches to achieving food security.},
}

*Rhizosphere
*Plant Roots/microbiology
*Microbiota
*Soil Microbiology
Astragalus Plant/microbiology
Plant Exudates/metabolism
Fungi/genetics/physiology
Crop Production/methods
Bacteria/genetics/metabolism

@article {pmid38671289,
year = {2024},
author = {Ślusarczyk, A and Ismail, H and Zapała, Ł and Piecha, T and Zapała, P and Radziszewski, P},
title = {ASO Visual Abstract: Changes in the Urinary Microbiome following Transurethral Resection of Non-muscle-invasive Bladder Cancer-Insights from a Prospective Observational Study.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1245/s10434-024-15340-7},
pmid = {38671289},
issn = {1534-4681},
}

@article {pmid38671238,
year = {2024},
author = {Juliyanti, V and Itakura, R and Kotani, K and Lim, SY and Suzuki, G and Chong, CW and Song, BK and Rahman, S},
title = {Comparative analysis of root associated microbes in tropical cultivated and weedy rice (Oryza spp.) and temperate cultivated rice.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9656},
pmid = {38671238},
issn = {2045-2322},
mesh = {*Oryza/microbiology/growth & development ; *Plant Roots/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Rhizosphere ; *Soil Microbiology ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Tropical Climate ; Plant Weeds/microbiology ; },
abstract = {Weedy rice is a major problem in paddy fields around the world. It is well known that weedy rice appears to grow faster and mature earlier than cultivated rice. It is possible that differences in the root microbial genetics are correlated with this characteristic. This study incorporated 16S rRNA amplicon sequencing to study the microbial composition in the rhizosphere and endosphere of rice root. No significant difference was found between the microbiota associated with weedy and cultivated rice lines grown in the same field. It was found that the endosphere had less microbial diversity compared to the rhizosphere. The major groups of bacteria found in the endosphere are from the phylum Proteobacteria, Myxococcota, Chloroflexota, and Actinobacteria. In addition, by analyzing the microbiome of japonica rice grown in the field in a temperate climate, we found that despite differences in genotype and location, some bacterial taxa were found to be common and these members of the putative rice core microbiome can also be detected by in situ hybridization. The delineation of a core microbiome in the endosphere of rice suggests that these bacterial taxa might be important in the life cycle of a wide range of rice types.},
}

*Oryza/microbiology/growth & development
*Plant Roots/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Rhizosphere
*Soil Microbiology
Bacteria/genetics/classification/isolation & purification
Phylogeny
Tropical Climate
Plant Weeds/microbiology

@article {pmid38670721,
year = {2024},
author = {Bracamonte-Baran, W and Kim, ST},
title = {The Current and Future of Biomarkers of Immune Related Adverse Events.},
journal = {Rheumatic diseases clinics of North America},
volume = {50},
number = {2},
pages = {201-227},
doi = {10.1016/j.rdc.2024.01.004},
pmid = {38670721},
issn = {1558-3163},
mesh = {Humans ; *Biomarkers ; *Immune Checkpoint Inhibitors/adverse effects ; Neoplasms/immunology ; Autoimmune Diseases/immunology ; },
abstract = {With their groundbreaking clinical responses, immune checkpoint inhibitors (ICIs) have ushered in a new chapter in cancer therapeutics. However, they are often associated with life-threatening or organ-threatening autoimmune/autoinflammatory phenomena, collectively termed immune-related adverse events (irAEs). In this review, we will first describe the mechanisms of action of ICIs as well as irAEs. Next, we will review biomarkers for predicting the development of irAEs or stratifying risks.},
}

Humans
*Biomarkers
*Immune Checkpoint Inhibitors/adverse effects
Neoplasms/immunology
Autoimmune Diseases/immunology

@article {pmid38670362,
year = {2024},
author = {Guo, D and Wang, Y and Li, Z and Zhang, DX and Wang, C and Wang, H and Liu, Z and Liu, F and Guo, X and Wang, N and Xu, B and Gao, Z},
title = {Effects of abamectin nanocapsules on bees through host physiology, immune function, and gut microbiome.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172738},
doi = {10.1016/j.scitotenv.2024.172738},
pmid = {38670362},
issn = {1879-1026},
abstract = {Pesticide usage is a common practice to increase crop yields. Nevertheless, the existence of pesticide residues in the surrounding environment presents a significant hazard to pollinators, specifically the potential undisclosed dangers related to emerging nanopesticides. This study examines the impact of abamectin nanocapsules (AbaNCs), created through electrostatic self-assembly, as an insecticide on honey bees. It was determined that AbaNCs upregulated detoxification genes, including CYP450, as well as antioxidant and immune genes in honey bees. Furthermore, AbaNCs affected the activity of crucial enzymes such as superoxide dismutase (SOD). Although no apparent damage was observed in bee gut tissue, AbaNCs significantly decreased digestive enzyme activity. Microbiome sequencing revealed that AbaNCs disrupted gut microbiome, resulting in a reduction of beneficial bacteria such as Bifidobacterium and Lactobacillus. Additionally, these changes in the gut microbiome were associated with decreased activity of digestive enzymes, including lipase. This study enhances our understanding of the impact of nanopesticides on pollinating insects. Through the revelation of the consequences arising from the utilization of abamectin nanocapsules, we have identified potential stress factors faced by these pollinators, enabling the implementation of improved protective measures.},
}

@article {pmid38670232,
year = {2024},
author = {Hoskinson, C and Medeleanu, MV and Reyna, ME and Dai, DL and Chowdhury, B and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Petersen, C and Turvey, SE and Subbarao, P},
title = {Antibiotics within first year are linked to infant gut microbiome disruption and elevated atopic dermatitis risk.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.03.025},
pmid = {38670232},
issn = {1097-6825},
abstract = {BACKGROUND: Atopic dermatitis (AD) is the most common chronic inflammatory skin disease in both pediatric and adult populations. The development of AD has been linked to antibiotic usage, which causes perturbation of the microbiome and has been associated with abnormal immune system function. However, imbalances in the gut microbiome itself associated with antibiotic usage have been inconsistently linked to AD.

OBJECTIVE: This study aimed to elucidate the timing and specific factors mediating the relationship between systemic (oral or intravenous) antibiotic usage and AD.

METHODS: We used statistical modelling and differential analysis to link CHILD participants' history of antibiotic usage and early-life gut microbiome alterations to atopic dermatitis.

RESULTS: Here we report that systemic antibiotics during the first year of life, as compared to later, are associated with AD risk (adjusted odds ratio (aOR) = 1.81 [95% CI = 1.28 - 2.57], p < 0.001), with an increased number of antibiotic courses corresponding to a dose-response-like increased risk of AD risk (1 course: aOR = 1.67 [95% CI = 1.17 - 2.38]; 2 or more courses: aOR = 2.16 [95% CI = 1.30 - 3.59]). Further, we demonstrate that microbiome alterations associated with both AD and systemic antibiotic usage fully mediate the effect of antibiotic usage on the development of AD (βindirect = 0.072, p < 0.001). Alterations in the 1-year infant gut microbiome of participants who would later develop AD included increased Tyzzerella nexilis, increased monosaccharide utilization, and parallel decreased Bifidobacterium, Eubacterium spp., and fermentative pathways.

CONCLUSION: Our findings indicate that early-life antibiotic usage, especially in the first year of life, modulates key gut microbiome components that may be used as markers to predict and possibly prevent the development of AD.},
}

@article {pmid38670215,
year = {2024},
author = {Zaatry, R and Herren, R and Gefen, T and Geva-Zatorsky, N},
title = {MICROBIOME and INFECTIOUS DISEASE: DIAGNOSTICS to THERAPEUTICS.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105345},
doi = {10.1016/j.micinf.2024.105345},
pmid = {38670215},
issn = {1769-714X},
abstract = {Over 300 years of research on the microbial world has revealed their importance in human health and disease. This review explores the impact and potential of microbial-based detection methods and therapeutic interventions, integrating research of early microbiologists, current findings, and future perspectives.},
}

@article {pmid38670070,
year = {2024},
author = {Wong, CC and Yu, J},
title = {Mapping the pancancer metastasis tumor microbiome.},
journal = {Cell},
volume = {187},
number = {9},
pages = {2126-2128},
doi = {10.1016/j.cell.2024.03.040},
pmid = {38670070},
issn = {1097-4172},
mesh = {Humans ; *Microbiota ; *Neoplasm Metastasis ; Neoplasms/pathology/microbiology ; },
abstract = {The landscape of the intratumoral microbiome in tumor metastases is largely unchartered. In this issue of Cell, Voest et al. profiled the tumor metastasis-associated microbiome in a pancancer cohort of 4,160 biopsies from 26 cancer types. This dataset offers a useful resource for understanding the role of the microbiome in metastatic cancers.},
}

Humans
*Microbiota
*Neoplasm Metastasis
Neoplasms/pathology/microbiology

@article {pmid38670037,
year = {2024},
author = {Wen, X and Xu, J and Wang, Y and Yang, X and Peng, G and Li, S and Ma, B and Zou, Y and Liao, X and Wang, Y and Worrich, A and Wu, Y},
title = {Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127734},
doi = {10.1016/j.micres.2024.127734},
pmid = {38670037},
issn = {1618-0623},
abstract = {The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10[-3] copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.},
}

@article {pmid38669694,
year = {2024},
author = {Ho, CC and Gilbert, MB and Urtecho, G and Lee, H and Drew, DA and Klempner, SJ and Cho, JS and Ryan, TJ and Rustgi, N and Lee, H and Lee, J and Caraballo, A and Magicheva-Gupta, MV and Rios, C and Shin, AE and Tseng, YY and Davis, JL and Chung, DC and Chan, AT and Wang, HH and Ryeom, S},
title = {Stool protein mass spectrometry identifies biomarkers for the early detection of diffuse-type gastric cancer.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-23-0449},
pmid = {38669694},
issn = {1940-6215},
abstract = {There is a high unmet need for early detection approaches for diffuse gastric cancer (DGC). We examined whether the stool proteome of mouse models of GC or individuals with hereditary diffuse GC (HDGC) have utility as biomarkers for early detection. Proteomic mass spectrometry of stool from a genetically engineered mouse model driven by oncogenic KrasG12D and loss of p53 and Cdh1 in gastric parietal cells (known as TCON mice) identified differentially abundant proteins compared to littermate controls. Immunoblot assays validated a panel of proteins including actinin alpha 4 (ACTN4), N-acylsphingosine amidohydrolase 2 (ASAH2), dipeptidyl peptidase 4 (DPP4), and valosin-containing protein (VCP) as enriched in TCON stool compared to littermate control stool. Immunofluorescence analysis of these proteins in TCON stomach sections revealed increased protein expression as compared to littermate controls. Proteomic mass spectrometry of stool obtained from HDGC patients with CDH1 mutations identified increased expression of ASAH2, DPP4, VCP, lactotransferrin (LTF), and tropomyosin-2 (TPM2) relative to stool from healthy sex and age-matched donors. Chemical inhibition of ASAH2 using C6-urea ceramide was toxic to GC cell lines and patient derived-GC organoids. This toxicity was reversed by adding downstream products of the S1P synthesis pathway, suggesting a dependency on ASAH2 activity in GC. An exploratory analysis of the HDGC stool microbiome identified features which correlated with patient tumors. Here we provide evidence supporting the potential of analyzing stool biomarkers for the early detection of DGC.},
}

@article {pmid38669258,
year = {2024},
author = {Zeber-Lubecka, N and Kulecka, M and Dabrowska, M and Baginska-Drabiuk, K and Glowienka-Stodolak, M and Nowakowski, A and Slabuszewska-Jozwiak, A and Bednorz, B and Jędrzejewska, I and Piasecka, M and Pawelec, J and Wojciechowska-Lampka, E and Ostrowski, J},
title = {Cervical microbiota dysbiosis associated with high-risk Human Papillomavirus infection.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302270},
doi = {10.1371/journal.pone.0302270},
pmid = {38669258},
issn = {1932-6203},
mesh = {Humans ; Female ; *Papillomavirus Infections/virology/microbiology/complications ; *Dysbiosis/microbiology/virology ; *Microbiota ; Adult ; *Cervix Uteri/microbiology/virology ; *Lactobacillus/isolation & purification/genetics ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Uterine Cervical Neoplasms/microbiology/virology ; Human papillomavirus 16/genetics/isolation & purification ; Case-Control Studies ; Human papillomavirus 18/genetics/isolation & purification ; Uterine Cervical Dysplasia/microbiology/virology ; },
abstract = {High-risk Human Papillomavirus (HR-HPV) genotypes, specifically HPV16 and HPV18, pose a significant risk for the development of cervical intraepithelial neoplasia and cervical cancer. In the multifaceted cervical microenvironment, consisting of immune cells and diverse microbiota, Lactobacillus emerges as a pivotal factor, wielding significant influence in both stabilizing and disrupting the microbiome of the reproductive tract. To analyze the distinction between the cervical microbiota and Lactobacillus-dominant/non-dominant status of HR-HPV and non-infected healthy women, sixty-nine cervical swab samples were analyzed, included 44 with HR-HPV infection and healthy controls. All samples were recruited from Human Papillomavirus-based cervical cancer screening program and subjected to 16s rRNA sequencing analysis. Alpha and beta diversity analyses reveal no significant differences in the cervical microbiota of HR-HPV-infected women, including 16 and 18 HPV genotypes, and those with squamous intraepithelial lesion (SIL), compared to a control group. In this study we identified significantly lower abundance of Lactobacillus mucosae in women with HR-HPV infection compared to the control group. Furthermore, changes in bacterial diversity were noted in Lactobacillus non-dominant (LND) samples compared to Lactobacillus-dominant (LD) in both HR-HPV-infected and control groups. LND samples in HR-HPV-infected women exhibited a cervical dysbiotic state, characterized by Lactobacillus deficiency. In turn, the LD HR-HPV group showed an overrepresentation of Lactobacillus helveticus. In summary, our study highlighted the distinctive roles of L. mucosae and L. helveticus in HR-HPV infections, signaling a need for further research to demonstrate potential clinical implications of cervical microbiota dysbiosis.},
}

Humans
Female
*Papillomavirus Infections/virology/microbiology/complications
*Dysbiosis/microbiology/virology
*Microbiota
Adult
*Cervix Uteri/microbiology/virology
*Lactobacillus/isolation & purification/genetics
*RNA, Ribosomal, 16S/genetics
Middle Aged
Uterine Cervical Neoplasms/microbiology/virology
Human papillomavirus 16/genetics/isolation & purification
Case-Control Studies
Human papillomavirus 18/genetics/isolation & purification
Uterine Cervical Dysplasia/microbiology/virology

@article {pmid38669216,
year = {2024},
author = {Wagner, MR},
title = {Identifying causes and consequences of rhizosphere microbiome heritability.},
journal = {PLoS biology},
volume = {22},
number = {4},
pages = {e3002604},
pmid = {38669216},
issn = {1545-7885},
mesh = {*Rhizosphere ; *Microbiota/genetics ; *Hordeum/microbiology/genetics ; Soil Microbiology ; Genotype ; Bacteria/genetics/classification ; Plant Roots/microbiology/genetics ; },
abstract = {Host genotype affects microbiome composition in many plants, but the mechanisms and implications of this phenomenon are understudied. New work in PLOS Biology illustrates how host genotype leads to differential gene expression and fitness in bacteria of the barley rhizosphere.},
}

*Rhizosphere
*Microbiota/genetics
*Hordeum/microbiology/genetics
Soil Microbiology
Genotype
Bacteria/genetics/classification
Plant Roots/microbiology/genetics

@article {pmid38669195,
year = {2024},
author = {Sengupta, S and Pabbaraja, S and Mehta, G},
title = {Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery.},
journal = {Organic & biomolecular chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4ob00236a},
pmid = {38669195},
issn = {1477-0539},
abstract = {Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.},
}

@article {pmid38668956,
year = {2024},
author = {Puga, MI and Poza-Carrión, C and Martinez-Hevia, I and Perez-Liens, L and Paz-Ares, J},
title = {Recent advances in research on phosphate starvation signaling in plants.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {38668956},
issn = {1618-0860},
abstract = {Phosphorus is indispensable for plant growth and development, with its status crucial for determining crop productivity. Plants have evolved various biochemical, morphological, and developmental responses to thrive under conditions of low P availability, as inorganic phosphate (Pi), the primary form of P uptake, is often insoluble in soils. Over the past 25 years, extensive research has focused on understanding these responses, collectively forming the Pi starvation response system. This effort has not only expanded our knowledge of strategies to cope with Pi starvation (PS) but also confirmed their adaptive significance. Moreover, it has identified and characterized numerous components of the intricate regulatory network governing P homeostasis. This review emphasizes recent advances in PS signaling, particularly highlighting the physiological importance of local PS signaling in inhibiting primary root growth and uncovering the role of TORC1 signaling in this process. Additionally, advancements in understanding shoot-root Pi allocation and a novel technique for studying Pi distribution in plants are discussed. Furthermore, emerging data on the regulation of plant-microorganism interactions by the PS regulatory system, crosstalk between the signaling pathways of phosphate starvation, phytohormones and immunity, and recent studies on natural variation in Pi homeostasis are addressed.},
}

@article {pmid38668878,
year = {2024},
author = {Farfour, E and Vasse, M and Vallée, A},
title = {Oligella spp.: A systematic review on an uncommon urinary pathogen.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38668878},
issn = {1435-4373},
abstract = {BACKGROUND: Oligella is an uncommon Gram-negative coccobacillus that was first thought to belong to the urogenital tract. The genus Oligella comprises two species that were recovered from various samples worldwide.

METHODS: We perform a systematic review focusing on Oligella microbiological characteristics, habitat, role in Human microbiome and infection, and antimicrobial susceptibility.

RESULTS: In humans, Oligella is mainly found as part of the microbiome of individuals with predisposing conditions. Oligella were also associated with invasive infections in patients with underlying diseases. Nevertheless, their prevalence remains to determine. Oligella culture requires up to 48 h on agar media in vitro, while urinary samples are usually incubated for 24 h. Consequently, microbiologists should be prompt to prolong the incubation of agar media when the direct examination showed Gram-negative coccobacilli. Oligella is accurately identified using MALDI-TOF mass spectrometry, but biochemical methods often provided inconsistent results. Specific guidelines for antimicrobial susceptibility testing of Oligella lack but the incubation could require up to 48 h of incubation. In contrast to O. urethralis, which is susceptible to third-generation cephalosporin, O. ureolytica is likely resistant to numerous antimicrobials. Genectic determinants of resistance were identified for beta-lactams and aminoglycosides.

CONCLUSION: Oligella is an uncommon pathogen that can be underrecognized. Microbiologists should be prompt to prolong the incubation of agar media plated with urines when the direct examination showed Gram-negative coccobacilli. Carbapenems should probably be given for the empirical treatment.},
}

@article {pmid38668783,
year = {2024},
author = {Shamjana, U and Vasu, DA and Hembrom, PS and Nayak, K and Grace, T},
title = {The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {71},
pmid = {38668783},
issn = {1572-9699},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Insecta/microbiology ; *Symbiosis ; Nutrients/metabolism ; Metagenomics ; Host Microbial Interactions ; Inactivation, Metabolic ; Bacteria/classification/genetics/metabolism ; },
abstract = {Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Insecta/microbiology
*Symbiosis
Nutrients/metabolism
Metagenomics
Host Microbial Interactions
Inactivation, Metabolic
Bacteria/classification/genetics/metabolism

@article {pmid38668709,
year = {2024},
author = {Mehdipour, A and Fateh, R and Fuladvand, F and Aghaali, M and Keykha, E and Hadilou, M},
title = {Association between sleep pattern, salivary cariogenic bacteria and fungi populations, pH and buffering capacity in children: A comparative study.},
journal = {Dental and medical problems},
volume = {61},
number = {2},
pages = {217-224},
doi = {10.17219/dmp/167411},
pmid = {38668709},
issn = {2300-9020},
mesh = {Humans ; Child ; *Saliva/microbiology/chemistry ; Hydrogen-Ion Concentration ; Cross-Sectional Studies ; Female ; Male ; *Dental Caries/microbiology ; Streptococcus mutans/isolation & purification ; Candida albicans/isolation & purification ; Buffers ; Lactobacillus/isolation & purification ; Sleep/physiology ; },
abstract = {BACKGROUND: Sleep quality has a significant impact on a child's health and is linked to oral and systemic diseases. It affects the circadian rhythm, which plays a crucial role in regulating the balance of the endocrine and hormonal systems. Current research has focused on exploring its role in the development of caries, which is influenced by inherent oral factors such as the composition of the oral microbiome and pH levels.

OBJECTIVES: This study aimed to investigate the relationship between bacterial population, pH, and buffering properties of saliva and sleep patterns in 8- to 12-year-old children.

MATERIAL AND METHODS: This cross-sectional study was conducted on 85 elementary school children aged 8-12 years. After obtaining written consent, non-stimulating saliva samples were collected using the spitting method. The participants' sleep pattern information was obtained with the use of the Persian version of the Children's Sleep Habits Questionnaire (CSHQ). Based on the results of the CSHQ, the participants were divided into 2 groups: those with appropriate sleep patterns; and those with inappropriate sleep patterns. The study compared the bacterial population of Streptococcus mutans, Lactobacillus spp. and Candida albicans, as well as the buffering capacity and pH of the saliva between the 2 groups. The statistical analysis employed the χ2 test, the independent samples t-test and Spearman's correlation.

RESULTS: The group with inappropriate sleep patterns had significantly lower pH and buffering capacity (p < 0.001) and significantly higher colony counts of Lactobacillus and S. mutans (p < 0.001 and p = 0.012, respectively). There was no association between C. albicans and sleep patterns (p = 0.121).

CONCLUSIONS: Inappropriate sleep patterns increase the population of caries-causing bacteria and reduce salivary pH and buffering capacity. This can be a significant factor in the development of dental caries in children aged 8-12 years.},
}

Humans
Child
*Saliva/microbiology/chemistry
Hydrogen-Ion Concentration
Cross-Sectional Studies
Female
Male
*Dental Caries/microbiology
Streptococcus mutans/isolation & purification
Candida albicans/isolation & purification
Buffers
Lactobacillus/isolation & purification
Sleep/physiology

@article {pmid38668434,
year = {2024},
author = {Chow, L and Flaherty, E and Pezzanite, L and Williams, M and Dow, S and Wotman, K},
title = {Impact of Equine Ocular Surface Squamous Neoplasia on Interactions between Ocular Transcriptome and Microbiome.},
journal = {Veterinary sciences},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/vetsci11040167},
pmid = {38668434},
issn = {2306-7381},
support = {N/a//Colorado State University Young Investigator Grant in Companion Animal Studies/ ; },
abstract = {Ocular surface squamous neoplasia (OSSN) represents the most common conjunctival tumor in horses and frequently results in vision loss and surgical removal of the affected globe. Multiple etiologic factors have been identified as contributing to OSSN progression, including solar radiation exposure, genetic mutations, and a lack of periocular pigmentation. Response to conventional treatments has been highly variable, though our recent work indicates that these tumors are highly responsive to local immunotherapy. In the present study, we extended our investigation of OSSN in horses to better understand how the ocular transcriptome responds to the presence of the tumor and how the ocular surface microbiome may also be altered by the presence of cancer. Therefore, we collected swabs from the ventral conjunctival fornix from 22 eyes in this study (11 with cytologically or histologically confirmed OSSN and 11 healthy eyes from the same horses) and performed RNA sequencing and 16S microbial sequencing using the same samples. Microbial 16s DNA sequencing and bulk RNA sequencing were both conducted using an Illumina-based platform. In eyes with OSSN, we observed significantly upregulated expression of genes and pathways associated with inflammation, particularly interferon. Microbial diversity was significantly reduced in conjunctival swabs from horses with OSSN. We also performed interactome analysis and found that three bacterial taxa (Actinobacillus, Helcococcus and Parvimona) had significant correlations with more than 100 upregulated genes in samples from animals with OSSN. These findings highlight the inflammatory nature of OSSN in horses and provide important new insights into how the host ocular surface interacts with certain microbial populations. These findings suggest new strategies for the management of OSSN in horses, which may entail immunotherapy in combination with ocular surface probiotics or prebiotics to help normalize ocular cell and microbe interactions.},
}

@article {pmid38668367,
year = {2024},
author = {Bajic, D and Wiens, F and Wintergerst, E and Deyaert, S and Baudot, A and Abbeele, PVD},
title = {HMOs Impact the Gut Microbiome of Children and Adults Starting from Low Predicted Daily Doses.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668367},
issn = {2218-1989},
abstract = {Recent studies suggest that the dietary intake of human milk oligosaccharides (HMOs) provides health benefits from infancy up to adulthood. Thus far, beneficial changes in the adult gut microbiome have been observed at oral doses of 5-20 g/day of HMOs. Efficacy of lower doses has rarely been tested. We assessed four HMO molecular species-2'Fucosyllactose (2'FL), Lacto-N-neotetraose (LNnT), 3'Sialyllactose (3'SL), and 6'Sialyllactose (6'SL)-at predicted doses from 0.3 to 5 g/day for 6-year-old children and adults (n = 6 each), using ex vivo SIFR[®] technology (Cryptobiotix, Ghent, Belgium). This technology employing bioreactor fermentation on fecal samples enables us to investigate microbial fermentation products that are intractable in vivo given their rapid absorption/consumption in the human gut. We found that HMOs significantly increased short-chain fatty acids (SCFAs), acetate, propionate (in children/adults), and butyrate (in adults) from predicted doses of 0.3-0.5 g/day onwards, with stronger effects as dosing increased. The fermentation of 6'SL had the greatest effect on propionate, LNnT most strongly increased butyrate, and 2'FL and 3'SL most strongly increased acetate. An untargeted metabolomic analysis revealed that HMOs enhanced immune-related metabolites beyond SCFAs, such as aromatic lactic acids (indole-3-lactic acid/3-phenyllactic acid) and 2-hydroxyisocaproic acid, as well as gut-brain-axis-related metabolites (γ-aminobutyric acid/3-hydroxybutyric acid/acetylcholine) and vitamins. The effects of low doses of HMOs potentially originate from the highly specific stimulation of keystone species belonging to, for example, the Bifidobacteriaceae family, which had already significantly increased at doses of only 0.5 g/day LNnT (adults) and 1 g/day 2'FL (children/adults).},
}

@article {pmid38668317,
year = {2024},
author = {Shen, W and Zhao, M and Xu, W and Shi, X and Ren, F and Tu, P and Gao, N and Shan, J and Gao, B},
title = {Sex-Specific Effects of Polystyrene Microplastic and Lead(II) Co-Exposure on the Gut Microbiome and Fecal Metabolome in C57BL/6 Mice.},
journal = {Metabolites},
volume = {14},
number = {4},
pages = {},
pmid = {38668317},
issn = {2218-1989},
support = {42107459//National Natural Science Foundation of China/ ; },
abstract = {The wide spread of microplastics has fueled growing public health concern globally. Due to their porous structure and large surface area, microplastics can serve as carriers for other environmental pollutants, including heavy metals. Although the toxic effects of microplastics or heavy metals have been reported previously, investigations into the sex-differential health effects of combined exposure to microplastics and heavy metals are lacking. In the present study, the effects of polystyrene microplastics and lead(II) co-exposure on the gut microbiome, intestinal permeability, and fecal metabolome were examined in both male and female mice. Combined exposure of polystyrene microplastics and lead(II) increased intestinal permeability in both male and female mice. Sex-specific responses to the co-exposure were found in gut bacteria, fungi, microbial metabolic pathways, microbial genes encoding antibiotic resistance and virulence factors, as well as fecal metabolic profiles. In particular, Shannon and Simpson indices of gut bacteria were reduced by the co-exposure only in female mice. A total of 34 and 13 fecal metabolites were altered in the co-exposure group in female and male mice, respectively, among which only three metabolites were shared by both sexes. These sex-specific responses to the co-exposure need to be taken into consideration when investigating the combined toxic effects of microplastics and heavy metals on the gut microbiota.},
}

@article {pmid38668232,
year = {2024},
author = {Liu, A and Garrett, S and Hong, W and Zhang, J},
title = {Staphylococcus aureus Infections and Human Intestinal Microbiota.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/pathogens13040276},
pmid = {38668232},
issn = {2076-0817},
abstract = {Staphylococcus aureus (S. aureus) is a common pathogen that can cause many human diseases, such as skin infection, food poisoning, endocarditis, and sepsis. These diseases can be minor infections or life-threatening, requiring complex medical management resulting in substantial healthcare costs. Meanwhile, as the critically ignored "organ," the intestinal microbiome greatly impacts physiological health, not only in gastrointestinal diseases but also in disorders beyond the gut. However, the correlation between S. aureus infection and intestinal microbial homeostasis is largely unknown. Here, we summarized the recent progress in understanding S. aureus infections and their interactions with the microbiome in the intestine. These summarizations will help us understand the mechanisms behind these infections and crosstalk and the challenges we are facing now, which could contribute to preventing S. aureus infections, effective treatment investigation, and vaccine development.},
}

@article {pmid38668046,
year = {2024},
author = {Capella, MP and Esfahani, K},
title = {A Review of Practice-Changing Therapies in Oncology in the Era of Personalized Medicine.},
journal = {Current oncology (Toronto, Ont.)},
volume = {31},
number = {4},
pages = {1913-1919},
pmid = {38668046},
issn = {1718-7729},
mesh = {Humans ; *Precision Medicine/methods ; *Neoplasms/therapy ; *Medical Oncology/methods/trends ; },
abstract = {In the past decade, a lot of insight was gathered into the composition of the host and tumor factors that promote oncogenesis and treatment resistance. This in turn has led to the ingenious design of multiple new classes of drugs, which have now become the new standards of care in cancer therapy. These include novel antibody-drug conjugates, chimeric antigen receptor T cell therapies (CAR-T), and bispecific T cell engagers (BitTE). Certain host factors, such as the microbiome composition, are also emerging not only as biomarkers for the response and toxicity to anti-cancer therapies but also as potentially useful tools to modulate anti-tumor responses. The field is slowly moving away from one-size-fits-all treatment options to personalized treatments tailored to the host and tumor. This commentary aims to cover the basic concepts associated with these emerging therapies and the promises and challenges to fight cancer.},
}

Humans
*Precision Medicine/methods
*Neoplasms/therapy
*Medical Oncology/methods/trends

@article {pmid38668025,
year = {2024},
author = {Parga, A and Pose-Rodríguez, JM and Muras, A and Baus-Domínguez, M and Otero-Casal, P and Ortega-Quintana, ML and Torres-Lagares, D and Otero, A},
title = {Do Concurrent Peri-Implantitis and Periodontitis Share Their Microbiotas? A Pilot Study.},
journal = {Dentistry journal},
volume = {12},
number = {4},
pages = {},
pmid = {38668025},
issn = {2304-6767},
support = {ED6481B-2023/117//Xunta de Galicia/ ; },
abstract = {The microbial compositions from concurrent peri-implant and periodontal lesions were compared, since the results reported in the literature on the etiological relationship between these oral pathologies are contradictory. Microbial compositions from nine patients were evaluated using Illumina MiSeq sequencing of 16S rRNA gene amplicons and Principal Components Analysis. Comparisons between the use of curettes or paper points as collection methods and between bacterial composition in both pathologies were performed. Paper points allowed the recovery of a higher number of bacterial genera. A higher bacterial diversity was found in peri-implantitis compared to periodontal samples from the same patient, while a greater number of operational taxonomic units (OTUs) were present in the corresponding periodontal samples. A higher abundance of oral pathogens, such as Porphyromonas or Treponema, was found in peri-implantitis sites. The opposite trend was observed for Aggregatibacter abundance, which was higher in periodontal than in peri-implantitis lesions, suggesting that both oral pathologies could be considered different but related diseases. Although the analysis of a higher number of samples would be needed, the differences regarding the microbial composition provide a basis for further understating the pathogenesis of peri-implant infections.},
}

@article {pmid38667474,
year = {2024},
author = {Ju, HM and Ahn, YW and Ok, SM and Jeong, SH and Na, HS and Chung, J},
title = {Microbial Profiles in Oral Lichen Planus: Comparisons with Healthy Controls and Erosive vs. Non-Erosive Subtypes.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {38667474},
issn = {2075-4418},
support = {NRF-2017M3A9B6062021//National Research Foundation of Korea/ ; },
abstract = {Recent studies have begun exploring the potential involvement of microbiota in the pathogenesis of oral lichen planus (OLP), yet comprehensive investigations remain limited. Hence, this study aimed to compare the microbial profiles in saliva samples obtained from patients with OLP against those from healthy controls (HC), along with a comparison between erosive (E) and non-erosive (NE) OLP patients. Saliva samples were collected from 60 OLP patients (E: n = 25, NE: n = 35) and 30 HC individuals. Analysis revealed no significant differences in alpha diversity, as assessed by the Chao1 and Shannon index, across the three groups. However, Bray-Curtis distance analysis indicated a significant disparity in microbiome composition distribution between HC and E-OLP, as well as HC and NE-OLP groups. The six most abundant phyla observed across the groups were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Saccharibacteria (TM7). Notably, OLP groups exhibited a higher prevalence of Bacteroidetes. Prevotella emerged as the predominant genus in the OLP groups, while Capnocytophaga showed a relatively higher prevalence in E-OLP compared to NE-OLP. This study's findings indicate a notable difference in microbiota composition between HC and patients with OLP. Additionally, differences in the microbiome were identified between the E-OLP and NE-OLP groups. The increase in the proportion of certain bacterial species in the oral microbiome suggests that they may exacerbate the inflammatory response and act as antigens for OLP.},
}

@article {pmid38667404,
year = {2024},
author = {Cai, Z and Zhao, X and Qian, Y and Zhang, K and Guo, S and Kan, Y and Wang, Y and Ayra-Pardo, C and Li, D},
title = {Transcriptomic and Metatranscriptomic Analyses Provide New Insights into the Response of the Pea Aphid Acyrthosiphon pisum (Hemiptera: Aphididae) to Acetamiprid.},
journal = {Insects},
volume = {15},
number = {4},
pages = {},
pmid = {38667404},
issn = {2075-4450},
support = {31970480//National Natural Science Foundation of China/ ; 212300410063//Natural Science Foundation of Henan province/ ; 231111111000//Key Research Project of Henan Province/ ; },
abstract = {Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14,858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analyses revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.},
}

@article {pmid38667044,
year = {2024},
author = {Lardenoije, CMJG and van Riel, SJJM and Peters, LJF and Wassen, MMLH and Cremers, NAJ},
title = {Medical-Grade Honey as a Potential New Therapy for Bacterial Vaginosis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antibiotics13040368},
pmid = {38667044},
issn = {2079-6382},
abstract = {The prevalence of bacterial vaginosis (BV) among women of reproductive age is 29%. BV arises from a vaginal imbalance marked by reduced levels of lactic acid-producing lactobacilli and an overgrowth of pathogenic anaerobes. The multifactorial nature of BV's pathogenesis complicates its treatment. Current antibiotic therapy exhibits a recurrence rate of about 60% within a year. Recurrence can be caused by antibiotic treatment failure (e.g., due to antimicrobial resistance), the persistence of residual infections (e.g., due to biofilm formation), and re-infection. Because of the high recurrence rates, alternative therapies are required. Medical-grade honey (MGH), known for its antimicrobial and wound healing properties in wound care, emerges as a potential novel therapy for BV. MGH exerts broad-spectrum antimicrobial activity, employing multiple mechanisms to eliminate the risk of resistance. For example, the low pH of MGH and the production of hydrogen peroxide benefit the microbiota and helps restore the natural vaginal balance. This is supported by in vitro studies demonstrating that MGH has an antibacterial effect on several pathogenic bacteria involved in the pathophysiology of BV, while lactobacilli and the vaginal microenvironment can be positively affected. In contrast to antibiotics, MGH exerts anti-biofilm activity, affects the microbiome as pre- and probiotic, and modulates the vaginal microenvironment through its anti-inflammatory, anti-oxidative, physicochemical, and immunomodulatory properties. More clinical research is required to confirm the positive effect of MGH on BV and to investigate the long-term cure rate.},
}

@article {pmid38667028,
year = {2024},
author = {Junaid, M and Lu, H and Din, AU and Yu, B and Liu, Y and Li, Y and Liu, K and Yan, J and Qi, Z},
title = {Deciphering Microbiome, Transcriptome, and Metabolic Interactions in the Presence of Probiotic Lactobacillus acidophilus against Salmonella Typhimurium in a Murine Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38667028},
issn = {2079-6382},
support = {31660713, 81903168//National Natural Science Foundation of China/ ; 20212014//The Nanning Science and Technology base Project/ ; 20210035, 20220026//The Project of Bama Country for Talents in Science and Technology/ ; },
abstract = {Salmonella enterica serovar Typhimurium (S. Typhimurium), a foodborne pathogen that poses significant public health risks to humans and animals, presents a formidable challenge due to its antibiotic resistance. This study explores the potential of Lactobacillus acidophilus (L. acidophilus 1.3251) probiotics as an alternative strategy to combat antibiotic resistance associated with S. Typhimurium infection. In this investigation, twenty-four BALB/c mice were assigned to four groups: a non-infected, non-treated group (CNG); an infected, non-treated group (CPG); a group fed with L. acidophilus but not infected (LAG); and a group fed with L. acidophilus and challenged with Salmonella (LAST). The results revealed a reduction in Salmonella levels in the feces of mice, along with restored weight and improved overall health in the LAST compared to the CPG. The feeding of L. acidophilus was found to downregulate pro-inflammatory cytokine mRNA induced by Salmonella while upregulating anti-inflammatory cytokines. Additionally, it influenced the expression of mRNA transcript, encoding tight junction protein, oxidative stress-induced enzymes, and apoptosis-related mRNA expression. Furthermore, the LEfSe analysis demonstrated a significant shift in the abundance of critical commensal genera in the LAST, essential for maintaining gut homeostasis, metabolic reactions, anti-inflammatory responses, and butyrate production. Transcriptomic analysis revealed 2173 upregulated and 506 downregulated differentially expressed genes (DEGs) in the LAST vs. the CPG. Functional analysis of these DEGs highlighted their involvement in immunity, metabolism, and cellular development. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis indicated their role in tumor necrosis factor (TNF), mitogen-activated protein kinase (MAPK), chemokine, Forkhead box O (FOXO), and transforming growth factor (TGF-β) signaling pathway. Moreover, the fecal metabolomic analysis identified 929 differential metabolites, with enrichment observed in valine, leucine, isoleucine, taurine, glycine, and other metabolites. These findings suggest that supplementation with L. acidophilus promotes the growth of beneficial commensal genera while mitigating Salmonella-induced intestinal disruption by modulating immunity, gut homeostasis, gut barrier integrity, and metabolism.},
}

@article {pmid38667016,
year = {2024},
author = {Twomey, E and O'Connor, PM and Coffey, A and Kiste, M and Guinane, CM and Hill, C and Field, D and Begley, M},
title = {Inhibition of Clinical MRSA Isolates by Coagulase Negative Staphylococci of Human Origin.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38667016},
issn = {2079-6382},
abstract = {Staphylococcus aureus is frequently highlighted as a priority for novel drug research due to its pathogenicity and ability to develop antibiotic resistance. Coagulase-negative staphylococci (CoNS) are resident flora of the skin and nares. Previous studies have confirmed their ability to kill and prevent colonization by S. aureus through the production of bioactive substances. This study screened a bank of 37 CoNS for their ability to inhibit the growth of methicillin-resistant S. aureus (MRSA). Deferred antagonism assays, growth curves, and antibiofilm testing performed with the cell-free supernatant derived from overnight CoNS cultures indicated antimicrobial and antibiofilm effects against MRSA indicators. Whole genome sequencing and BAGEL4 analysis of 11 CoNS isolates shortlisted for the inhibitory effects they displayed against MRSA led to the identification of two strains possessing complete putative bacteriocin operons. The operons were predicted to encode a nukacin variant and a novel epilancin variant. From this point, strains Staphylococcus hominis C14 and Staphylococcus epidermidis C33 became the focus of the investigation. Through HPLC, a peptide identical to previously characterized nukacin KQU-131 and a novel epilancin variant were isolated from cultures of C14 and C33, respectively. Mass spectrometry confirmed the presence of each peptide in the active fractions. Spot-on-lawn assays demonstrated both bacteriocins could inhibit the growth of an MRSA indicator. The identification of natural products with clinically relevant activity is important in today's climate of escalating antimicrobial resistance and a depleting antibiotic pipeline. These findings also highlight the prospective role CoNS may play as a source of bioactive substances with activity against critical pathogens.},
}

@article {pmid38666993,
year = {2024},
author = {Olson, S and Welton, L and Jahansouz, C},
title = {Perioperative Considerations for the Surgical Treatment of Crohn's Disease with Discussion on Surgical Antibiotics Practices and Impact on the Gut Microbiome.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
pmid = {38666993},
issn = {2079-6382},
abstract = {Crohn's disease, a chronic inflammatory process of the gastrointestinal tract defined by flares and periods of remission, is increasing in incidence. Despite advances in multimodal medical therapy, disease progression often necessitates multiple operations with high morbidity. The inability to treat Crohn's disease successfully is likely in part because the etiopathogenesis is not completely understood; however, recent research suggests the gut microbiome plays a critical role. How traditional perioperative management, including bowel preparation and preoperative antibiotics, further changes the microbiome and affects outcomes is not well described, especially in Crohn's patients, who are unique given their immunosuppression and baseline dysbiosis. This paper aims to outline current knowledge regarding perioperative management of Crohn's disease, the evolving role of gut dysbiosis, and how the microbiome can guide perioperative considerations with special attention to perioperative antibiotics as well as treatment of Mycobacterium avium subspecies paratuberculosis. In conclusion, dysbiosis is common in Crohn's patients and may be exacerbated by malnutrition, steroids, narcotic use, diarrhea, and perioperative antibiotics. Dysbiosis is also a major risk factor for anastomotic leak, and special consideration should be given to limiting factors that further perturb the gut microbiota in the perioperative period.},
}

@article {pmid38666955,
year = {2024},
author = {Bilski, K and Żeber-Lubecka, N and Kulecka, M and Dąbrowska, M and Bałabas, A and Ostrowski, J and Dobruch, A and Dobruch, J},
title = {Microbiome Sex-Related Diversity in Non-Muscle-Invasive Urothelial Bladder Cancer.},
journal = {Current issues in molecular biology},
volume = {46},
number = {4},
pages = {3595-3609},
pmid = {38666955},
issn = {1467-3045},
support = {2019/33/B/NZ5/02447//National Science Center/ ; },
abstract = {Sex-specific discrepancies in bladder cancer (BCa) are reported, and new studies imply that microbiome may partially explain the diversity. We aim to provide characterization of the bladder microbiome in both sexes diagnosed with non-muscle-invasive BCa with specific insight into cancer grade. In our study, 16S rRNA next-generation sequencing was performed on midstream urine, bladder tumor sample, and healthy-appearing bladder mucosa. Bacterial DNA was isolated using QIAamp Viral RNA Mini Kit. Metagenomic analysis was performed using hypervariable fragments of the 16S rRNA gene on Ion Torrent Personal Genome Machine platform. Of 41 sample triplets, 2153 taxa were discovered: 1739 in tumor samples, 1801 in healthy-appearing bladder mucosa and 1370 in midstream urine. Women were found to have smaller taxa richness in Chao1 index than men (p = 0.03). In comparison to low-grade tumors, patients with high-grade lesions had lower bacterial diversity and richness in urine. Significant differences between sexes in relative abundance of communities at family level were only observed in high-grade tumors.},
}

@article {pmid38666797,
year = {2024},
author = {Llorenç-Vicedo, A and Lluesma Gomez, M and Zeising, O and Kleiner, T and Freitag, J and Martinez-Hernandez, F and Wilhelms, F and Martinez-Garcia, M},
title = {New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0007324},
doi = {10.1128/msphere.00073-24},
pmid = {38666797},
issn = {2379-5042},
abstract = {UNLABELLED: The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell technologiesand metagenomics, we have been able to sequence frozen microbial DNA (≈300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g., Nitrosopumilus spp.), followed by Actinobacteria (e.g., Actinomarinales), were abundant. Remarkably, our data allow us to "travel to the past" and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice (≈300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated.

IMPORTANCE: Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.},
}

@article {pmid38666794,
year = {2024},
author = {Zaher, A and Elsaygh, J and Peterson, SJ and Weisberg, IS and Parikh, MA and Frishman, WH},
title = {The Interplay of Microbiome Dysbiosis and Cardiovascular Disease.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000000701},
pmid = {38666794},
issn = {1538-4683},
abstract = {The intricate ecosystem of the mammalian gut, which hosts a diverse microbiome, plays a vital role in various physiological functions. Trillions of bacteria within the gut contribute to host metabolism, immune modulation, energy homeostasis, and more. Emerging research highlights the gut microbiota's significant impact on cardiovascular diseases (CVDs), with intestinal dysbiosis identified as a risk factor for conditions such as obesity and diabetes, both linked to atherosclerosis. Chronic inflammation, pivotal in atherosclerosis, is influenced by the gut microbiome, where microbial signals, such as lipopolysaccharides, can translocate from the gut to trigger inflammatory responses. Diet has major effects on the gut microbiota, with the Western diet, rich in saturated fats, contributing to dysbiosis and elevated cardiovascular risks. Probiotics and prebiotics offer therapeutic potential in CVD management. Probiotics, or live microorganisms, exhibit antioxidant, anti-inflammatory, and cholesterol-lowering effects. Probiotics are most effective when given with prebiotics, with the former acting on the latter as substrate. Understanding the dynamic interplay between diet, gut microbiota, and CVD provides insights into preventive and therapeutic strategies.},
}

@article {pmid38666460,
year = {2024},
author = {Campbell, A and Bae, J and Hein, M and Hillis, SL and Rebeck, ON and Rakel, BA and Grice, E and Gardner, SE},
title = {The heterogeneous wound microbiome varies with wound care pain, dressing type, and inflammatory gene expression.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/wrr.13184},
pmid = {38666460},
issn = {1524-475X},
support = {R01NR015639/NR/NINR NIH HHS/United States ; R01NR015642/NR/NINR NIH HHS/United States ; UL1TR002537/TR/NCATS NIH HHS/United States ; },
abstract = {Wound dressing changes are essential procedures for wound management. However, ~50% of patients experience severe pain during these procedures despite the availability of analgesic medications, indicating a need for novel therapeutics that address underlying causes of pain. Along with other clinical factors, wound pathogens and inflammatory immune responses have previously been implicated in wound pain. To test whether these factors could contribute to severe pain during wound dressing changes, we conducted an exploratory, cross-sectional analysis of patient-reported pain, inflammatory immune responses, and wound microbiome composition in 445 wounds at the time of a study dressing change. We profiled the bacterial composition of 406 wounds using 16S ribosomal RNA amplicon sequencing and quantified gene expression of 13 inflammatory markers in wound fluid using quantitative real-time polymerase chain reaction (qPCR). Neither inflammatory gene expression nor clinically observed inflammation were associated with severe pain, but Corynebacterium and Streptococcus were of lower relative abundance in wounds of patients reporting severe pain than those reporting little or no pain. Wound microbiome composition differed by wound location, and correlated with six of the inflammatory markers, including complement receptor C5AR1, pro-inflammatory cytokine interleukin (IL)1β, chemokine IL-8, matrix metalloproteinase MMP2, and the antimicrobial peptide encoding cathelicidin antimicrobial peptide. Interestingly, we found a relationship between the wound microbiome and vacuum-assisted wound closure (VAC). These findings identify preliminary, associative relationships between wound microbiota and host factors which motivate future investigation into the directional relationships between wound care pain, wound closure technologies, and the wound microbiome.},
}

@article {pmid38666261,
year = {2024},
author = {Li, M and Kopylova, E and Mao, J and Namkoong, J and Sanders, J and Wu, J},
title = {Microbiome and lipidomic analysis reveal the interplay between skin bacteria and lipids in a cohort study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383656},
pmid = {38666261},
issn = {1664-302X},
abstract = {Human skin acts as a protective barrier between the body and the external environment. Skin microbiome and intercellular lipids in the stratum corneum (SC) are essential for maintaining skin barrier function. However, the interplay between skin bacteria and the lipids is not fully understood. In this study, we characterized the skin microbiome and SC lipid profiles from the forearm and face in a cohort of 57 healthy participants. 16S rRNA gene sequencing showed the skin microbial composition is significantly different between body locations and genders. Female forearm samples have the highest microbial diversity. The relative abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium tuberculostearicum, Finegoldia magna, and Moraxellaceae sp. are significantly higher in the forearm than the face. The predictive functional analysis of 16S rRNA gene sequencing by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and ANCOM-BC showed different bacterial metabolic pathway profiles between body locations or genders, and identified 271 differential pathways, including arginine and polyamine biosynthesis, chorismate biosynthesis pathways, which are more abundant in the female forearm, and sulfur oxidation pathway, which is more abundant in the male face. The SC lipid profiles differ between the body locations as well. Total free fatty acids (FFA), cholesterol sulfate and sphingosine are more abundant in the face. Dihydro-/6-hydroxy/phyto-ceramides are more abundant in the forearm. The correlation analysis of 16S rRNA gene sequencing and lipids revealed novel interplay between the bacteria and skin lipids. Shannon entropy and S. hominis negatively correlated with FFA, cholesterol sulfate and sphingosine; while positively correlated with dihydro-/6-hydroxy/phyto-ceramides. The correlation of predictive pathway profiles and lipids identified pathways involved in amino acids metabolism, carbohydrates degradation, aromatic compounds metabolism and fatty acid degradation metabolism are positively correlated with dihydro-/6-hydroxy/phyto-ceramides and negatively correlated with FFA, cholesterol sulfate and sphingosine. This study provides insights on the potential correlation between skin microbiome and lipids.},
}

@article {pmid38666257,
year = {2024},
author = {Wang, Z and Xu, L and Lu, X and Wang, R and Han, J and Yan, A},
title = {The endophytic microbiome response patterns of Juglans regia to two pathogenic fungi.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1378273},
pmid = {38666257},
issn = {1664-302X},
abstract = {The endophytic microbial community reassembles to participate in plant immune balance when the host plants are stressed by pathogens. However, it remains unclear whether this assembly is pathogen-specific and how regulatory pathways are coordinated in multi-pathogens. In order to investigate the effects of infection with Colletotrichum gloeosporioides (Cg treatment) and Fusarium proliferatum (Fp treatment) on walnut leaf endophytic microbiome in their assembly, co-occurrence pattern, and on comprehensive chemical function of the internal environment of leaf, an interaction system of the walnut-pathogenic fungi was constructed using seed embryo tissue culture technology. The study showed differences in the assembly of endophytic microbial communities in walnut trees across three groups (control group, Ck; Cg; Fp) after Cg and Fp treatments. Despite changes in relative abundances, the dominant communities in phyla and genera remained comparable during the infection of the two pathogens. Endophyte fungi were more sensitive to the pathogen challenge than endophyte bacteria. Both promoted the enrichment of beneficial bacteria such as Bacillus and Pseudomonas, changed the modularity of the community, and reduced the stability and complexity of the endophyte community. Pathogenic fungi infection mainly affects the metabolism of porphyrin and chlorophyll, purine metabolism, phenylpropane metabolism, and amino acid metabolism. However, there was no significant difference in the secondary metabolites for the different susceptible plants. By screening endogenous antagonistic bacteria, we further verified that Pseudomonas psychrotolerans and Bacillus subtilis had inhibitory effects on the two pathogenic fungi and participated in the interaction between the leaves and pathogenic fungi. The antibacterial substances may be 1-methylnaphthalene, 1,3-butadiene, 2,3-butanediol, and toluene aldehyde.},
}

@article {pmid38666212,
year = {2024},
author = {Pujolassos, M and Susín, A and Calle, ML},
title = {Microbiome compositional data analysis for survival studies.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {2},
pages = {lqae038},
pmid = {38666212},
issn = {2631-9268},
abstract = {The growing interest in studying the relationship between the human microbiome and our health has also extended to time-to-event studies where researchers explore the connection between the microbiome and the occurrence of a specific event of interest. The analysis of microbiome obtained through high throughput sequencing techniques requires the use of specialized Compositional Data Analysis (CoDA) methods designed to accommodate its compositional nature. There is a limited availability of statistical tools for microbiome analysis that incorporate CoDA, and this is even more pronounced in the context of survival analysis. To fill this methodological gap, we present coda4microbiome for survival studies, a new methodology for the identification of microbial signatures in time-to-event studies. The algorithm implements an elastic-net penalized Cox regression model adapted to compositional covariates. We illustrate coda4microbiome algorithm for survival studies with a case study about the time to develop type 1 diabetes for non-obese diabetic mice. Our algorithm identified a bacterial signature composed of 21 genera associated with diabetes development. coda4microbiome for survival studies is integrated in the R package coda4microbiome as an extension of the existing functions for cross-sectional and longitudinal studies.},
}

@article {pmid38666051,
year = {2024},
author = {Kicic-Starcevich, E and Hancock, DG and Iosifidis, T and Agudelo-Romero, P and Caparros-Martin, JA and Karpievitch, YV and Silva, D and Turkovic, L and Le Souef, PN and Bosco, A and Martino, DJ and Kicic, A and Prescott, SL and Stick, SM},
title = {Airway epithelium respiratory illnesses and allergy (AERIAL) birth cohort: study protocol.},
journal = {Frontiers in allergy},
volume = {5},
number = {},
pages = {1349741},
pmid = {38666051},
issn = {2673-6101},
abstract = {INTRODUCTION: Recurrent wheezing disorders including asthma are complex and heterogeneous diseases that affect up to 30% of all children, contributing to a major burden on children, their families, and global healthcare systems. It is now recognized that a dysfunctional airway epithelium plays a central role in the pathogenesis of recurrent wheeze, although the underlying mechanisms are still not fully understood. This prospective birth cohort aims to bridge this knowledge gap by investigating the influence of intrinsic epithelial dysfunction on the risk for developing respiratory disorders and the modulation of this risk by maternal morbidities, in utero exposures, and respiratory exposures in the first year of life.

METHODS: The Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) study is nested within the ORIGINS Project and will monitor 400 infants from birth to 5 years. The primary outcome of the AERIAL study will be the identification of epithelial endotypes and exposure variables that influence the development of recurrent wheezing, asthma, and allergic sensitisation. Nasal respiratory epithelium at birth to 6 weeks, 1, 3, and 5 years will be analysed by bulk RNA-seq and DNA methylation sequencing. Maternal morbidities and in utero exposures will be identified on maternal history and their effects measured through transcriptomic and epigenetic analyses of the amnion and newborn epithelium. Exposures within the first year of life will be identified based on infant medical history as well as on background and symptomatic nasal sampling for viral PCR and microbiome analysis. Daily temperatures and symptoms recorded in a study-specific Smartphone App will be used to identify symptomatic respiratory illnesses.

DISCUSSION: The AERIAL study will provide a comprehensive longitudinal assessment of factors influencing the association between epithelial dysfunction and respiratory morbidity in early life, and hopefully identify novel targets for diagnosis and early intervention.},
}

@article {pmid38665319,
year = {2024},
author = {Ganesan, A and Kumar, G and Gauthaman, J and Lakshmi, KC and Kumbalaparambil, YA},
title = {Exploring the Relationship between Psychoneuroimmunology and Oral Diseases: A Comprehensive Review and Analysis.},
journal = {Journal of lifestyle medicine},
volume = {14},
number = {1},
pages = {13-19},
pmid = {38665319},
issn = {2234-8549},
abstract = {The relationship between psychoneuroimmunology (PNI) and oral health has recently garnered increasing attention due to the intricate interaction among psychological factors, the nervous system, immune responses, and oral diseases. This comprehensive review aims to elucidate the multifaceted connections between PNI and various oral conditions and conduct an in-depth analysis. Psychological factors, such as stress, anxiety, and depression, have been linked to oral microbiome alterations and immune function and the development and progression of oral diseases, such as periodontal disorders, oral ulcers, and temporomandibular disorders. Conversely, oral health conditions, particularly chronic periodontitis, have been associated with systemic inflammation, affecting mental health and overall well-being through neuroendocrine-immune pathways. Moreover, neural mechanisms, including the brain-gut axis and the autonomic nervous system, significantly influenced oral health through immune modulation and inflammatory responses. Understanding these complex interactions has implications for therapeutic interventions that target both psychological well-being and oral health outcomes. This review synthesizes current research findings from various disciplines, including immunology, neuroscience, dentistry, and psychology, to offer a comprehensive understanding of the bidirectional relationship between PNI and oral diseases. The implications of these interactions on treatment strategies, preventive measures, and interdisciplinary approaches underscore the need for integrated healthcare models that address psychological and oral health aspects to improve outcomes and quality of life in patients.},
}

@article {pmid38665315,
year = {2024},
author = {Ismail, A and Yogarajah, A and Falconer, JL and Dworakowski, R and Watson, S and Breeze, J and Gunning, M and Khan, H and Hussain, A and Howard, JP and Cheong, P and Shah, M and Nibali, L and Sousa, V},
title = {Insights into microorganisms, associated factors, and the oral microbiome in infective endocarditis patients.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1270492},
pmid = {38665315},
issn = {2673-4842},
abstract = {INTRODUCTION: Infective Endocarditis (IE) is a rare, life-threatening infection of the endocardium with multisystem effects. Culprit microorganisms derived from different niches circulate through the bloodstream and attach to the endocardium, particularly the heart valves. This study aimed to investigate culprit microorganisms among a cross-sectional cohort of IE patients, their associated factors, and to explore the potential relationship to the oral microbiome.

METHODS: In this observational study, we undertook a cross-sectional analysis of 392 medical records from patients diagnosed with IE. The primary outcome of this study was to analyse the association between the IE culprit microorganisms and the underlying anatomical types of IE (native valve (NVE), prosthetic valve (PVE), or cardiac device-related (CDE)). Secondary outcomes encompassed a comparative analysis of additional factors, including: the treatment approaches for IE, and the categorisation of blood cultures, extending to both genus and species levels. Additionally, we cross-referenced and compared the species-level identification of IE bacteraemia outcome measures with data from the expanded Human Oral Microbiome Database (eHOMD).

RESULTS: A culprit microorganism was identified in 299 (76.28%) case participants. Staphylococcal infections were the most common (p < 0.001), responsible for 130 (33.16%) hospitalisations. There were 277 (70.66%) cases of NVE, 104 (26.53%) cases of PVE, and 11 (2.81%) cases of CDE. The majority of PVE occurred on prosthetic aortic valves (78/104, 75%), of which 72 (93.5%) were surgical aortic valve replacements (SAVR), 6 (7.8%) were transcatheter aortic valve implants, and one transcatheter pulmonary valve implant. Overall, underlying anatomy (p = 0.042) as well as the treatment approaches for IE (p < 0.001) were significantly associated with IE culprit microorganisms. Cross-reference between IE bacteraemia outcomes with the eHOMD was observed in 267/392 (68.11%) cases.

CONCLUSIONS: This study demonstrated that IE patients with a history of stroke, smoking, intravenous drug use, or dialysis were more likely to be infected with Staphylococcus aureus. CDE case participants and patients who had previous SAVR were most associated with Staphylococcus epidermidis. IE patients aged 78+ were more likely to develop enterococci IE than other age groups. Oral microorganisms indicated by the eHOMD are significantly observed in the IE population. Further research, through enhanced dental and medical collaboration, is required to correlate the presence of oral microbiota as causative factor for IE.},
}

@article {pmid38665301,
year = {2024},
author = {Esperança, VJR and Moreira, PIO and Chávez, DWH and Freitas-Silva, O},
title = {Evaluation of the safety and quality of Brazil nuts (Bertholletia excelsa) using the tools of dna sequencing technology and aflatoxin profile.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1357778},
pmid = {38665301},
issn = {2296-861X},
abstract = {INTRODUCTION: Brazil nuts (BNs) result from sustainable extraction and are widely exploited in the Amazon region. Due to the production characteristics in the forest and the nutritional characteristics of these nuts, the occurrence of fungal contamination and the presence of aflatoxins are extensively discussed in the literature as a great aspect of interest and concern. This study aims to evaluate the microbial profile through DNA sequencing and amplification of 16S and ITS genes for bacterial and fungal analysis, respectively, and the presence of mycotoxins using high-performance liquid chromatography with fluorescence detection (HPLC-FD) from different fractions of the nuts processed.

METHODS: The BN samples, harvest A (HA) and harvest B (HB), from two different harvests were collected in an extractive cooperative in the Amazon region for microbiological analysis (from DNA extraction and amplification of 16S genes, bacteria analysis, and ITS for fungi) and mycotoxins (aflatoxins AFB1, AFB2, AFG1, and AFG2) using HPLC-FD/KobraCell[®].

RESULTS AND DISCUSSION: The samples showed a very different microbiome and aflatoxin profile. Genera such as Rothia (HA) and Cronobacter (HB) were abundant during the analysis of bacteria; as for fungi, the genera Aspergillus, Fusarium, Penicillium, and Alternaria were also considered prevalent in these samples. Soil microorganisms, including those pathogenic and related to inadequate hygienic-sanitary production practices, as well as aflatoxins, were found in the samples. However, they were within the established limits permitted by Brazilian legislation. Nuts have a diverse microbiota and are not restricted to fungi of the genus Aspergillus. The microbiological and toxicological profile can vary significantly within the same nut in the same extraction region and can be exacerbated by global climate changes. Therefore, it is necessary to advance sanitary educational actions by applying good production practices and inspection programs to ensure the sustainability and quality of the BN production chain.},
}

@article {pmid38665235,
year = {2024},
author = {Cossart, P and Hacker, J and Holden, DH and Normark, S and Vogel, J},
title = {Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg.},
journal = {microLife},
volume = {5},
number = {},
pages = {uqae008},
pmid = {38665235},
issn = {2633-6693},
abstract = {On September 20-22 September 2023, the international conference 'Microbiology 2023: from single cell to microbiome and host' convened microbiologists from across the globe for a very successful symposium, showcasing cutting-edge research in the field. Invited lecturers delivered exceptional presentations covering a wide range of topics, with a major emphasis on phages and microbiomes, on the relevant bacteria within these ecosystems, and their multifaceted roles in diverse environments. Discussions also spanned the intricate analysis of fundamental bacterial processes, such as cell division, stress resistance, and interactions with phages. Organized by four renowned Academies, the German Leopoldina, the French Académie des sciences, the Royal Society UK, and the Royal Swedish Academy of Sciences, the symposium provided a dynamic platform for experts to share insights and discoveries, leaving participants inspired and eager to integrate new knowledge into their respective projects. The success of Microbiology 2023 prompted the decision to host the next quadrennial academic meeting in Sweden. This choice underscores the commitment to fostering international collaboration and advancing the frontiers of microbiological knowledge. The transition to Sweden promises to be an exciting step in the ongoing global dialogue and specific collaborations on microbiology, a field where researchers will continue to push the boundaries of knowledge, understanding, and innovation not only in health and disease but also in ecology.},
}

@article {pmid38665155,
year = {2024},
author = {Babalola, OO and Adedayo, AA and Akinola, SA},
title = {High-throughput metagenomic assessment of Cango Cave microbiome-A South African limestone cave.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110381},
pmid = {38665155},
issn = {2352-3409},
abstract = {Microorganisms inhabiting caves exhibit medical or biotechnological promise, most of which have been attributed to factors such as antimicrobial activity or the induction of mineral precipitation. This dataset explored the shotgun metagenomic sequencing of the Cango cave microbial community in Oudtshoorn, South Africa. The aimed to elucidate both the structure and function of the microbial community linked to the cave. DNA sequencing was conducted using the Illumina NovaSeq platform, a next-generation sequencing. The data comprises 4,738,604 sequences, with a cumulative size of 1,180,744,252 base pairs and a GC content of 52%. Data derived from the metagenome sequences can be accessed through the bioproject number PRJNA982691 on NCBI. Using an online metagenome server, MG-RAST, the subsystem database revealed that bacteria displayed the highest taxonomical representation, constituting about 98.66%. Archaea accounted for 0.05%, Eukaryotes at 1.20%, viruses were 0.07%, while unclassified sequences had a representation of 0.02%. The most abundant phyla were Proteobacteria (81.74%), Bacteroidetes (10.57%), Actinobacteria (4.16%), Firmicutes (SK‒1.03%), Acidobacteria (0.20), and Planctomycetes (SK‒0.16%). Functional annotation using subsystem analysis revealed that clustering based on subsystems had 13.44%, while amino acids and derivatives comprised 11.41%. Carbohydrates sequences constituted 9.55%, along with other advantageous functional traits essential for growth promotion and plant management.},
}

@article {pmid38665074,
year = {2024},
author = {Gao, J and Lv, D and Wu, Z and Sun, Z and Sun, X and Liu, S and Tan, Z and Zhu, W and Cheng, Y},
title = {Dietary supplementing phytosterols improves the metabolic status of perinatal cows revealed by plasma metabolomics and faecal microbial metabolism.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.23.0422},
pmid = {38665074},
issn = {2765-0189},
abstract = {OBJECTIVE: Previous research reported that dietary addition with phytosterols improved the energy utilisation of the rumen microbiome, suggesting its potential to alleviate the negative energy balance of perinatal cows. This experiment aimed to explore the effects of feeding phytosterols on the metabolic status of perinatal cows through plasma metabolomics and faecal bacteria metabolism.

METHODS: Ten perinatal Holstein cows (multiparous, 2 parities) with a similar calving date were selected four weeks before calving. After 7 days for adaptation, cows were allocated to two groups (n=5), which respectively received the basal rations supplementing commercial phytosterols at 0 and 200 mg/d during a 42-day experiment. The milk yield of each cow was recorded daily after calving. On days 1 and 42, blood and faeces samples were all collected from perinatal cows before morning feeding for analysing plasma biochemicals and metabolome, and faecal bacteria metabolism.

RESULTS: Dietary addition with phytosterols at 200 mg/d had no effects on plasma cholesterol and numerically increased milk yield by 1.82 kg/d (p>0.10) but attenuated their negative energy balance in perinatal cows as observed from the significantly decreased plasma level of β-hydroxybutyric acid (p=0.002). Dietary addition with phytosterols significantly altered 12 and 15 metabolites (p<0.05) within the plasma and faeces of perinatal cows, respectively. Of these metabolites, 5 upregulated plasma fatty acids indicated an improved energy status (i.e., C18:1T, C14:0, C17:0, C18:0, and C16:0). Milk yield negatively correlated with plasma concentrations of ketone bodies (p=0.035) and 5-methoxytryptamine (p=0.039). Furthermore, dietary addition with phytosterols at 200 mg/d had no effects on fermentation characteristics and bacterial diversity of cow faeces (p>0.10) but improved potentially beneficial bacteria such as Christensenellaceae family (p<0.05) that positively correlated with feed efficiency.

CONCLUSION: Dietary addition with phytosterols at 200 mg/d could effectively improve the energy status in perinatal cows by attenuating their negative energy balance.},
}

@article {pmid38664929,
year = {2024},
author = {Fu, Q and Ma, X and Li, S and Shi, M and Song, T and Cui, J},
title = {New insights into the interactions between the gut microbiota and the inflammatory response to ulcerative colitis in a mouse model of dextran sodium sulfate and possible mechanisms of action for treatment with PE&AFWE.},
journal = {Animal models and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/ame2.12405},
pmid = {38664929},
issn = {2576-2095},
support = {81774449//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a heterogeneous state of chronic intestinal inflammation. Intestinal innate immunity, including innate immune cells, defends against pathogens and excessive entry of gut microbiota, while preserving immune tolerance to resident intestinal microbiota, and may be characterized by its capacity to produce a rapid and nonspecific reaction. The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic. When the intestinal ecosystem is in dysbiosis, the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota. The aim of our study was to comprehensively assess the relationship between microbial populations within UC, the signaling pathways of pathogenic gut microbe therein and the inflammatory response, as well as to understand the effects of using PE&AFWE (poppy extract [Papaver nudicaule L.] and Artemisia frigida Willd. extract) on UC modulation.

METHODS: A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate (DSS). Based on metagenomic sequencing to characterize the gut microbiome, the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods, as well as histopathological analysis.

RESULTS: (1) We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria. There were three types of abundance changes in the model groups: increases (Chlamydiae/Proteobacteria and Deferribacteres), decreases (Firmicutes), and no significant changes (Bacteroidetes). The UC model group was significantly different from the control group, with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold. (2) The proportion of the fecal flora in the UC group decreased by 37.5% in the Firmicutes and increased by 14.29% in the proportion of Proteobacteria compared to the control group before treatment. (3) The significantly enriched and increased signaling pathways screened were the 'arachidonic acid metabolic pathway' and the 'phagosomal pathway', which both showed a decreasing trend after drug administration. (4) Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration, screening for directly relevant OTU networks, the UC group was found to directly affect OTU69, followed by a cascade of effects on OTU12, OTU121, OTU93, and OTU7, which may be the pathway of action that initiated the pathological changes in normal mice. (5) We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre- and post-PE&AFWE-treated groups. Thereby, we learned that PE&AFWE can directly affect OTU90, after which it inhibits UC, inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118, which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7. (6) Histopathological observation and scoring (HS) of the colon showed that there was a significant difference between the model group and the control group (p < 0.001), and that there was a significant recovery in both the sulfasalazine (SASP)and the PE&AFWE groups after the administration of the drug (p < 0.0001).

CONCLUSION: We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD, with five opportunistic pathogens directly contributing to IBD. PE&AFWE reduced the abundance of proteobacteria in the gut microbiota, and histopathology showed significant improvement.},
}

@article {pmid38664737,
year = {2024},
author = {Dang, YR and Cha, QQ and Liu, SS and Wang, SY and Li, PY and Li, CY and Wang, P and Chen, XL and Tian, JW and Xin, Y and Chen, Y and Zhang, YZ and Qin, QL},
title = {Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {77},
pmid = {38664737},
issn = {2049-2618},
mesh = {*Polysaccharides/metabolism ; *Seawater/microbiology ; *Phytoplankton/metabolism/genetics ; *Nutrients/metabolism ; *Peptidoglycan/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microbiota ; },
abstract = {BACKGROUND: The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS: In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS: Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.},
}

*Polysaccharides/metabolism
*Seawater/microbiology
*Phytoplankton/metabolism/genetics
*Nutrients/metabolism
*Peptidoglycan/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenomics
Microbiota

@article {pmid38664617,
year = {2024},
author = {Vergine, M and Vita, F and Casati, P and Passera, A and Ricciardi, L and Pavan, S and Aprile, A and Sabella, E and De Bellis, L and Luvisi, A},
title = {Characterization of the olive endophytic community in genotypes displaying a contrasting response to Xylella fastidiosa.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {337},
pmid = {38664617},
issn = {1471-2229},
mesh = {*Olea/microbiology ; *Xylella/physiology/genetics ; *Endophytes/physiology/genetics ; *Genotype ; *Plant Diseases/microbiology ; Microbiota ; Bacteria/genetics/classification ; Fungi/physiology/genetics ; },
abstract = {BACKGROUND: Endophytes mediate the interactions between plants and other microorganisms, and the functional aspects of interactions between endophytes and their host that support plant-growth promotion and tolerance to stresses signify the ecological relevance of the endosphere microbiome. In this work, we studied the bacterial and fungal endophytic communities of olive tree (Olea europaea L.) asymptomatic or low symptomatic genotypes sampled in groves heavily compromised by Xylella fastidiosa subsp. pauca, aiming to characterize microbiota in genotypes displaying differential response to the pathogen.

RESULTS: The relationships between bacterial and fungal genera were analyzed both separately and together, in order to investigate the intricate correlations between the identified Operational Taxonomic Units (OTUs). Results suggested a dominant role of the fungal endophytic community compared to the bacterial one, and highlighted specific microbial taxa only associated with asymptomatic or low symptomatic genotypes. In addition, they indicated the occurrence of well-adapted genetic resources surviving after years of pathogen pressure in association with microorganisms such as Burkholderia, Quambalaria, Phaffia and Rhodotorula.

CONCLUSIONS: This is the first study to overview endophytic communities associated with several putatively resistant olive genotypes in areas under high X. fastidiosa inoculum pressure. Identifying these negatively correlated genera can offer valuable insights into the potential antagonistic microbial resources and their possible development as biocontrol agents.},
}

*Olea/microbiology
*Xylella/physiology/genetics
*Endophytes/physiology/genetics
*Genotype
*Plant Diseases/microbiology
Microbiota
Bacteria/genetics/classification
Fungi/physiology/genetics

@article {pmid38664512,
year = {2024},
author = {Ahammad, I and Bhattacharjee, A and Chowdhury, ZM and Rahman, A and Hossain, MU and Dewan, G and Talukder, S and Das, KC and Keya, CA and Salimullah, M},
title = {Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {500},
pmid = {38664512},
issn = {2399-3642},
support = {MoST-2020//Ministry of Science and Technology, Government of the People's Republic of Bangladesh (Ministry of Science and Technology)/ ; },
mesh = {Bangladesh ; Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Ethnicity ; Bacteria/genetics/classification ; Female ; Adult ; Male ; Indigenous Peoples ; *South Asian People ; },
abstract = {Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.},
}

Bangladesh
Humans
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
Feces/microbiology
Ethnicity
Bacteria/genetics/classification
Female
Adult
Male
Indigenous Peoples
*South Asian People

@article {pmid38664490,
year = {2024},
author = {Kolobaric, A and Andreescu, C and Jašarević, E and Hong, CH and Roh, HW and Cheong, JY and Kim, YK and Shin, TS and Kang, CS and Kwon, CO and Yoon, SY and Hong, SW and Aizenstein, HJ and Karim, HT and Son, SJ},
title = {Gut microbiome predicts cognitive function and depressive symptoms in late life.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {38664490},
issn = {1476-5578},
abstract = {Depression in older adults with cognitive impairment increases progression to dementia. Microbiota is associated with current mood and cognition, but the extent to which it predicts future symptoms is unknown. In this work, we identified microbial features that reflect current and predict future cognitive and depressive symptoms. Clinical assessments and stool samples were collected from 268 participants with varying cognitive and depressive symptoms. Seventy participants underwent 2-year follow-up. Microbial community diversity, structure, and composition were assessed using high-resolution 16 S rRNA marker gene sequencing. We implemented linear regression to characterize the relationship between microbiome composition, current cognitive impairment, and depressive symptoms. We leveraged elastic net regression to discover features that reflect current or future cognitive function and depressive symptoms. Greater microbial community diversity associated with lower current cognition in the whole sample, and greater depression in participants not on antidepressants. Poor current cognitive function associated with lower relative abundance of Bifidobacterium, while greater GABA degradation associated with greater current depression severity. Future cognitive decline associated with lower cognitive function, lower relative abundance of Intestinibacter, lower glutamate degradation, and higher baseline histamine synthesis. Future increase in depressive symptoms associated with higher baseline depression and anxiety, lower cognitive function, diabetes, lower relative abundance of Bacteroidota, and lower glutamate degradation. Our results suggest cognitive dysfunction and depression are unique states with an overall biological effect detectable through gut microbiota. The microbiome may present a noninvasive readout and prognostic tool for cognitive and psychiatric states.},
}

@article {pmid38664425,
year = {2024},
author = {Chui, ZSW and Chan, LML and Zhang, EWH and Liang, S and Choi, EPH and Lok, KYW and Tun, HM and Kwok, JYY},
title = {Effects of microbiome-based interventions on neurodegenerative diseases: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9558},
pmid = {38664425},
issn = {2045-2322},
mesh = {Humans ; *Neurodegenerative Diseases/microbiology/therapy ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation/methods ; Probiotics/therapeutic use ; Microbiota ; },
abstract = {Neurodegenerative diseases (NDDs) are characterized by neuronal damage and progressive loss of neuron function. Microbiome-based interventions, such as dietary interventions, biotics, and fecal microbiome transplant, have been proposed as a novel approach to managing symptoms and modulating disease progression. Emerging clinical trials have investigated the efficacy of interventions modulating the GM in alleviating or reversing disease progression, yet no comprehensive synthesis have been done. A systematic review of the literature was therefore conducted to investigate the efficacy of microbiome-modulating methods. The search yielded 4051 articles, with 15 clinical trials included. The overall risk of bias was moderate in most studies. Most microbiome-modulating interventions changed the GM composition. Despite inconsistent changes in GM composition, the meta-analysis showed that microbiome-modulating interventions improved disease burden (SMD, - 0.57; 95% CI - 0.93 to - 0.21; I[2] = 42%; P = 0.002) with a qualitative trend of improvement in constipation. However, current studies have high methodological heterogeneity and small sample sizes, requiring more well-designed and controlled studies to elucidate the complex linkage between microbiome, microbiome-modulating interventions, and NDDs.},
}

Humans
*Neurodegenerative Diseases/microbiology/therapy
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation/methods
Probiotics/therapeutic use
Microbiota

@article {pmid38664180,
year = {2024},
author = {Knorr, J and Lone, Z and Werneburg, G and Adler, A and Agudelo, J and Suryavanshi, M and Campbell, RA and Ericson, K and Qiu, H and Bajic, P and Haber, GP and Weight, CJ and Ahern, PP and Almassi, N and Miller, AW and Lee, BH},
title = {An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.04.011},
pmid = {38664180},
issn = {1873-2496},
abstract = {PURPOSE: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response.

MATERIALS AND METHODS: Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations.

RESULTS: Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction.

CONCLUSION: A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.},
}

@article {pmid38663906,
year = {2024},
author = {Zhu, J and Fan, X and Ding, L and Song, T},
title = {Idiopathic gingival fibromatosis and primary analysis of dominant bacteria in subgingival biofilm: a case report.},
journal = {The Journal of international medical research},
volume = {52},
number = {4},
pages = {3000605241245302},
pmid = {38663906},
issn = {1473-2300},
mesh = {Humans ; *Biofilms/growth & development ; *Fibromatosis, Gingival/diagnosis/pathology/microbiology ; *Gingiva/microbiology/pathology ; Female ; Adult ; Male ; Bacteria/isolation & purification ; Gingivectomy/methods ; },
abstract = {Idiopathic gingival fibromatosis (IGF), a rare fibroproliferative disease of unknown etiology, affects gingival tissue and has substantial adverse effects on patients. Therefore, the pathogenesis of IGF requires more extensive and in-depth research. In this case, a patient with confirmed IGF underwent initial nonsurgical periodontal therapy and gingivectomy, and the prognosis was good. The patient had no loss of periodontal attachment but had a history of swelling and bleeding of the gingiva prior to fibrous enlargement, which prompted further investigation. We explored the patient's subgingival microbiome and found a high abundance of periodontal pathogens. Gingival tissue biopsy revealed abundant fibrous tissue containing multiple inflammatory cell infiltrates. These results suggest that gingival inflammation secondary to periodontal pathogens can contribute to IGF onset.},
}

Humans
*Biofilms/growth & development
*Fibromatosis, Gingival/diagnosis/pathology/microbiology
*Gingiva/microbiology/pathology
Female
Adult
Male
Bacteria/isolation & purification
Gingivectomy/methods

@article {pmid38663780,
year = {2024},
author = {Dinat, S and Orchard, A and Van Vuuren, S},
title = {Antimicrobial activity of Southern African medicinal plants on Helicobacter pylori and Lactobacillus species.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118238},
doi = {10.1016/j.jep.2024.118238},
pmid = {38663780},
issn = {1872-7573},
abstract = {Numerous medicinal plants have been used traditionally in South Africa for gastric ulcer treatment. Helicobacter pylori is known for causing inflammation and the onset of gastric ulcers. While several studies explored medicinal plants against H. pylori, investigation of medicinal plants used for gastric ulcers has been neglected, as well as the effects these plants would have on bacteria occurring naturally in the gut microbiome.

AIM OF THE STUDY: This study aimed to investigate Southern African medicinal plants used traditionally for treating gastric ulcers against H. pylori and against Lactobacillus species, as well as the effects of these plants combined with the Lactobacillus species against H. pylori.

METHODOLOGY: Based on evidence from the ethnobotanical literature, 21 plants were collected. Their antimicrobial activity was assessed against five clinical H. pylori strains, and in combination with each of three Lactobacillus species, using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) broth microdilution assays. Toxicity was assessed using the brine shrimp lethality assay.

RESULTS: Noteworthy activity was observed against at least one H. pylori strain for 12 plant species. The lowest mean MICs were from organic extracts of Carissa edulis Vahl (0.18 mg/mL) and Chironia baccifera L. (0.20 mg/mL), and aqueous extracts of Sansevieria hyacinthoides (L.) Druce (0.26 mg/mL) and Dodonaea viscosa Jacq. (0.30 mg/mL). Aqueous extracts of the investigated plants were combined with Lactobacillus species, and the majority of combinations showed increased antimicrobial activity compared with the extracts alone. Combinations of Lactobacillus rhamnosus with 18 of the 21 aqueous plant extracts showed at least a two-fold decrease in the mean MBC against all H. pylori strains tested. Lactobacillus acidophilus combined with either Protea repens L., Carpobrotus edulis (L.) L.Bolus or Warburgia salutaris (Bertol.f.) Chiov. aqueous extracts had the best anti-H. pylori activity (mean MBCs of 0.10 mg/mL for each combination). Only four organic and one aqueous extract(s) were considered toxic.

CONCLUSION: These results highlight the potential of medicinal plants to inhibit H. pylori growth and their role in traditional treatments for the management of ulcers. The results also indicate that aqueous extracts of these plants do not hinder the growth of bacteria that occur naturally in the gut microbiome and play a role in maintaining gut health, as well as show the potential benefit of including Lactobacillus species in treatment as potentiators of H. pylori activity.},
}

@article {pmid38663650,
year = {2024},
author = {Fang, H and Hou, Q and Zhang, W and Su, Z and Zhang, J and Li, J and Lin, J and Wang, Z and Yu, X and Yang, Y and Wang, Q and Li, X and Li, Y and Hu, L and Li, S and Wang, X and Liao, L},
title = {Fecal Microbiota Transplantation Improves Clinical Symptoms of Fibromyalgia: An open-label, Randomized, Nonplacebo-Controlled Study.},
journal = {The journal of pain},
volume = {},
number = {},
pages = {104535},
doi = {10.1016/j.jpain.2024.104535},
pmid = {38663650},
issn = {1528-8447},
abstract = {Fibromyalgia (FM) is a complex and poorly understood disorder characterized by chronic and widespread musculoskeletal pain, of which the etiology remains unknown. Now, the disorder of the gut microbiome is considered as one of the main causes of FM. This study was aimed to investigate the potential benefits of fecal microbiota transplantation (FMT) in patients with FM. A total of 45 patients completed this open-label randomized, nonplacebo-controlled clinical study. The Numerical Rating Scale (NRS) scores in the FMT group were slightly lower than the control group at 1 month (P> 0.05), and they decreased significantly at 2, 3, 6, and 12 months after treatment (P < 0.001). Besides, compared with the control group, the Widespread Pain Index (WPI), Symptom Severity (SS), Hospital Anxiety and Depression Scale (HADS) and Pittsburgh Sleep Quality Index (PSQI) scores were significantly lower in the FMT group at different time points (P < 0.001). After 6 months of treatment, there was a significant increase in serotonin (5-HT) and gamma-aminobutyric acid (GABA) levels (P < 0.001), while glutamate levels significantly decreased in the FMT group (P < 0.001). The total effective rate was higher in the FMT group (90.9%) compared to the control group (56.5%) after 6 months of treatment (P < 0.05). FMT can effectively improve the clinical symptoms of FM. With the close relations between the changes of neurotransmitters and FM, certain neurotransmitters may serve as a diagnostic marker or potential target for FM patients. PERSPECTIVE: Fecal microbiota transplantation (FMT) is a novel therapy that aims to restore the gut microbial balance and modulate the gut-brain axis. It is valuable to further explore the therapeutic effect of FMT on FM. Furthermore, certain neurotransmitters may become a diagnostic marker or a new therapeutic target for FM patients.},
}

@article {pmid38663637,
year = {2024},
author = {Mao, X and Li, J and Meng, E and Jin, W and Han, W},
title = {Responses of physiological, microbiome and lipid metabolism to lignocellulose wastes in gut of yellow mealworm (Tenebrio molitor).},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130731},
doi = {10.1016/j.biortech.2024.130731},
pmid = {38663637},
issn = {1873-2976},
abstract = {There is limited research on physiological and degradation mechanisms of yellow mealworm, a novel organic waste converter, in processing lignocellulosic wastes. This study has selected two types of lignocellulosic wastes, distillers' grains (DG) and maize straw (MS), to feed yellow mealworms. This study investigated the effects of lignocellulosic wastes on the growth, antioxidant system, microbiome, and lipidome of yellow mealworms. The relative growth of lignocellulosic waste group was not significantly different from wheat bran. The antioxidant level was elevated in DG. MS was significantly enriched in cellulose-degrading bacteria in the gut and was accompanied by disturbances in lipid metabolism. The correlation coefficients were used to construct a network connecting diet, microbiota, and lipids. The correlation analysis indicated that two sphingolipids, hexylglyceramide and dihydroglyceramide, were strongly and positively linked with the dominating species. This study provides comprehensive information on physiological and mechanism of mealworms in process of treating lignocellulosic waste.},
}

@article {pmid38663293,
year = {2024},
author = {Li, N and Wang, X and Li, X and Yi, S and Guo, Y and Wu, N and Lin, H and Zhong, B and Wu, WM and He, Y},
title = {Anthropogenic and biological activities elevate microplastics pollution in headwater ecosystem of Yangtze tributaries in Hindu Kush-Himalayan region.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134395},
doi = {10.1016/j.jhazmat.2024.134395},
pmid = {38663293},
issn = {1873-3336},
abstract = {Microplastic (MP) pollution is widely spread in oceans, freshwater, and terrestrial environments but MPs in mountainous headwater ecosystem are rarely reported. This study focuses on the headwater of Yangtze tributaries of the Hindu Kush-Himalayan (HKH) region. Five streams at elevations of 900 to 3300 m were selected to investigate the distribution of MPs in water and sediments across altitudes. MPs were found in all water and sediment samples from top stream zone nearly in absence of anthropogenic activity, low anthropogenic zone, and high anthropogenic zone, increased from 12-54, 81-185 to 334-847 items/L, and 2-35, 26-84 to 124-428 items/kg, respectively. This elevation-dependent MP distribution indicated that as elevation decreased, anthropogenic activities intensified and increased MPs input and their abundance, size, and diversity. Notably, hydraulic projects, such as damming, were identified as potential barriers to the migration of MPs downstream. Microbiome analyses revealed the presence of bacterial genes associated with plastic biodegradation in all sediment samples. The study indicates that Shangri-la mountainous streams have been polluted with MPs for years with potential risk of generation of nano-sized particles via natural fragmentation and biodegradation, and thus raises concern on MPs pollution in headwaters streams in mountainous regions.},
}

@article {pmid38662827,
year = {2024},
author = {Giampazolias, E and Pereira da Costa, M and Lam, KC and Lim, KHJ and Cardoso, A and Piot, C and Chakravarty, P and Blasche, S and Patel, S and Biram, A and Castro-Dopico, T and Buck, MD and Rodrigues, RR and Poulsen, GJ and Palma-Duran, SA and Rogers, NC and Koufaki, MA and Minutti, CM and Wang, P and Vdovin, A and Frederico, B and Childs, E and Lee, S and Simpson, B and Iseppon, A and Omenetti, S and Kelly, G and Goldstone, R and Nye, E and Suárez-Bonnet, A and Priestnall, SL and MacRae, JI and Zelenay, S and Patil, KR and Litchfield, K and Lee, JC and Jess, T and Goldszmid, RS and Reis E Sousa, C},
title = {Vitamin D regulates microbiome-dependent cancer immunity.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6694},
pages = {428-437},
doi = {10.1126/science.adh7954},
pmid = {38662827},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Vitamin D/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bacteroides fragilis ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Neoplasms/immunology/microbiology ; Mice, Inbred C57BL ; Immunotherapy ; Female ; Intestinal Mucosa/immunology/microbiology/metabolism ; Male ; },
abstract = {A role for vitamin D in immune modulation and in cancer has been suggested. In this work, we report that mice with increased availability of vitamin D display greater immune-dependent resistance to transplantable cancers and augmented responses to checkpoint blockade immunotherapies. Similarly, in humans, vitamin D-induced genes correlate with improved responses to immune checkpoint inhibitor treatment as well as with immunity to cancer and increased overall survival. In mice, resistance is attributable to the activity of vitamin D on intestinal epithelial cells, which alters microbiome composition in favor of Bacteroides fragilis, which positively regulates cancer immunity. Our findings indicate a previously unappreciated connection between vitamin D, microbial commensal communities, and immune responses to cancer. Collectively, they highlight vitamin D levels as a potential determinant of cancer immunity and immunotherapy success.},
}

Animals
Mice
*Vitamin D/pharmacology
*Gastrointestinal Microbiome/drug effects
Humans
*Bacteroides fragilis
Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Neoplasms/immunology/microbiology
Mice, Inbred C57BL
Immunotherapy
Female
Intestinal Mucosa/immunology/microbiology/metabolism
Male

@article {pmid38662573,
year = {2024},
author = {Bosch, TCG and Wigley, M and Colomina, B and Bohannan, B and Meggers, F and Amato, KR and Azad, MB and Blaser, MJ and Brown, K and Dominguez-Bello, MG and Ehrlich, SD and Elinav, E and Finlay, BB and Geddie, K and Geva-Zatorsky, N and Giles-Vernick, T and Gros, P and Guillemin, K and Haraoui, LP and Johnson, E and Keck, F and Lorimer, J and McFall-Ngai, MJ and Nichter, M and Pettersson, S and Poinar, H and Rees, T and Tropini, C and Undurraga, EA and Zhao, L and Melby, MK},
title = {The potential importance of the built-environment microbiome and its impact on human health.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {20},
pages = {e2313971121},
doi = {10.1073/pnas.2313971121},
pmid = {38662573},
issn = {1091-6490},
support = {HMB program//Canadian Institute for Advanced Research (ICRA)/ ; },
mesh = {Humans ; *Built Environment ; *Microbiota/physiology ; Animals ; },
abstract = {There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments.},
}

Humans
*Built Environment
*Microbiota/physiology
Animals

@article {pmid38662328,
year = {2024},
author = {Snelson, M and Vanuytsel, T and Marques, FZ},
title = {Breaking the Barrier: The Role of Gut Epithelial Permeability in the Pathogenesis of Hypertension.},
journal = {Current hypertension reports},
volume = {},
number = {},
pages = {},
pmid = {38662328},
issn = {1534-3111},
support = {106698/WT_/Wellcome Trust/United Kingdom ; 105663/WT_/Wellcome Trust/United Kingdom ; },
abstract = {PURPOSE OF THE REVIEW: To review what intestinal permeability is and how it is measured, and to summarise the current evidence linking altered intestinal permeability with the development of hypertension.

RECENT FINDINGS: Increased gastrointestinal permeability, directly measured in vivo, has been demonstrated in experimental and genetic animal models of hypertension. This is consistent with the passage of microbial substances to the systemic circulation and the activation of inflammatory pathways. Evidence for increased gut permeability in human hypertension has been reliant of a handful of blood biomarkers, with no studies directly measuring gut permeability in hypertensive cohorts. There is emerging literature that some of these putative biomarkers may not accurately reflect permeability of the gastrointestinal tract. Data from animal models of hypertension support they have increased gut permeability; however, there is a dearth of conclusive evidence in humans. Future studies are needed that directly measure intestinal permeability in people with hypertension.},
}

@article {pmid38662310,
year = {2024},
author = {Keum, GB and Pandey, S and Kim, ES and Doo, H and Kwak, J and Ryu, S and Choi, Y and Kang, J and Kim, S and Kim, HB},
title = {Understanding the Diversity and Roles of the Ruminal Microbiome.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38662310},
issn = {1976-3794},
support = {NRF-2019M3A9F3065227//Ministry of Education/ ; },
abstract = {The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.},
}

@article {pmid38662051,
year = {2024},
author = {Reuben, RC and Torres, C},
title = {Bacteriocins: potentials and prospects in health and agrifood systems.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {233},
pmid = {38662051},
issn = {1432-072X},
support = {101034288//H2020 Marie Skłodowska-Curie Actions/ ; 101034288//H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {*Bacteriocins/metabolism/pharmacology ; Humans ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism/drug effects/genetics ; Food Microbiology ; Microbiota ; Food Packaging ; Food Safety ; },
abstract = {Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.},
}

*Bacteriocins/metabolism/pharmacology
Humans
Animals
*Anti-Bacterial Agents/pharmacology
Bacteria/metabolism/drug effects/genetics
Food Microbiology
Microbiota
Food Packaging
Food Safety

@article {pmid38661414,
year = {2024},
author = {Alexander, CC and Gaudier-Diaz, MM and Kleinschmit, AJ and Dihle, PJ and Salger, SA and Vega, N and Robertson, SD},
title = {A case study to engage students in the research design and ethics of high-throughput metagenomics.},
journal = {Journal of microbiology & biology education},
volume = {25},
number = {1},
pages = {e0007423},
pmid = {38661414},
issn = {1935-7877},
abstract = {Case studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today's Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled "You Are What You Eat." Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students' perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the "You Are What You Eat" case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.},
}

@article {pmid38661383,
year = {2023},
author = {Bechberger, M and Eigenbrod, T and Boutin, S and Heeg, K and Bode, KA},
title = {IL-1β knockout increases the intestinal abundancy of Akkermansia muciniphila.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {361-370},
doi = {10.1163/18762891-20220042},
pmid = {38661383},
issn = {1876-2891},
mesh = {Animals ; Mice ; *Akkermansia/genetics ; Colon/microbiology ; *Gastrointestinal Microbiome ; *Interleukin-1beta/genetics/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Ribonuclease, Pancreatic/genetics/metabolism ; },
abstract = {The proinflammatory cytokine interleukin-1β (IL-1β) is known to be upregulated in patients suffering from metabolic syndrome. IL-1β contributes to insulin resistance in obesity and type 2 diabetes, yet its influence on the intestinal microbiome is incompletely understood. The data presented here demonstrate that mice genetically deficient in IL-1β show a specific alteration of intestinal colonisation of a small group of bacteria. Especially Akkermansia muciniphila, a bacterium reported to be inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation, showed increased colonisation in IL-1β knockout mice. In comparative microarray analysis from mucus scrapings of the colon mucosa of IL-1β knockout and wildtype mice, angiogenin 4 mRNA was strongly reduced in IL-1β knockout animals. Since the presence of angiogenin 4 in the culture medium showed a significant growth inhibition on A. muciniphila which was not detectable for other bacteria tested, IL-1β induced expression of angiogenin 4 is a strong candidate to be responsible for the IL-1β induced suppression of A. muciniphila colonisation. Thus, the data presented here indicate that IL-1β might be the lacking link between inflammation and suppression of A. muciniphila abundance as observed in a variety of chronic inflammatory disorders.},
}

Animals
Mice
*Akkermansia/genetics
Colon/microbiology
*Gastrointestinal Microbiome
*Interleukin-1beta/genetics/metabolism
Intestinal Mucosa/microbiology/metabolism
Mice, Inbred C57BL
Ribonuclease, Pancreatic/genetics/metabolism

@article {pmid38661361,
year = {2023},
author = {Hendrickx, DM and An, R and Boeren, S and Mutte, SK and , and Wopereis, H and Belzer, C},
title = {Trackability of proteins from probiotic Bifidobacterium spp. in the gut using metaproteomics.},
journal = {Beneficial microbes},
volume = {14},
number = {3},
pages = {269-280},
doi = {10.1163/18762891-20220137},
pmid = {38661361},
issn = {1876-2891},
mesh = {Humans ; *Feces/microbiology ; *Bifidobacterium/genetics/metabolism ; *Probiotics ; *Gastrointestinal Microbiome ; Infant ; *Proteomics ; *Synbiotics ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Prebiotics/analysis ; Infant Formula ; Male ; DNA, Bacterial/genetics ; Female ; },
abstract = {Beneficial effects of Bifidobacterium spp. on gut microbiota development and infant health have been reported earlier. Therefore, supplementation of infant formulas with probiotic bifidobacteria, as well as prebiotics stimulating bifidobacterial growth, has been proposed. Here, we studied the faecal microbiome of infants supplemented with specialized nutrition, of which some received a standard amino acid-based formula (AAF) and others an AAF with a specific mixture of prebiotics and a probiotic (synbiotics) using metaproteomics and 16S rRNA gene sequencing. Faecal samples were taken at baseline, as well as after 6 and 12 months fed with the specialized formula. The aim was to compare microbial differences between infants treated with the standard AAF and those who received the additional synbiotics. Our findings show that infants who received AAF with synbiotics have significantly higher levels of Bifidobacteriaceae DNA as well as significantly increased levels of Coriobacteriaceae proteins, over time. Moreover, at visit 12 months higher levels of some bifidobacterial carbohydrate-active enzymes, known to metabolize oligosaccharides, were observed in the synbiotic group compared to the non-synbiotic group. The results indicate that the synbiotics provided in our study are trackable in faecal samples on the DNA and protein level during the intervention period.},
}

Humans
*Feces/microbiology
*Bifidobacterium/genetics/metabolism
*Probiotics
*Gastrointestinal Microbiome
Infant
*Proteomics
*Synbiotics
*RNA, Ribosomal, 16S/genetics
Bacterial Proteins/genetics/metabolism
Prebiotics/analysis
Infant Formula
Male
DNA, Bacterial/genetics
Female

@article {pmid38661353,
year = {2023},
author = {Zhu, Z and Hu, C and Liu, Y and Wang, F and Zhu, B},
title = {Inulin has a beneficial effect by modulating the intestinal microbiome in a BALB/c mouse model.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {371-383},
doi = {10.1163/18762891-20220094},
pmid = {38661353},
issn = {1876-2891},
mesh = {Animals ; *Inulin/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred BALB C ; Mice ; *Ovalbumin/immunology ; *Disease Models, Animal ; *Immunoglobulin E/blood/immunology ; *Food Hypersensitivity/microbiology/immunology/drug therapy ; Female ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/drug effects/isolation & purification/genetics ; Immunoglobulin A, Secretory ; Immunoglobulin A/blood ; },
abstract = {Food allergy is an important health problem that affects human quality of life and socioeconomic development, and its treatment requires improvement. Intestinal flora dysbiosis is closely associated with food allergies. A sensitised mouse model was established by the intraperitoneal injection of ovalbumin (OVA). The mice were randomly divided into four groups: control, model, high-dose (H), and low-dose (L) inulin. The mice were administered water containing different concentrations of inulin four weeks before the OVA injection. Body weight changes were monitored. After the last OVA injection, the mice were scored for allergic reactions. The levels of total immunoglobulin E (IgE) and diamine oxidase (DAO) in the serum and secretory IgA (sIgA) in the small intestinal mucus were measured, and 16S rRNA sequencing of the faecal flora was performed to evaluate microbial parameters. The intestinal flora biomarkers, correlations between them, and biochemical indicators were analysed. Inulin treatment had no effect on the body weight of OVA-sensitised mice but attenuated allergic reactions and intestinal injury in mice. Compared with the control group, the model group had significantly higher levels of serum DAO and IgE and significantly lower levels of intestinal mucus IgA. IgA levels in the intestinal mucus of mice treated with inulin prior to OVA sensitisation were higher than those in non-inulin-treated OVA-sensitised mice. Furthermore, analysis of operational taxonomic units showed that inulin treatment decreased the abundance of Alloprevotella, Rikenellaceae RC9, Eubacterium siraeum, and Eubacterium xylanophilum, and increased the abundance of Blautia and Lachnospiraceae. Serum DAO levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, and Odoribacter and negatively associated with Blautia, Tyzzerella, Alistipes, Desulfovibrionaceae, and Ruminococcaceae UCG005. In addition, IgE levels were positively associated with Eubacterium siraeum, Alloprevotella, Eubacterium xylanophilum, Odoribacter, and Citrobacter and negatively associated with Blautia, unclassified Ruminococcaceae, and Alistipes. IgA exhibited significant positive correlation with Blautia, norank_f_Eubacterium coprostanoligenes, Alistipes, norank Desulfovibrionaceae, Muribaculum, and Ruminococcaceae U C G 005 and significant negative correlation with Eubacterim siraeum, Eubacterium xylanophilum, Odoribacter, and Citrobacter. Inulin exerts a protective effect against food allergies in mice, which is partially mediated by alterations in the gut microbiota.},
}

Animals
*Inulin/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Mice, Inbred BALB C
Mice
*Ovalbumin/immunology
*Disease Models, Animal
*Immunoglobulin E/blood/immunology
*Food Hypersensitivity/microbiology/immunology/drug therapy
Female
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Bacteria/classification/drug effects/isolation & purification/genetics
Immunoglobulin A, Secretory
Immunoglobulin A/blood

@article {pmid38661345,
year = {2023},
author = {Jackson, PPJ and Wijeyesekera, A and Theis, S and Van Harsselaar, J and Rastall, RA},
title = {Effects of food matrix on the prebiotic efficacy of inulin-type fructans: a randomised trial.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {317-334},
doi = {10.1163/18762891-20220120},
pmid = {38661345},
issn = {1876-2891},
mesh = {*Prebiotics ; *Inulin/pharmacology ; Humans ; *Bifidobacterium/genetics/drug effects ; *Feces/microbiology ; *Fructans/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Oryza ; Female ; Male ; Gastrointestinal Microbiome/drug effects ; Adult ; Chocolate ; Young Adult ; In Situ Hybridization, Fluorescence ; },
abstract = {Recently there is much debate in the scientific community over the impact of the food matrix on prebiotic efficacy of inulin-type fructans. Previous studies suggest that prebiotic selectivity of inulin-type fructans towards bifidobacteria is unaffected by the food matrix. Due to differences in study design, definitive conclusions cannot be drawn from these findings with any degree of certainty. In this randomised trial, we aimed to determine the effects that different food matrices had on the prebiotic efficacy of inulin-type fructans following a standardised 10-day, 4-arm, parallel, randomised protocol with inulin either in pure form or incorporated into shortbread biscuits, milk chocolate or a rice drink. Similar increases in Bifidobacterium counts were documented across all four interventions using both fluorescence in situ hybridisation (pure inulin: +0.63; shortbread: +0.59; milk chocolate: +0.65 and rice drink: +0.71 (log10 cells/g wet faeces) and 16S rRNA sequencing quantitative microbiome profiling data (pure inulin: +1.21 × 109; shortbread: +1.47 × 109; milk chocolate: +8.59 × 108 and rice drink: +1.04 × 109 (cells/g wet faeces) (all P ≤ 0.05). From these results, we can confirm that irrespective of the food matrix, the selectivity of inulin-type fructans towards Bifidobacterium is unaffected, yet the compositional make-up of the food matrix may have implications regarding wider changes in the microbiota.},
}

*Prebiotics
*Inulin/pharmacology
Humans
*Bifidobacterium/genetics/drug effects
*Feces/microbiology
*Fructans/pharmacology
*RNA, Ribosomal, 16S/genetics
Oryza
Female
Male
Gastrointestinal Microbiome/drug effects
Adult
Chocolate
Young Adult
In Situ Hybridization, Fluorescence

@article {pmid38661344,
year = {2024},
author = {Phan, J and Calvo, DC and Nair, D and Jain, S and Montagne, T and Dietsche, S and Blanchard, K and Treadwell, S and Adams, J and Krajmalnik-Brown, R},
title = {Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050324},
doi = {10.1128/msystems.00503-24},
pmid = {38661344},
issn = {2379-5077},
abstract = {UNLABELLED: The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms.

IMPORTANCE: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.},
}

@article {pmid38661014,
year = {2024},
author = {Dalgard, F and Bewley, A},
title = {New insights to the mind-body connection: The importance of the brain-gut microbiome for inflammatory skin diseases.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {38},
number = {5},
pages = {784-785},
doi = {10.1111/jdv.19946},
pmid = {38661014},
issn = {1468-3083},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Brain-Gut Axis/physiology ; Skin Diseases/microbiology ; Brain ; },
}

Humans
*Gastrointestinal Microbiome/physiology
Brain-Gut Axis/physiology
Skin Diseases/microbiology
Brain

@article {pmid38660637,
year = {2024},
author = {Qi, JH and Huang, SL and Jin, SZ},
title = {Novel milestones for early esophageal carcinoma: From bench to bed.},
journal = {World journal of gastrointestinal oncology},
volume = {16},
number = {4},
pages = {1104-1118},
pmid = {38660637},
issn = {1948-5204},
abstract = {Esophageal cancer (EC) is the seventh most common cancer worldwide, and esophageal squamous cell carcinoma (ESCC) accounts for the majority of cases of EC. To effectively diagnose and treat ESCC and improve patient prognosis, timely diagnosis in the initial phase of the illness is necessary. This article offers a detailed summary of the latest advancements and emerging technologies in the timely identification of ECs. Molecular biology and epigenetics approaches involve the use of molecular mechanisms combined with fluorescence quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology (next-generation sequencing), and digital PCR technology to study endogenous or exogenous biomolecular changes in the human body and provide a decision-making basis for the diagnosis, treatment, and prognosis of diseases. The investigation of the microbiome is a swiftly progressing area in human cancer research, and microorganisms with complex functions are potential components of the tumor microenvironment. The intratumoral microbiota was also found to be connected to tumor progression. The application of endoscopy as a crucial technique for the early identification of ESCC has been essential, and with ongoing advancements in technology, endoscopy has continuously improved. With the advancement of artificial intelligence (AI) technology, the utilization of AI in the detection of gastrointestinal tumors has become increasingly prevalent. The implementation of AI can effectively resolve the discrepancies among observers, improve the detection rate, assist in predicting the depth of invasion and differentiation status, guide the pericancerous margins, and aid in a more accurate diagnosis of ESCC.},
}

@article {pmid38660491,
year = {2024},
author = {Serrage, HJ and O' Neill, CA and Uzunbajakava, NE},
title = {Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1307374},
pmid = {38660491},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; *Skin/microbiology/radiation effects ; *Light ; Skin Diseases/microbiology ; Dysbiosis/microbiology ; Animals ; Blue Light ; },
abstract = {Cutaneous diseases (such as atopic dermatitis, acne, psoriasis, alopecia and chronic wounds) rank as the fourth most prevalent human disease, affecting nearly one-third of the world's population. Skin diseases contribute to significant non-fatal disability globally, impacting individuals, partners, and society at large. Recent evidence suggests that specific microbes colonising our skin and its appendages are often overrepresented in disease. Therefore, manipulating interactions of the microbiome in a non-invasive and safe way presents an attractive approach for management of skin and hair follicle conditions. Due to its proven anti-microbial and anti-inflammatory effects, blue light (380 - 495nm) has received considerable attention as a possible 'magic bullet' for management of skin dysbiosis. As humans, we have evolved under the influence of sun exposure, which comprise a significant portion of blue light. A growing body of evidence indicates that our resident skin microbiome possesses the ability to detect and respond to blue light through expression of chromophores. This can modulate physiological responses, ranging from cytotoxicity to proliferation. In this review we first present evidence of the diverse blue light-sensitive chromophores expressed by members of the skin microbiome. Subsequently, we discuss how blue light may impact the dialog between the host and its skin microbiome in prevalent skin and hair follicle conditions. Finally, we examine the constraints of this non-invasive treatment strategy and outline prospective avenues for further research. Collectively, these findings present a comprehensive body of evidence regarding the potential utility of blue light as a restorative tool for managing prevalent skin conditions. Furthermore, they underscore the critical unmet need for a whole systems approach to comprehend the ramifications of blue light on both host and microbial behaviour.},
}

Humans
*Microbiota
*Skin/microbiology/radiation effects
*Light
Skin Diseases/microbiology
Dysbiosis/microbiology
Animals
Blue Light

@article {pmid38660490,
year = {2024},
author = {Ramos Peña, DE and Pillet, S and Grupioni Lourenço, A and Pozzetto, B and Bourlet, T and Motta, ACF},
title = {Human immunodeficiency virus and oral microbiota: mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1364002},
pmid = {38660490},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology/complications/virology ; *Microbiota ; *Gingiva/microbiology/virology ; Mouth/microbiology/virology ; Disease Reservoirs/microbiology/virology ; Periodontitis/microbiology/virology ; Virome ; Dysbiosis/microbiology ; Anti-Retroviral Agents/therapeutic use ; HIV ; },
abstract = {The role of the oral microbiota in the overall health and in systemic diseases has gained more importance in the recent years, mainly due to the systemic effects that are mediated by the chronic inflammation caused by oral diseases, such as periodontitis, through the microbial communities of the mouth. The chronic infection by the human immunodeficiency virus (HIV) interacts at the tissue level (e.g. gut, genital tract, brain) to create reservoirs; the modulation of the gut microbiota by HIV infection is a good example of these interactions. The purpose of the present review is to assess the state of knowledge on the oral microbiota (microbiome, mycobiome and virome) of HIV-infected patients in comparison to that of HIV-negative individuals and to discuss the reciprocal influence of HIV infection and oral microbiota in patients with periodontitis on the potential establishment of a viral gingival reservoir. The influence of different clinical and biological parameters are reviewed including age, immune and viral status, potent antiretroviral therapies, smoking, infection of the airway and viral coinfections, all factors that can modulate the oral microbiota during HIV infection. The analysis of the literature proposed in this review indicates that the comparisons of the available studies are difficult due to their great heterogeneity. However, some important findings emerge: (i) the oral microbiota is less influenced than that of the gut during HIV infection, although some recurrent changes in the microbiome are identified in many studies; (ii) severe immunosuppression is correlated with altered microbiota and potent antiretroviral therapies correct partially these modifications; (iii) periodontitis constitutes a major factor of dysbiosis, which is exacerbated in HIV-infected patients; its pathogenesis can be described as a reciprocal reinforcement of the two conditions, where the local dysbiosis present in the periodontal pocket leads to inflammation, bacterial translocation and destruction of the supporting tissues, which in turn enhances an inflammatory environment that perpetuates the periodontitis cycle. With the objective of curing viral reservoirs of HIV-infected patients in the future years, it appears important to develop further researches aimed at defining whether the inflamed gingiva can serve of viral reservoir in HIV-infected patients with periodontitis.},
}

Humans
*HIV Infections/drug therapy/microbiology/complications/virology
*Microbiota
*Gingiva/microbiology/virology
Mouth/microbiology/virology
Disease Reservoirs/microbiology/virology
Periodontitis/microbiology/virology
Virome
Dysbiosis/microbiology
Anti-Retroviral Agents/therapeutic use
HIV

@article {pmid38660489,
year = {2024},
author = {Zhang, J and Wang, H and Liu, Y and Shi, M and Zhang, M and Zhang, H and Chen, J},
title = {Advances in fecal microbiota transplantation for the treatment of diabetes mellitus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1370999},
pmid = {38660489},
issn = {2235-2988},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus/therapy/microbiology ; Dysbiosis/therapy ; Animals ; Feces/microbiology ; },
abstract = {Diabetes mellitus (DM) refers to a group of chronic diseases with global prevalence, characterized by persistent hyperglycemia resulting from various etiologies. DM can harm various organ systems and lead to acute or chronic complications, which severely endanger human well-being. Traditional treatment mainly involves controlling blood sugar levels through replacement therapy with drugs and insulin; however, some patients still find a satisfactory curative effect difficult to achieve. Extensive research has demonstrated a close correlation between enteric dysbacteriosis and the pathogenesis of various types of DM, paving the way for novel therapeutic approaches targeting the gut microbiota to manage DM. Fecal microbiota transplantation (FMT), a method for re-establishing the intestinal microbiome balance, offers new possibilities for treating diabetes. This article provides a comprehensive review of the correlation between DM and the gut microbiota, as well as the current advancements in FMT treatment for DM, using FMT as an illustrative example. This study aims to offer novel perspectives and establish a theoretical foundation for the clinical diagnosis and management of DM.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Gastrointestinal Microbiome
*Diabetes Mellitus/therapy/microbiology
Dysbiosis/therapy
Animals
Feces/microbiology

@article {pmid38660030,
year = {2024},
author = {Lourenço, KS and Suleiman, AKA and Pijl, A and Dimitrov, MR and Cantarella, H and Kuramae, EE},
title = {Mix-method toolbox for monitoring greenhouse gas production and microbiome responses to soil amendments.},
journal = {MethodsX},
volume = {12},
number = {},
pages = {102699},
pmid = {38660030},
issn = {2215-0161},
abstract = {In this study, we adopt an interdisciplinary approach, integrating agronomic field experiments with soil chemistry, molecular biology techniques, and statistics to investigate the impact of organic residue amendments, such as vinasse (a by-product of sugarcane ethanol production), on soil microbiome and greenhouse gas (GHG) production. The research investigates the effects of distinct disturbances, including organic residue application alone or combined with inorganic N fertilizer on the environment. The methods assess soil microbiome dynamics (composition and function), GHG emissions, and plant productivity. Detailed steps for field experimental setup, soil sampling, soil chemical analyses, determination of bacterial and fungal community diversity, quantification of genes related to nitrification and denitrification pathways, measurement and analysis of gas fluxes (N2O, CH4, and CO2), and determination of plant productivity are provided. The outcomes of the methods are detailed in our publications (Lourenço et al., 2018a; Lourenço et al., 2018b; Lourenço et al., 2019; Lourenço et al., 2020). Additionally, the statistical methods and scripts used for analyzing large datasets are outlined. The aim is to assist researchers by addressing common challenges in large-scale field experiments, offering practical recommendations to avoid common pitfalls, and proposing potential analyses, thereby encouraging collaboration among diverse research groups.•Interdisciplinary methods and scientific questions allow for exploring broader interconnected environmental problems.•The proposed method can serve as a model and protocol for evaluating the impact of soil amendments on soil microbiome, GHG emissions, and plant productivity, promoting more sustainable management practices.•Time-series data can offer detailed insights into specific ecosystems, particularly concerning soil microbiota (taxonomy and functions).},
}

@article {pmid38659993,
year = {2024},
author = {He, J and Mao, N and Lyu, W and Zhou, S and Zhang, Y and Liu, Z and Xu, Z},
title = {Association between oral microbiome and five types of respiratory infections: a two-sample Mendelian randomization study in east Asian population.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1392473},
pmid = {38659993},
issn = {1664-302X},
abstract = {OBJECTIVE: To explore the causal relationship between the oral microbiome and specific respiratory infections including tonsillitis, chronic sinusitis, bronchiectasis, bronchitis, and pneumonia, assessing the impact of genetic variations associated with the oral microbiome.

METHODS: Mendelian randomization was used to analyze genetic variations, leveraging data from genome-wide association studies in an East Asian cohort to identify connections between specific oral microbiota and respiratory infections.

RESULTS: Our analysis revealed that Prevotella, Streptococcus, Fusobacterium, Pauljensenia, and Capnocytophaga play crucial roles in influencing respiratory infections. Prevotella is associated with both promoting bronchitis and inhibiting pneumonia and tonsillitis, with a mixed effect on chronic sinusitis. Streptococcus and Fusobacterium show varied impacts on respiratory diseases, with Fusobacterium promoting chronic sinusitis, bronchiectasis, and bronchitis. Conversely, Pauljensenia and Capnocytophaga are linked to reduced bronchitis and tonsillitis, and inhibited pneumonia and bronchitis, respectively.

DISCUSSION: These findings underscore the significant impact of the oral microbiome on respiratory health, suggesting potential strategies for disease prevention and management through microbiome targeting. The study highlights the complexity of microbial influences on respiratory infections and the importance of further research to elucidate these relationships.},
}

@article {pmid38659992,
year = {2024},
author = {Qiu, Y and Hou, Y and Wei, X and Wang, M and Yin, Z and Xie, M and Duan, A and Ma, C and Si, K and Wang, Z},
title = {Causal association between gut microbiomes and different types of aneurysms: a Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1267888},
pmid = {38659992},
issn = {1664-302X},
abstract = {BACKGROUND: Previous studies suggests that gut microbiomes are associated with the formation and progression of aneurysms. However, the causal association between them remains unclear.

METHODS: A two-sample Mendelian randomization was conducted to investigate whether gut microbiomes have a causal effect on the risk of intracerebral aneurysm (IA), thoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA), and aortic aneurysm (AA). Single nucleotide polymorphisms (SNPs) smaller than the locus-wide significance level (1 × 10[-5]) were selected as instrumental variables. We used inverse-variance weighted (IVW) test as the primary method for the evaluation of causal association. MR-Egger, weighted median, weighted mode, and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO) methods were conducted for sensitive analysis. The p-value was adjusted by the false discovery rate (FDR) which adjust the results of multiple comparisons, a p < 0.05 and q < 0.1 was considered a significant causal association. Additionally, a p < 0.05 and q > 0.1 was considered a suggestive causal effect. Additionally, reverse MR was also performed to exclude the possibility of reverse causality.

RESULTS: The phylum Firmicutes (OR = 0.62; 95% CI, 0.48-0.81), class Lentisphaeria (OR = 0.75; 95% CI, 0.62-0.89), and order Victivallales (OR = 0.75; 95% CI, 0.62-0.89) have a causal protective effect on the risk of AAA. Additionally, class Verrucomicrobia, class Deltaproteobacteria, order Verrucomicrobiale, family Verrucomicrobiacea, genus Eubacterium rectale group, genus Akkermansia, and genus Clostridium innocuum group were negatively associated with the risk of different types of aneurysms, whereas class Negativicutes, order Selenomonadales, and genus Roseburia had positive causal association with different types of aneurysms (p < 0.05; q > 0.1). Further sensitivity analysis validated the robustness of our MR results, and no reverse causality was found with these gut microbiomes (p > 0.05).

CONCLUSION: Our MR analysis confirmed the causal association of specific gut microbiomes with AAA, and these microbiomes were considered as protective factors. Our result may provide novel insights and theoretical basis for the prevention of aneurysms through regulation of gut microbiomes.},
}

@article {pmid38659984,
year = {2024},
author = {Ovsepian, A and Kardaras, FS and Skoulakis, A and Hatzigeorgiou, AG},
title = {Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383404},
pmid = {38659984},
issn = {1664-302X},
}

@article {pmid38659980,
year = {2024},
author = {Sarpong, N and Seifert, J and Bennewitz, J and Rodehutscord, M and Camarinha-Silva, A},
title = {Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1354537},
pmid = {38659980},
issn = {1664-302X},
abstract = {As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.},
}

@article {pmid38659839,
year = {2024},
author = {Chen, T and Way, R and Templeton, H and Ball, D and Cheng, MH and Tobet, S},
title = {A Microphysiological System for Studying Barrier Health of Live Tissues in Real Time.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4078220/v1},
pmid = {38659839},
abstract = {Epithelial cells create barriers that protect many different components in the body from their external environment. The gut in particular carries bacteria and other infectious agents. A healthy gut epithelial barrier prevents unwanted substances from accessing the underlying lamina propria while maintaining the ability to digest and absorb nutrients. Increased gut barrier permeability, better known as leaky gut , has been linked to several chronic inflammatory diseases. Yet understanding the cause of leaky gut and developing effective interventions are still elusive due to the lack of tools to maintain tissue's physiological environment while elucidating cellular functions under various stimuli ex vivo. This paper presents a microphysiological system capable of recording real-time barrier permeability of mouse gut tissues in a realistic physiological environment over extended durations. Key components of the microphysiological system include a microfluidic chamber designed to hold the live tissue explant and create a sufficient microphysiological environment to maintain tissue viability; proper media composition that preserves a microbiome and creates necessary oxygen gradients across the barrier; integrated sensor electrodes and supporting electronics for acquiring and calculating transepithelial electrical resistance (TEER); and a scalable system architecture to allow multiple chambers running in parallel for increased throughput. The experimental results demonstrate that the system can maintain tissue viability for up to 72 hours. The results also show that the custom-built and integrated TEER sensors are sufficiently sensitive to distinguish differing levels of barrier permeability when treated with collagenase and low pH media compared to control. Permeability variations in tissue explants from different positions in the intestinal tract were also investigated using TEER revealing their disparities in permeability. Finally, the results also quantitatively determine the effect of the muscle layer on total epithelial resistance.},
}

@article {pmid38659779,
year = {2024},
author = {Moraes, JGN and Gull, TB and Ericsson, AC and Caldeira, MO and Evans, TJ and Poock, SE and Lucy, MC},
title = {Systemic antibiotic treatment of cows with metritis early postpartum does not change the progression of uterine disease or the uterine microbiome at 1 month postpartum.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4233045/v1},
pmid = {38659779},
abstract = {Background: Postpartum uterine disease (metritis) is common in dairy cows. The disease develops within 1 week after calving and is associated with microbial dysbiosis, fever, and fetid uterine discharge. Cows with metritis have a greater likelihood of developing endometritis and infertility later postpartum. Antibiotic treatment is used to relieve symptoms of metritis but the capacity of antibiotic treatment to improve fertility later postpartum is inconsistent across published studies. We hypothesized that an antibiotic has only a short-term effect on the uterine microbiome and does not change the progression of disease from metritis to endometritis. To test this hypothesis, we studied the effects of systemic antibiotic given to cows diagnosed with metritis and healthy cows early postpartum on the development of endometritis and the uterine microbiome at 1 month postpartum. Results: Cows diagnosed with metritis were compared to healthy ones in a 2 x 2 factorial design, where they were either treated with an antibiotic (ceftiofur hydrochloride) at 7 to 10 days postpartum or left untreated. Cows were slaughtered at one month postpartum and the uterus was assessed for endometritis (presence of purulent material in the uterine lumen and inflammation in the endometrium) and uterine samples were collected for bacteriology and metagenomics (16S rRNA gene sequencing). As expected, the uterine microbiome at disease diagnosis had dysbiosis of typical metritis pathogens (e.g., Fusobacterium , Bacteroides , and Porphyromonas) in diseased compared with healthy cows. At one month postpartum, there was a tendency for more endometritis in metritis cows compared with healthy but antibiotic treatment had no effect on endometritis prevalence regardless of the original disease diagnosis. Likewise, when bacteria were cultured or sequenced, there were a greater number of species (culture) or amplicon sequence variants (ASV; sequencing) in the uterine lumen of cows with metritis. However, antibiotic treatment had no effect on the prevalence of cultured species or the composition of the detected ASV. The uterine microbiome at 1 month postpartum was associated with the clinical observation of the uterus (endometritis or healthy). Conclusions: Early postpartum antibiotic treatment only provides temporary resolution of uterine dysbiosis that is not sustained long-term. Failure to resolve the dysbiosis is associated with a greater prevalence of endometritis in cows with metritis, and the occurrence of endometritis significantly impacts fertility later postpartum.},
}

@article {pmid38659758,
year = {2024},
author = {Occhino, JA and D O, JNB and Wu, PY and Walther-Antonio, MR and Chen, J},
title = {Preoperative Vaginal Microbiome as a Predictor of Postoperative Urinary Tract Infection.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4069233/v1},
pmid = {38659758},
abstract = {This is a single Institute, prospective cohort study. We collected twenty- two postmenopausal women with pelvic organ prolapse planning to undergo vaginal hysterectomy with transvaginal pelvic reconstructive surgery, with or without a concomitant anti-incontinence procedure. Vaginal swabs and urine samples were longitudinally collected at five time points: preoperative consult visit (T1), day of surgery prior to surgical scrub (T2), immediately postoperative (T3), day of hospital discharge (T4), and at the postoperative exam visit (T5). Women experiencing urinary tract infection symptoms provided a sample set prior to antibiotic administration (T6). Microbiome analysis on vaginal and urinary specimens at each time point. Region V3-V5 of the 16S ribosomal RNA gene was amplified and sequenced. Sample DNA was analyzed with visit T1, T2, T5 and T6. Six (27.3%) participants developed postoperative urinary tract infection whose vaginal sample at first clinical visit (T1) revealed beta-diversity analysis with significant differences in microbiome structure and composition. Women diagnosed with a postoperative urinary tract infection had a vaginal microbiome characterized by low abundance of Lactobacillus and high prevalence of Prevotella and Gardnerella species. In our cohort, preoperative vaginal swabs can predict who will develop a urinary tract infection following transvaginal surgery for pelvic organ prolapse.},
}