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28 Sep 2021 at 01:48
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 28 Sep 2021 at 01:48 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-09-27

Pacheco AP, Cedernaes J, C Benedict (2021)

Gut microbiome as a therapeutic target in the treatment of sleep disorders: where we are.

RevDate: 2021-09-27

Hu B, Liu C, Jiang W, et al (2021)

Chronic in vitro fermentation and in vivo metabolism: Extracellular polysaccharides from Sporidiobolus pararoseus regulate the intestinal microbiome of humans and mice.

International journal of biological macromolecules pii:S0141-8130(21)02056-0 [Epub ahead of print].

The fungus Sporidiobolus pararoseus not only produces carotenoids, but also produces bioactive extracellular polysaccharides (SPP). However, the relationship between SPP and the metabolism of gut microbiome is unclear. The aim of this study was to investigate the mechanism of SPP regulating intestinal health in vivo and in vitro. Results showed that SPP are nondigestible polysaccharides after the digestion with simulated stomach and small intestinal juice in vitro. After SPP was cultured in an in vitro intestinal simulation system for seven days, the concentration of short-chain fatty acids (SCFAs) increased; the microbial diversity changed; the relative abundance of Bifidobacterium and Streptococcus increased; and that of Escherichia Shigella and Lachnospiraceae NK4A136 decreased. In addition, metabolism of SPP by the mice colonic microbiome showed SPP decreased the relative abundance of Firmicutes and Bacteroidota, while the relative abundance of Verrucomicrobiota, Desulfobacterota, and Actinobacteriota increased. Finally, predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolism results also showed that SPP can enhance the metabolism of cofactors, vitamins, amino acids, starch, and sucrose. In conclusion, SPP can multiply the intestinal beneficial bacteria of humans and mice, promote the production of SCFAs and metabolism of amino acids, and promote intestinal health.

RevDate: 2021-09-27

Rui M, Zhang X, Huang J, et al (2021)

The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study.

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology pii:S0167-8140(21)06736-0 [Epub ahead of print].

PURPOSE: Among oral squamous cell carcinoma (OSCC) patients who receive docetaxel, cisplatin, and 5-fluorouracil (TPF) induction chemotherapy, those with a favorable pathological response tend to obtain satisfactory clinical outcomes, while the total population exhibit no survival benefit. Thus, there is an urgent need to improve the therapeutic effect of TPF by applying personalized treatment according to distinct biomarkers.

METHODS AND MATERIALS: In the present study, we collected oral rinse samples from 44 OSCC patients enrolled in our prospective multicenter random phase II trial before TPF induction chemotherapy to conduct 16S rRNA gene sequencing and metagenomic analysis. Patients were administrated with two cycles of TPF induction chemotherapy (75 mg/m2 cisplatin and 75 mg/m2 docetaxel on day 1 and 750 mg/m2 fluorouracil from the first to the fifth day), and then divided into responsive and nonresponsive groups according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1.

RESULTS: In the 16S rRNA gene sequence analysis, Fusobacterium and Mycoplasma were more enriched in the nonresponsive group, while Slackia was more enriched in the responder group at the genus level. In the metagenomic shotgun sequencing analysis, Fusobacterium nucleatum was more enriched in the nonresponsive group. Functional analysis showed that the platinum drug resistance pathway and microRNAs in cancer and RNA degradation pathways were remarkably associated with patient sensitivity to induction chemotherapy.

CONCLUSIONS: Our data suggest that the oral microbiome may play an important role in the OSCC patient sensitivity to TPF induction chemotherapy and offer novel potential biomarkers for predicting the response to TPF induction chemotherapy.

RevDate: 2021-09-27

Patel V, Lee S, McPhail M, et al (2021)

Rifaximin reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial.

Journal of hepatology pii:S0168-8278(21)02040-7 [Epub ahead of print].

BACKGROUND: Rifaximin is efficacious in the prevention of recurrent hepatic encephalopathy (HE) but its mechanism of action remains unclear. We postulated that rifaximin reduces gut microbiota-derived endotoxemia and systemic inflammation, a known driver of HE.

DESIGN: A randomised placebo-controlled double-blind mechanistic study of rifaximin versus placebo was performed in cirrhotic patients with HE. Rifaximin-α 550mg (TARGAXAN) twice daily (n=19) or placebo (n=19) was administered for 90-days.

PRIMARY OUTCOME: 50% reduction in neutrophil oxidative burst (OB) at 30-days.

SECONDARY OUTCOMES: Psychometric Hepatic Encephalopathy Scale (PHES), shotgun metagenomic sequencing of saliva and faeces, plasma and faecal metabolome, blood bacterial DNA, neutrophil toll-like receptor (TLR)-2/4/9 and interleukin-8 expression, and plasma and faecal cytokine analysis.

RESULTS: Patients were well-matched: median MELD [11 rifaximin-α versus 10 placebo]. Day 30 HE grade normalised on rifaximin-α but not placebo (p=0.014) with an improvement in PHES score; p=0.009. Rifaximin-α reduced circulating neutrophil TLR-4 expression on day-30 (p=0.021) with a reduction in plasma tumour necrosis factor-α (TNF-α); p<0.001. Rifaximin-α suppressed oralisation of the gut, reducing the mucin-degrading sialidase-rich species Streptococcus spp, Veillonella atypica and parvula, Akkermansia and Hungatella. Rifaximin-α promoted a TNF-α and IL-17E enriched intestinal microenvironment augmenting anti-bacterial responses to invading pathobionts and promoting gut barrier repair. Those on rifaximin-α were less likely to develop infection [odds ratio 0.21(0.05-0.96)].

CONCLUSION: Rifaximin-treated patients were less likely to develop infection with resolution of overt and covert HE. Rifaximin-α reduced oralisation of the gut with mucin-degrading species attenuating systemic inflammation. These data link rifaximin-α as having a role in gut barrier repair as a mechanism by which it ameliorates bacterial translocation and systemic endotoxemia in cirrhosis.

LAY SUMMARY: This clinical trial examined the underlying mechanism of action of an antibiotic called rifaximin which has been shown to be an effective treatment for a complication of chronic liver disease which effects the brain (termed encephalopathy). It shows that rifaximin suppresses gut bacteria that translocate from the mouth to the intestine which causes the intestinal wall to become leaky by breaking down the protective mucus barrier. This resolves encephalopathy and reduces inflammation in the blood preventing the development of infection.

CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT02019784.

RevDate: 2021-09-27

Kitsou C, Foor SD, Dutta S, et al (2021)

Tick gut barriers impacting tick-microbe interactions and pathogen persistence.

Molecular microbiology [Epub ahead of print].

Ticks are regarded as one of the most ancient, unique, and highly evolved ectoparasites. They can parasitize diverse vertebrates and transmit a number of widespread infections. Once acquired from infected hosts, many tick-borne pathogens, like Borrelia burgdorferi, are confined within the tick gut lumen and are surrounded by discrete gut barriers. Such barriers include the peritrophic membrane (PM) and the dityrosine network (DTN), which are in close contact with resident microbiota and invading pathogens, influencing their survival within the vector. Herein, we review our current state of knowledge about tick-microbe interactions involving the PM and DTN structures. As a model, we will focus on Ixodes ticks, their microbiome, and the pathogen of Lyme disease. We will address the most salient findings on the structural and physiological roles of these Ixodes gut barriers on microbial interactions, with a comparison to analogous functions in other model vectors, such as mosquitoes. We will distill how this information could be leveraged towards a better understanding of the basic mechanisms of gut biology and tick-microbial interactions, which could contribute to potential therapeutic strategies in response to ticks and tick-borne infections.

RevDate: 2021-09-27

Karlicki M, Antonowicz S, A Karnkowska (2021)

Tiara: Deep learning-based classification system for eukaryotic sequences.

Bioinformatics (Oxford, England) pii:6375939 [Epub ahead of print].

MOTIVATION: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards a better understanding of eukaryotic diversity.

RESULTS: We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analysing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.

AVAILABILITY: Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2021-09-27

Katz J, H Gao (2021)

The Alzheimer-E. coli Axis: What Can We Learn from an Electronic Health Record Platform.

Journal of Alzheimer's disease : JAD pii:JAD215004 [Epub ahead of print].

BACKGROUND: Alzheimer's disease (AD) is a neurodegenerative disease with unclear etiology. Recent studies have demonstrated a potential role for gut microbiome. There is, however, a significant dearth in epidemiological correlation between gut bacteria and AD.

OBJECTIVE: To investigate the association between Escherichia coli (E. coli) infection and AD.

METHODS: Counts of patients with ICD 10 diagnoses of AD, E. coli, urinary tract infection, and comorbidities were retrieved from the electronic health records at the University of Florida Health Center.

RESULTS: The relative risk for AD with a previous event of E. coli was 5.17 (95%CI 4.0786 to 6.5446, p < 0.0001). In the unadjusted association, patients with E. coli infection had odds ratio (OR) of 20.83 to have AD (95%CI, 17.7-24.34; p < 0.0001); after adjusting for gender (OR = 12.71; 95%CI, 10.82-14.83; p < 0.0001), race (OR = 13.97; 95%CI, 11.84-16.36; p < 0.0001), age group (OR = 11.51; 95%CI, 9.73-13.54; p < 0.0001), diabetes (OR = 9.23; 95%CI, 7.79-10.87; p < 0.0001), stroke (OR = 5.31; 95%CI, 4.47-6.28; p < 0.0001), and hypertension (OR = 4.55; 95%CI, 3.86-5.32; p < 0.0001).

CONCLUSION: These results should be taken cautiously. This retrospective cross-sectional study cannot infer causality and had used aggregate data that did not allow simultaneous adjustments of covariates. Future studies are warranted to investigate the link between gut bacteria and AD.

RevDate: 2021-09-27

Sousa C, Ferreira R, Azevedo NF, et al (2021)

Helicobacter pylori infection: from standard to alternative treatment strategies.

Critical reviews in microbiology [Epub ahead of print].

Helicobacter pylori is the major component of the gastric microbiome of infected individuals and one of the aetiological factors of chronic gastritis, peptic ulcer disease and gastric cancer. The increasing resistance to antibiotics worldwide has made the treatment of H. pylori infection a challenge. As a way to overhaul the efficacy of currently used H. pylori antibiotic-based eradication therapies, alternative treatment strategies are being devised. These include probiotics and prebiotics as adjuvants in H. pylori treatment, antimicrobial peptides as alternatives to antibiotics, photodynamic therapy ingestible devices, microparticles and nanoparticles applied as drug delivery systems, vaccines, natural products, and phage therapy. This review provides an updated synopsis of these emerging H. pylori control strategies and discusses the advantages, hurdles, and challenges associated with their development and implementation. An effective human vaccine would be a major achievement although, until now, projects regarding vaccine development have failed or were discontinued. Numerous natural products have demonstrated anti-H. pylori activity, mostly in vitro, but further clinical studies are needed to fully disclose their role in H. pylori eradication. Finally, phage therapy has the potential to emerge as a valid alternative, but major challenges remain, namely the isolation of more H. pylori strictly virulent bacterio(phages).

RevDate: 2021-09-27

Tchernin N, Paran M, Funkaz L, et al (2021)

Biliary Tract Instrumentations Prior to Elective Cholecystectomy: Effect on Biliary Microbiome.

Surgical infections [Epub ahead of print].

Background: Calculus biliary disease is a common condition that requires invasive procedures in complicated cases. The effect of biliary instrumentation on the biliary microbiome and its impact on surgical complications after elective cholecystectomy remains unclear. This study aimed to assess the impact of prior biliary instrumentation on the biliary microbiome, as well as on the clinical outcomes of cholecystectomy. Patients and Methods: This retrospective study included all patients who underwent elective cholecystectomy for calculus biliary disease between 2015 and 2020 in a single medical center. Data regarding biliary instrumentation prior to cholecystectomy, biliary cultures obtained during cholecystectomy, and clinical outcomes were collected. A comparison between patients with and without prior instrumentation was performed with regard to biliary cultures and clinical outcomes. Results: Of the 508 patients studied, 109 patients underwent biliary instrumentation prior to cholecystectomy. Patients with prior instrumentation were older and more likely to be men (p < 0.0001). Prior instrumentation was also associated with higher rates of conversion to open surgery (p < 0.0001). Positive biliary cultures and polymicrobial growth were both more common among patients with prior instrumentation (p < 0.0001). Prior instrumentation was associated with longer length of hospital stay, as well as higher rates of perioperative complications and surgical site infection (p < 0.0001). Conclusions: Prior instrumentation was associated with poorer clinical outcomes and affected the biliary microbiome. The different results of biliary cultures in these patients may suggest that an alternative empiric antibiotic regimen should be considered when treating patients with biliary instrumentation.

RevDate: 2021-09-27

Wan SJ, Datta A, Flandrin O, et al (2021)

Nerve-associated transient receptor potential ion channels can contribute to intrinsic resistance to bacterial adhesion in vivo.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 35(10):e21899.

The cornea of the eye differs from other mucosal surfaces in that it lacks a viable bacterial microbiome and by its unusually high density of sensory nerve endings. Here, we explored the role of corneal nerves in preventing bacterial adhesion. Pharmacological and genetic methods were used to inhibit the function of corneal sensory nerves or their associated transient receptor potential cation channels TRPA1 and TRPV1. Impacts on bacterial adhesion, resident immune cells, and epithelial integrity were examined using fluorescent labeling and quantitative confocal imaging. TRPA1/TRPV1 double gene-knockout mice were more susceptible to adhesion of environmental bacteria and to that of deliberately-inoculated Pseudomonas aeruginosa. Supporting the involvement of TRPA1/TRPV1-expressing corneal nerves, P. aeruginosa adhesion was also promoted by treatment with bupivacaine, or ablation of TRPA1/TRPV1-expressing nerves using RTX. Moreover, TRPA1/TRPV1-dependent defense was abolished by enucleation which severs corneal nerves. High-resolution imaging showed normal corneal ultrastructure and surface-labeling by wheat-germ agglutinin for TRPA1/TRPV1 knockout murine corneas, and intact barrier function by absence of fluorescein staining. P. aeruginosa adhering to corneas after perturbation of nerve or TRPA1/TRPV1 function failed to penetrate the surface. Single gene-knockout mice showed roles for both TRPA1 and TRPV1, with TRPA1-/- more susceptible to P. aeruginosa adhesion while TRPV1-/- corneas instead accumulated environmental bacteria. Corneal CD45+/CD11c+ cell responses to P. aeruginosa challenge, previously shown to counter bacterial adhesion, also depended on TRPA1/TRPV1 and sensory nerves. Together, these results demonstrate roles for corneal nerves and TRPA1/TRPV1 in corneal resistance to bacterial adhesion in vivo and suggest that the mechanisms involve resident immune cell populations.

RevDate: 2021-09-27

Theofilis P, Vordoni A, Koukoulaki M, et al (2021)

Dyslipidemia in Chronic Kidney Disease: Contemporary Concepts and Future Therapeutic Perspectives.

American journal of nephrology pii:000518456 [Epub ahead of print].

BACKGROUND: Chronic kidney disease (CKD) is an increasingly prevalent disease state met with great morbidity and mortality primarily resulting from the high incidence of adverse cardiovascular outcomes. Therapeutic strategies in this patient population aim at controlling modifiable cardiovascular risk factors, including dyslipidemia.

SUMMARY: In this review article, we first provide the latest pathophysiologic evidence regarding the altered dyslipidemia pattern in CKD, followed by its contemporary management according to the latest guidelines. Moreover, we present the current progress regarding the emerging therapeutic strategies. Key Messages: The presence of renal impairment leads to alterations in cholesterol structure, metabolism, and reverse transport paired with increased oxidative stress. Statins remain the cornerstone of dyslipidemia management in patients with kidney dysfunction who are at risk for cardiovascular events. However, their efficacy is debatable in end-stage renal disease under renal replacement therapy. Therefore, novel treatment approaches aiming at hypertriglyceridemia, proprotein convertase subtilisin/kexin type 9, and lipoprotein(a) are under rigorous investigation while the research of gut microbiome might provide additional mechanistic and therapeutic insight.

RevDate: 2021-09-27

Valentino TR, Vechetti IJ, Mobley CB, et al (2021)

Dysbiosis of the gut microbiome impairs mouse skeletal muscle adaptation to exercise.

The Journal of physiology [Epub ahead of print].

KEY POINTS: Dysbiosis of the gut microbiome caused by continuous antibiotic treatment did not affect running activity. Continuous treatment with antibiotics did not result in systemic inflammation as indicated by serum cytokine levels. Gut microbiome dysbiosis was associated with blunted fiber-type specific hypertrophy in the soleus and plantaris muscles in response to progressive weighted wheel running (PoWeR). Gut microbiome dysbiosis was associated with impaired PoWeR-induced fiber-type shift in the plantaris muscle. Gut microbiome dysbiosis was associated with a loss of PoWeR-induced myonuclei accretion in the plantaris muscle.

ABSTRACT: There is emerging evidence of a gut microbiome-skeletal muscle axis. The purpose of this study was to determine if an intact gut microbiome was necessary for skeletal muscle adaption to exercise. Forty-two, four-month old female C57BL/6J mice were randomly assigned to either untreated (U) or antibiotic-treated (T), non-running controls (CU or CT, respectively) or progressive weighted wheel running (PoWeR, P) untreated (PU) or antibiotic-treated (PT). Antibiotic treatment resulted in disruption of the gut microbiome as indicated by a significant depletion of gut microbiome bacterial species in both CT and PT groups. The training stimulus was the same between PU and PT groups as assessed by weekly (12.35 ± 2.06 km/wk vs 11.09 ± 1.76 km/week, respectively) and total (778.9 ± 130.5 km vs 703.8 ± 112.9 km, respectively) running activity. In response to PoWeR, PT showed less hypertrophy of soleus Type 1 and 2a fibers and plantaris Type 2b/x fibers compared to PU. The higher satellite cell and myonuclei abundance of PU plantaris muscle after PoWeR was not observed in PT. The fiber-type shift of PU plantaris muscle to a more oxidative Type 2a fiber composition following PoWeR was blunted in PT. There was no difference in serum cytokine levels among all groups suggesting disruption of the gut microbiome did not induce systemic inflammation. The results of this study provide the first evidence that an intact gut microbiome is necessary for skeletal muscle adaptation to exercise. This article is protected by copyright. All rights reserved.

RevDate: 2021-09-27

Wang X, Yao Y, Wang G, et al (2021)

Comprehensive Analysis of the Influence of Fulvic Acid from Paper Mill Effluent on Soil Properties, Soil Microbiome, and Growth of Malus hupehensis Rehd. Seedlings under Replant Conditions.

ACS omega, 6(37):24027-24038.

In this study, the potential regulatory effects of fulvic acid extracted from paper mill effluent (PFA) in apple replant disease (ARD) were investigated through a comprehensive experimental evaluation of the effects of PFA on soil properties, growth inhibition of apple replant pathogens, and growth of replanted Malus hupehensis Rehd. seedlings. PFA with a relatively lower molecular weight was mainly composed of carbohydrates, lignin derivatives, and polysaccharides and was rich in functional groups such as carboxyl and phenolic hydroxyl groups. Treatment with PFA dosages ranging from 2 to 3 g/pot significantly increased available phosphorus (P) in soil by 47.5 to 57.5% when compared with the control without PFA, indicating that PFA had a positive effect in activating P. In addition, PFA stimulated the growth of replanted seedlings by promoting root elongation, enhancing leaf photosynthesis, and increasing the activity of root antioxidant enzymes including superoxide dismutase, peroxidase, and catalase. However, no convincing evidence was found that application of different dosages of PFA had remarkable effects on soil pH, inorganic nitrogen, available potassium, organic matter, and the numbers of bacteria and fungi. Notably, PFA had no effect on the copy number of the main pathogenic fungi causing ARD, including Fusarium oxysporum, Fusarium solani, Fusarium proliferatum, and Fusarium moniliforme. Overall, PFA can alleviate ARD to a certain extent mainly through its effects on improving the resilience of replanted young seedlings rather than by affecting soil microorganisms or providing nutrients.

RevDate: 2021-09-27

Wang Q, Yi S, Su G, et al (2021)

Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease via Adjuvant Effects.

Frontiers in cell and developmental biology, 9:716760.

Behcet's disease (BD) is associated with considerable gut microbiome changes. However, it still remains unknown how the composition of the gut microbiome exactly affects the development of this disease. In this study, transplantation of stool samples from patients with active ocular BD to mice via oral gavage was performed. This resulted in decreases of three short chain fatty acids (SCFAs) including butyric acid, propionic acid and valeric acid in the feces of the BD-recipient group. Intestinal barrier integrity of mice receiving BD feces was damaged as shown by a decreased expression of tight junction proteins and was associated with the release of Lipopolysaccharides (LPS) in the circulation. The mice also showed a higher frequency of splenic neutrophils as well as an enrichment of genes associated with innate immune responses in the neutrophils and CD4 + T cells as identified by single cell RNA sequencing. Analysis of neutrophils and T cells functions in these mice showed an enhanced mesenteric lymph node and splenic Th1 and Th17 cell differentiation in association with activation of neutrophils. Transplantation of BD feces to mice and subsequent induction of experimental uveitis (EAU) or encephalomyelitis (EAE) led to an exacerbation of disease in both models, suggesting a microbial adjuvant effect. These findings suggest that the gut microbiome may regulate an autoimmune response via adjuvant effects including increased gut permeability and enhancement of innate immunity.

RevDate: 2021-09-27

Baleeiro FCF, Ardila MS, Kleinsteuber S, et al (2021)

Effect of Oxygen Contamination on Propionate and Caproate Formation in Anaerobic Fermentation.

Frontiers in bioengineering and biotechnology, 9:725443 pii:725443.

Mixed microbial cultures have become a preferred choice of biocatalyst for chain elongation systems due to their ability to convert complex substrates into medium-chain carboxylates. However, the complexity of the effects of process parameters on the microbial metabolic networks is a drawback that makes the task of optimizing product selectivity challenging. Here, we studied the effects of small air contaminations on the microbial community dynamics and the product formation in anaerobic bioreactors fed with lactate, acetate and H2/CO2. Two stirred tank reactors and two bubble column reactors were operated with H2/CO2 gas recirculation for 139 and 116 days, respectively, at pH 6.0 and 32°C with a hydraulic retention time of 14 days. One reactor of each type had periods with air contamination (between 97 ± 28 and 474 ± 33 mL O2 L-1 d-1, lasting from 4 to 32 days), while the control reactors were kept anoxic. During air contamination, production of n-caproate and CH4 was strongly inhibited, whereas no clear effect on n-butyrate production was observed. In a period with detectable O2 concentrations that went up to 18%, facultative anaerobes of the genus Rummeliibacillus became predominant and only n-butyrate was produced. However, at low air contamination rates and with O2 below the detection level, Coriobacteriia and Actinobacteria gained a competitive advantage over Clostridia and Methanobacteria, and propionate production rates increased to 0.8-1.8 mmol L-1 d-1 depending on the reactor (control reactors 0.1-0.8 mmol L-1 d-1). Moreover, i-butyrate production was observed, but only when Methanobacteria abundances were low and, consequently, H2 availability was high. After air contamination stopped completely, production of n-caproate and CH4 recovered, with n-caproate production rates of 1.4-1.8 mmol L-1 d-1 (control 0.7-2.1 mmol L-1 d-1). The results underline the importance of keeping strictly anaerobic conditions in fermenters when consistent n-caproate production is the goal. Beyond that, micro-aeration should be further tested as a controllable process parameter to shape the reactor microbiome. When odd-chain carboxylates are desired, further studies can develop strategies for their targeted production by applying micro-aerobic conditions.

RevDate: 2021-09-27

Yang Y, Yu X, Yang X, et al (2021)

Oral Microbiota Profile of Individuals Who Abuse Methamphetamine.

Frontiers in cellular and infection microbiology, 11:706961.

The poor oral health condition of individuals who abuse methamphetamine (MA) is well known. The roles of the oral and fecal microbiomes in addiction and nervous system diseases have been the focus of many studies. However, changes in the microbiota composition of MA users have not been reported. This was addressed in the present study in 20 MA users and 14 sex-matched healthy subjects. Saliva samples were collected and high-throughput 16S rRNA sequencing and bioinformatic analysis were performed to evaluate oral microbiome profiles. The results showed that species richness was significantly lower in the MA group than in the control group. Bacterial taxa that are known to be related to oral diseases such as Negativicutes, Veillonellaceae, Veillonella, and Selenomonadales had higher relative abundance in the MA group than in the control group, and the relative abundance of Prevotella melaninogenica-a putative etiologic agent of periodontal disease-was also higher. Avoiding MA use and improving oral hygiene practices over a short term (i.e., during hospitalization for 2 weeks) did not alter the oral microbiota composition of MA users. Although the causal relationship between changes in oral microbiome profile and MA abuse remains to be determined, our results suggest that oral disease prevention and treatment strategies are important for MA users.

RevDate: 2021-09-27

Guo Y, Guo H, Qiu L, et al (2021)

Appetite Suppression and Interleukin 17 Receptor Signaling Activation of Colonic Mycobiota Dysbiosis Induced by High Temperature and High Humidity Conditions.

Frontiers in cellular and infection microbiology, 11:657807.

It is known that the microbiome affects human physiology, emotion, disease, growth, and development. Most humans exhibit reduced appetites under high temperature and high humidity (HTHH) conditions, and HTHH environments favor fungal growth. Therefore, we hypothesized that the colonic mycobiota may affect the host's appetite under HTHH conditions. Changes in humidity are also associated with autoimmune diseases. In the current study mice were fed in an HTHH environment (32°C ± 2°C, relative humidity 95%) maintained via an artificial climate box for 8 hours per day for 21 days. Food intake, the colonic fungal microbiome, the feces metabolome, and appetite regulators were monitored. Components of the interleukin 17 pathway were also examined. In the experimental groups food intake and body weight were reduced, and the colonic mycobiota and fecal metabolome were substantially altered compared to control groups maintained at 25°C ± 2°C and relative humidity 65%. The appetite-related proteins LEPT and POMC were upregulated in the hypothalamus (p < 0.05), and NYP gene expression was downregulated (p < 0.05). The expression levels of PYY and O-linked β-N-acetylglucosamine were altered in colonic tissues (p < 0.05), and interleukin 17 expression was upregulated in the colon. There was a strong correlation between colonic fungus and sugar metabolism. In fimo some metabolites of cholesterol, tromethamine, and cadaverine were significantly increased. There was significant elevation of the characteristic fungi Solicoccozyma aeria, and associated appetite suppression and interleukin 17 receptor signaling activation in some susceptible hosts, and disturbance of gut bacteria and fungi. The results indicate that the gut mycobiota plays an important role in the hypothalamus endocrine system with respect to appetite regulation via the gut-brain axis, and also plays an indispensable role in the stability of the gut microbiome and immunity. The mechanisms involved in these associations require extensive further studies.

RevDate: 2021-09-27

Dilnaz F, Zafar F, Afroze T, et al (2021)

Mediterranean Diet and Physical Activity: Two Imperative Components in Breast Cancer Prevention.

Cureus, 13(8):e17306.

Despite tremendous advances in medicine over the past few decades and significantly improved understanding of the symptomology and contributors to breast cancer (BC) incidence, BC rates continue to rise worldwide, with BC being a leading cause of cancer-related death among women. To reduce BC incidence, it is necessary to focus on promoting prevention strategies through a population-based approach of lowering exposure to modifiable risk factors in addition to the application of newer drug interventions (chemoprevention) for prevention in high-risk populations. Currently, available data suggest that lifestyle modifications through a healthy diet and increased physical activity (PA) play a crucial role in BC prevention; specifically, there is growing evidence to indicate that the Mediterranean diet (MeD) lowers cancer risk. This review summarizes the potential role of the MeD and PA in reducing BC risk, with an additional focus on microbial modulation in BC prevention, based on the current evidence obtained from PubMed. After reviewing the immunomodulatory and anticarcinogenic effects of both the MeD and PA, we conclude that further evaluation and proper implementation of both interventions can significantly reduce the risk of BC and associated mortality in the general population.

RevDate: 2021-09-27

Wongpayak P, Meesungnoen O, Saejang S, et al (2021)

A highly effective and self-transmissible CRISPR antimicrobial for elimination of target plasmids without antibiotic selection.

PeerJ, 9:e11996 pii:11996.

The use of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) for sequence-specific elimination of bacteria or resistance genes is a powerful tool for combating antibiotic resistance. However, this approach requires efficient delivery of CRISPR/Cas DNA cassette(s) into the targeted bacterial population. Compared to phage transduction, plasmid conjugation can deliver DNA to a broader host range but often suffers from low delivery efficiency. Here, we developed multi-plasmid conjugation systems for efficient CRISPR/Cas delivery, target DNA elimination and plasmid replacement. The CRISPR/Cas system, delivered via a broad-host-range R1162 mobilizable plasmid, specifically eliminated the targeted plasmid in recipient cells. A self-transmissible RK2 helper plasmid facilitated the spread of mobilizable CRISPR/Cas. The replacement of the target plasmid with another plasmid from the same compatibility group helped speed up target plasmid elimination especially when the target plasmid was also mobilizable. Together, we showed that up to 100% of target plasmid from the entire recipient population could be replaced even at a low (1:180) donor-to-recipient ratio and in the absence of transconjugant selection. Such an ability to modify genetic content of microbiota efficiently in the absence of selection will be critical for future development of CRISPR antimicrobials as well as genetic tools for in situ microbiome engineering.

RevDate: 2021-09-27

Spatz LA, Silverman GJ, JA James (2021)

Editorial: Pathogens, Pathobionts, and Autoimmunity.

Frontiers in immunology, 12:752980.

RevDate: 2021-09-27

Calle-Tobón A, Holguin-Rocha AF, Moore C, et al (2021)

Blood Meals With Active and Heat-Inactivated Serum Modifies the Gene Expression and Microbiome of Aedes albopictus.

Frontiers in microbiology, 12:724345.

The Asian "tiger mosquito" Aedes albopictus is currently the most widely distributed disease-transmitting mosquito in the world. Its geographical expansion has also allowed the expansion of multiple arboviruses like dengue, Zika, and chikungunya, to higher latitudes. Due to the enormous risk to global public health caused by mosquitoes species vectors of human disease, and the challenges in slowing their expansion, it is necessary to develop new and environmentally friendly vector control strategies. Among these, host-associated microbiome-based strategies have emerged as promising options. In this study, we performed an RNA-seq analysis on dissected abdomens of Ae. albopictus females from Manhattan, KS, United States fed with sugar and human blood containing either normal or heat-inactivated serum, to evaluate the effect of heat inactivation on gene expression, the bacteriome transcripts and the RNA virome of this mosquito species. Our results showed at least 600 genes with modified expression profile when mosquitoes were fed with normal vs. heat-inactivated-containing blood. These genes were mainly involved in immunity, oxidative stress, lipid metabolism, and oogenesis. Also, we observed bacteriome changes with an increase in transcripts of Actinobacteria, Rhodospirillaceae, and Anaplasmataceae at 6 h post-feeding. We also found that feeding with normal blood seems to particularly influence Wolbachia metabolism, demonstrated by a significant increase in transcripts of this bacteria in mosquitoes fed with blood containing normal serum. However, no differences were observed in the virome core of this mosquito population. These results suggest that heat and further inactivation of complement proteins in human serum may have profound effect on mosquito and microbiome metabolism, which could influence interpretation of the pathogen-host interaction findings when using this type of reagents specially when measuring the effect of Wolbachia in vector competence.

RevDate: 2021-09-27

Abdelhafiz Y, Fernandes JMO, Larger S, et al (2021)

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System.

Frontiers in microbiology, 12:709611.

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

RevDate: 2021-09-27

Matar GK, Ali M, Bagchi S, et al (2021)

Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged.

Frontiers in microbiology, 12:708531.

The relative importance of different ecological processes controlling biofilm community assembly over time on membranes with different surface characteristics has never been investigated in membrane bioreactors (MBRs). In this study, five ultrafiltration hollow-fiber membranes - having identical nominal pore size (0.1μm) but different hydrophobic or hydrophilic surface characteristics - were operated simultaneously in the same MBR tank with a constant flux of 10 liters per square meter per hour (LMH). In parallel, membrane modules operated without permeate flux (0 LMH) were submerged in the same MBR tank, to investigate the passive microbial adsorption onto different hydrophobic or hydrophilic membranes. Samples from the membrane biofilm were collected after 1, 10, 20, and 30days of continuous filtration. The membrane biofilm microbiome were investigated using 16S rRNA gene amplicon sequencing from DNA and cDNA samples. Similar beta diversity trends were observed for both DNA- and cDNA-based analyses. Beta diversity analyses revealed that the nature of the membrane surface (i.e., hydrophobic vs. hydrophilic) did not seem to have an effect in shaping the bacterial community, and a similar biofilm microbiome evolved for all types of membranes. Similarly, membrane modules operated with and without permeate flux did not significantly influence alpha and beta diversity of the membrane biofilm. Nevertheless, different-aged membrane biofilm samples exhibited significant differences. Proteobacteria was the most dominant phylum in early-stage membrane biofilm after 1 and 10days of filtration. Subsequently, the relative reads abundance of the phyla Bacteroidetes and Firmicutes increased within the membrane biofilm communities after 20 and 30days of filtration, possibly due to successional steps that lead to the formation of a relatively aged biofilm. Our findings indicate distinct membrane biofilm assembly patterns with different-aged biofilm. Ecological null model analyses revealed that the assembly of early-stage biofilm community developed after 1 and 10days of filtration was mainly governed by homogenous selection. As the biofilm aged (days 20 and 30), stochastic processes (e.g., ecological drift) started to become important in shaping the assembly of biofilm community.

RevDate: 2021-09-27

Ye P, Zhang X, Xu Y, et al (2021)

Alterations of the Gut Microbiome and Metabolome in Patients With Proliferative Diabetic Retinopathy.

Frontiers in microbiology, 12:667632.

Diabetic retinopathy (DR) has been reported to associate with gut microbiota alterations in murine models and thus "gut-retina-axis" has been proposed. However, the role of gut microbiome and the associated metabolism in DR patients still need to be elucidated. In this study, we collected fecal samples from 45 patients with proliferative diabetic retinopathy (PDR) and 90 matched diabetic patients (1:2 according to age, sex, and duration of diabetes) without DR (NDR) and performed 16S rRNA gene sequencing and untargeted metabolomics. We observed significantly lower bacterial diversity in the PDR group than that in the NDR group. Differential gut bacterial composition was also found, with significant depletion of 22 families (e.g., Coriobacteriaceae, Veillonellaceae, and Streptococcaceae) and enrichment of two families (Burkholderiaceae and Burkholderiales_unclassified) in the PDR group as compared with the NDR group. There were significantly different fecal metabolic features, which were enriched in metabolic pathways such as arachidonic acid and microbial metabolism, between the two groups. Among 36 coabundance metabolite clusters, 11 were positively/negatively contributed to PDR using logistic regression analysis. Fifteen gut microbial families were significantly correlated with the 11 metabolite clusters. Furthermore, a fecal metabolite-based classifier was constructed to distinguish PDR patients from NDR patients accurately. In conclusion, PDR is associated with reduced diversity and altered composition of gut microbiota and specific microbe-metabolite interplay. Our findings help to better understand the disease pathogenesis and provide novel diagnostic and therapeutic targets for PDR.

RevDate: 2021-09-27

Büttiker P, Weissenberger S, Stefano GB, et al (2021)

SARS-CoV-2, Trait Anxiety, and the Microbiome.

Frontiers in psychiatry, 12:720082.

During the COVID-19 pandemic, research on the relationships between the virus and its human host has become fundamental to understand this pathology and its effects. Attaining this profound understanding is critical for the effective containment and treatment of infections caused by the virus. In this review, we present some possible mechanisms by which psychopathological symptoms emerge following viral infections of the central nervous system (CNS). These proposed mechanisms are based on microbial communication and the induced priming of microglial antibody activation within the CNS through Toll-like receptor signaling. In this process, chronic microglial activation causes increased glutamate release in virally-altered, high-density neuronal structures, thereby modulating cognitive networks and information integration processes. This modulation, in turn, we suggest, affects the accuracy of sensory integration and connectivity of major control networks, such as the default mode network. The chronic activation of immunological responses and neurochemical shifts toward an elevated glutamate/gamma-aminobutyric acid ratio lead to negative reinforcement learning and suboptimal organismic functioning, for example, maintaining the body in an anxious state, which can later become internalized as trait anxiety. Therefore, we hypothesize that the homeostatic relationship between host, microbiome, and virome, would be decisive in determining the efficiency of subsequent immunological responses, disease susceptibility, and long-term psychopathological effects of diseases that impact the CNS, such as the COVID-19.

RevDate: 2021-09-27

Busing JD, Buendia M, Choksi Y, et al (2021)

Microbiome in Eosinophilic Esophagitis-Metagenomic, Metatranscriptomic, and Metabolomic Changes: A Systematic Review.

Frontiers in physiology, 12:731034.

Background: Our understanding of human gut microbiota has expanded in recent years with the introduction of high-throughput sequencing methods. These technologies allow for the study of metagenomic, metatranscriptomic, and metabolomic bacterial alterations as they relate to human disease. Work in this area has described the human gut microbiome in both healthy individuals and those with chronic gastrointestinal diseases, such as eosinophilic esophagitis (EoE). Objectives: A systematic review of the current available literature on metagenomic, metatranscriptomic, and metabolomic changes in EoE was performed. Methods: This review was performed following the PRISMA guidelines for reporting systematic reviews and meta-analyses. All relevant publications up to March 2021 were retrieved using the search engines PubMed, Google Scholar, and Web of Science. They were then extracted, assessed, and reviewed. Only original studies published in English were included. Results: A total of 46 potential manuscripts were identified for review. Twelve met criteria for further review based on relevance screening and 9 met criteria for inclusion, including 6 studies describing the microbiome in EoE and 3 detailing metabolomic/tissue biochemistry alterations in EoE. No published studies examined metatranscriptomic changes. Samples for microbiome analysis were obtained via esophageal biopsy (n = 3), esophageal string test (n = 1), salivary sampling (n = 1), or stool specimen (n = 1). Samples analyzing tissue biochemistry were obtained via esophageal biopsy (n = 2) and blood plasma (n = 1). There were notable differences in how samples were collected and analyzed. Metabolomic and tissue biochemical alterations were described using Raman spectroscopy, which demonstrated distinct differences in the spectral intensities of glycogen, lipid, and protein content compared to controls. Finally, research in proteomics identified an increase in the pro-fibrotic protein thrombospondin-1 in patients with EoE compared with controls. Conclusions: While there are notable changes in the microbiome, these differ with the collection technique and method of analysis utilized. Techniques characterizing metabolomics and tissue biochemistry are now being utilized to further study patients with EoE. The lack of published data related to the human microbiome, metagenome, metatranscriptome, and metabolome in patients with EoE highlights the need for further research in these areas.

RevDate: 2021-09-27

Vasileva VY, Sultanova RF, Sudarikova AV, et al (2021)

Insights Into the Molecular Mechanisms of Polycystic Kidney Diseases.

Frontiers in physiology, 12:693130.

Autosomal dominant (AD) and autosomal recessive (AR) polycystic kidney diseases (PKD) are severe multisystem genetic disorders characterized with formation and uncontrolled growth of fluid-filled cysts in the kidney, the spread of which eventually leads to the loss of renal function. Currently, there are no treatments for ARPKD, and tolvaptan is the only FDA-approved drug that alleviates the symptoms of ADPKD. However, tolvaptan has only a modest effect on disease progression, and its long-term use is associated with many side effects. Therefore, there is still a pressing need to better understand the fundamental mechanisms behind PKD development. This review highlights current knowledge about the fundamental aspects of PKD development (with a focus on ADPKD) including the PC1/PC2 pathways and cilia-associated mechanisms, major molecular cascades related to metabolism, mitochondrial bioenergetics, and systemic responses (hormonal status, levels of growth factors, immune system, and microbiome) that affect its progression. In addition, we discuss new information regarding non-pharmacological therapies, such as dietary restrictions, which can potentially alleviate PKD.

RevDate: 2021-09-27

Wang Y, Baumdicker F, Schweiger P, et al (2021)

Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila.

BMC biology, 19(1):187.

BACKGROUND: How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS).

RESULTS: We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT).

CONCLUSION: Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation.

RevDate: 2021-09-27

Tsan L, Sun S, Hayes AMR, et al (2021)

Early life Western diet-induced memory impairments and gut microbiome changes in female rats are long-lasting despite healthy dietary intervention.

Nutritional neuroscience [Epub ahead of print].

OBJECTIVE: Western diet consumption during adolescence results in hippocampus (HPC)-dependent memory impairments and gut microbiome dysbiosis. Whether these adverse outcomes persist in adulthood following healthy dietary intervention is unknown. Here we assessed the short- and long-term effects of adolescent consumption of a Western diet enriched with either sugar or both sugar and fat on metabolic outcomes, HPC function, and gut microbiota.

METHODS: Adolescent female rats (PN 26) were fed a standard chow diet (CHOW), chow with access to 11% sugar solution (SUG), or a junk food cafeteria-style diet (CAF) containing various foods high in fat and/or sugar. During adulthood (PN 65+), metabolic outcomes, HPC-dependent memory, and gut microbial populations were evaluated. In a subsequent experiment, these outcomes were evaluated following a 5-week dietary intervention where CAF and SUG groups were maintained on standard chow alone.

RESULTS: Both CAF and SUG groups demonstrated impaired HPC-dependent memory, increased adiposity, and altered gut microbial populations relative to the CHOW group. However, impaired peripheral glucose regulation was only observed in the SUG group. When examined following a healthy dietary intervention in a separate experiment, metabolic dysfunction was not observed in either the CAF or SUG group, whereas HPC-dependent memory impairments were observed in the CAF but not the SUG group. In both groups the composition of the gut microbiota remained distinct from CHOW rats after the dietary intervention.

CONCLUSIONS: While the metabolic impairments associated with adolescent junk food diet consumption are not present in adulthood following dietary intervention, the HPC-dependent memory impairments and the gut microbiome dysbiosis persist.

RevDate: 2021-09-26

James SC, Fraser K, Young W, et al (2021)

Concentrations of Fecal Bile Acids in Participants with Functional Gut Disorders and Healthy Controls.

Metabolites, 11(9): pii:metabo11090612.

Bile acids are metabolites involved in nutrient absorption and signaling with levels influenced by dietary intake, metabolic processes, and the gut microbiome. We aimed to quantify 23 bile acids in fecal samples to ascertain if concentrations differed between healthy participants and those with functional gut disorders. Fecal bile acids were measured using liquid chromatography-mass spectrometry (LC-MS) in the COMFORT (The Christchurch IBS cohort to investigate mechanisms for gut relief and improved transit) cohort of 250 participants with Rome IV IBS (IBS-constipation (C), IBS-diarrhea (D), IBS-mixed (M)), functional gut disorders (functional constipation (FC), functional diarrhea (FD)) and healthy controls (FC n = 35, FD n = 13, IBS-C n = 24, IBS-D n = 52, IBS-M n = 29, and control n = 97). Dietary information was recorded to ascertain three-day dietary intake before fecal samples were collected. Fecal bile acid concentrations, predominantly primary bile acids, were significantly different between all functional gut disorder participants and healthy controls (CDCA p = 0.011, CA p = 0.003) and between constipation (FC + IBS-C) and diarrhea (FD + IBS-D) groups (CDCA p = 0.001, CA p = 0.0002). Comparison of bile acids between all functional groups showed four metabolites were significantly different, although analysis of combined groups (FC + IBS-C vs. FD + IBS-D) showed that 10 metabolites were significantly different. The bile acid profiles of FD individuals were similar to those with IBS-D, and likewise, those with FC were similar to IBS-C. Individuals with a diarrhea phenotype (FD + IBS-D) had higher concentrations of bile acids compared to those with constipation (FC + IBS-C). Bile acid metabolites distinguish between individuals with functional gut disorders and healthy controls but are similar in constipation (or diarrhea) whether classified as IBS or not.

RevDate: 2021-09-26

Chiu K, Bashir ST, Gao L, et al (2021)

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice.

Toxics, 9(9): pii:toxics9090215.

Di-2-ethylhexyl phthalate (DEHP) is a plasticizer commonly found in polyvinyl chloride, medical equipment, and food packaging. DEHP has been shown to target the reproductive system and alter the gut microbiome in humans and experimental animals. However, very little is known about the impact of DEHP-induced microbiome changes and its effects during pregnancy. Thus, the objective of this study was to investigate the effects of DEHP exposure during pregnancy on the cecal microbiome and pregnancy outcomes. Specifically, this study tested the hypothesis that subacute exposure to DEHP during pregnancy alters the cecal microbiome in pregnant mice, leading to changes in birth outcomes. To test this hypothesis, pregnant dams were orally exposed to corn oil vehicle or 20 µg/kg/day DEHP for 10 days and euthanized 21 days after their last dose. Cecal contents were collected for 16S Illumina and shotgun metagenomic sequencing. Fertility studies were also conducted to examine whether DEHP exposure impacted birth outcomes. Subacute exposure to environmentally relevant doses of DEHP in pregnant dams significantly increased alpha diversity and significantly altered beta diversity. Furthermore, DEHP exposure during pregnancy significantly increased the relative abundance of Bacteroidetes and decreased the relative abundance of Firmicutes and Deferribacteres compared with controls. The affected taxonomic families included Deferribacteraceae, Lachnospiraceae, and Mucisprillum. In addition to changes in the gut microbiota, DEHP exposure significantly altered 14 functional pathways compared with the control. Finally, DEHP exposure did not significantly impact the fertility and birth outcomes compared with the control. Collectively, these data indicate that DEHP exposure during pregnancy shifts the cecal microbiome, but the shifts do not impact fertility and birth outcomes.

RevDate: 2021-09-26

Kanoute A, Gare J, Meda N, et al (2021)

Effect of Oral Prophylactic Measures on the Occurrence of Pre-Eclampsia (OP-PE) in High-Risk Pregnant Women: A Cluster Randomized Controlled Trial.

Methods and protocols, 4(3): pii:mps4030061.

Pre-eclampsia (PE), a pregnancy-specific hypertensive disorder, characterized by the development of placental endothelial dysfunction, remains a major source of maternal and perinatal morbidity and mortality, especially in low- and middle-income settings. Periodontal disorders during pregnancy, and particularly periodontal pathogens, may be related to the risk of PE. Standard oral hygiene methods, based mainly on the joint use of toothbrushes and interdental brushes, reduce periodontal inflammatory risk and modulate the dysbiosis of the oral microbiome. The aim of this trial is to compare the PE outcomes in high-risk pregnant women receiving oral prophylactic measures to a control group. This trial is designed as a two-arm, parallel, cluster randomized controlled trial with the antenatal obstetric clinic as the unit of randomization and an allocation ratio of 1:1. The pregnant women will be included at 3 months of pregnancy and will be followed throughout the pregnancy. The primary outcome measure will be the incidence of PE from a baseline during the pregnancy. Secondary outcomes measures will include changes from the baseline in quantification of the pathogenic bacterial load of the interdental microbiota, the severity scores of periodontal indicators, and the incidence of adverse perinatal outcomes. This trial should demonstrate that the implementation of daily oral hygiene reduces oral dysbiosis, the incidence of periodontal disease, and the risk of PE.

RevDate: 2021-09-26

Kayani MUR, Yu K, Qiu Y, et al (2021)

Corrigendum to "Environmental concentrations of antibiotics alter zebrafish gut microbiome structure and potential functions" [Environ. Pollut. 278 (2021) 116760].

RevDate: 2021-09-26

Mngomezulu K, Mzobe G, Mtshali A, et al (2021)

The use of PSA as a biomarker of recent semen exposure in female reproductive health studies.

Journal of reproductive immunology, 148:103381 pii:S0165-0378(21)00111-X [Epub ahead of print].

Semen contains potent soluble proteins, bacteria, viruses, activated immune cells as well as anti- and pro-inflammatory cytokines that may influence the inflammatory response and alter microbial composition of the female genital tract. The presence of semen in the female genital mucosa may be a significant confounder that most studies have failed to control for in their analysis. Prostate-specific antigen (PSA), a protein secreted by the prostate into the urethra during ejaculation, is a well-established biomarker of semen exposure. Several studies have demonstrated discordance between self-reports of sexual behavior and the presence of PSA. Recent semen exposure has been shown to promote pro-inflammatory responses, stimulate the recruitment of activated immune cells and decrease Lactobacilli abundance in the female genital mucosa. As a result, it is important to understand the concordance between self-reported consistent condom use and the presence of semen biomarkers. Furthermore, to ensure that the interpretation of data in clinical studies of the immunological and microbial environment in the female genital mucosa are accurate, it is essential to establish whether semen is present in the vaginal fluid. This review explores the impact of semen exposure on the mucosal microenvironment and assesses the use of the PSA as an objective biomarker of semen exposure to reduce reliance on self-reported sexual intercourse.

RevDate: 2021-09-26

Xu Y, Shao M, Fang X, et al (2021)

Antipsychotic-induced gastrointestinal hypomotility and the alteration in gut microbiota in patients with schizophrenia.

Brain, behavior, and immunity pii:S0889-1591(21)00558-4 [Epub ahead of print].

AIM: Gut microbiota play an important role in the pathogenesis of gut hypomotility and are critical for the production of the intestinal immune system and the maintenance of the intestinal homeostasis. Patients with psychotic disorders are at a high risk of antipsychotic-induced constipation. However, the mechanisms might be more than neurotransmission properties of antipsychotics.

METHODS: We recruited a total of 45 patients with constipation according to Rome IV criteria and objective test for colonic motility and the other 45 gender- and age-matching patients without constipation and investigated their differences in composition of gut microbiota. The demographic and serum metabolic indices were collected. The subjective constipation assessment scale (CAS) and the Bristol stool classification (BSS) were also used to evaluate the degree of constipation in both groups. The fecal samples were analysed using the 16S rRNA gene sequencing.

RESULTS: The constipation group had a significantly increased alpha diversity in Observed species, Chao 1, and ACE as compared to the non-constipation group. At the phylum levels, the relative abundances of Bacteroidetes and Fusobacteria decreased significantly, while those of Firmicutes, Verrucomicrobia, and Synergistetes increased significantly in the constipation group. At the genus level, the relative abundances of Christensenella and Desulfovibrio were higher in the constipation group. The α-diversity indices of gut microbiota were correlated positively with the levels of serum total bile acid and correlated negatively with BSS scores. The BSS scores were positively correlated with the relative abundance of Bacteroidetes but negatively correlated with the relative abundance of Firmicutes. PICRUSt analysis revealed the potential metabolic pathways of lipopolysaccharide, vitamin B6, riboflavin, pyruvate, and propionate functions.

CONCLUSIONS: The alternation of the gut microbiota in schizophrenia patients with antipsychotic-induced constipation indicates antipsychotic agents might affect gastrointestinal motility via varying microbiome-related metabolites, and the specific bacteria, such as Synergistetes which might act as an anti-inflammatory factor in the healthy human gut, related to colonic transit motility seem inconsistent to the findings from previous literature in gastroenterology. However, the causal effects are still unknown. Our study provides a new possibility to understand the mechanisms of antipsychotic-induced constipation.

RevDate: 2021-09-26

Park SY, Faraci G, Nanda S, et al (2021)

Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses.

Microbial pathogenesis pii:S0882-4010(21)00483-6 [Epub ahead of print].

People living with HIV have a high incidence of cardiovascular and neurological diseases as comorbid disorders that are commonly linked to inflammation. While microbial translocation can augment inflammation during HIV infection, functional microbiome shifts that may increase pro-inflammatory responses have not been fully characterized. In addition, defining HIV-induced microbiome changes has been complicated by high variability among individuals. Here we conducted functional annotation of previously-published 16 S ribosomal RNA gene sequences of 305 HIV positive and 249 negative individuals, with adjustment for geographic region, sex, sexual behavior, and age. Metagenome profiles were inferred from these individuals'16 S data. HIV infection was associated with impaired microbial vitamin B synthesis; around half of the gene families in thiamine and folate biosynthesis pathways were significantly less abundant in the HIV positive group than the negative control. These results are consistent with the high prevalence of thiamine and folate deficiencies in HIV infections. These HIV-induced microbiota shifts have the potential to influence cardiovascular and neurocognitive diseases, given the documented associations between B-vitamin deficiencies, inflammation, and these diseases. We also observed that most essential amino acid biosynthesis pathways were downregulated in the microbiome of HIV-infected individuals. Microbial vitamin B and amino acid synthesis pathways were not significantly recovered by antiretroviral treatment when we compared 262 ART positive and 184 ART negative individuals. Our meta-analysis provides a new outlook for understanding vitamin B and amino acid deficiencies in HIV patients, suggesting that interventions for reversing HIV-induced microbiome shifts may aid in lessening the burdens of HIV comorbidities.

RevDate: 2021-09-26

Wang Y, Yang Y, Zhang Y, et al (2021)

Milk replacer supplementation in early life optimizes the development of intestinal microbes in Yimeng black goats.

Microbial pathogenesis pii:S0882-4010(21)00484-8 [Epub ahead of print].

Colonization and development of the gut microbiome during early life is important in establishing a host-microbial symbiotic relationship. It contributes to maintaining health and well-being throughout the life span. To date, early longitudinal development of intestinal microflora in the ileum micro-ecology of the Yimeng black goats (YBGs) is rare. The purpose of this research was to study the effect of milk replacer with age on ileal microbiota growth and maturation in YBGs throughout the post-weaning phase. The newborn YBGs (n = 24) were divided into two groups, i.e., milk replacer (R group) and control group (B group). The microbiome of Ileum was observed on days 15, 25, 45, and 75. When compared with baseline (B group), the R group's alpha diversity was lower (day 15, 25, 45), but it gradually approached and exceeded the baseline in the later stages (day 75). On the time axis, the richness of intestinal microflora was increased with age, but there was no statistically significant difference. The relative abundances of Proteobacteria, Firmicutes, Peptoclustridium, Lachnospiraceae, and Prevotellaceae showed a continuous trend of increase initially and then decreased except Ruminococcaceae, which reflected the gradual maturity of intestinal microbial development. Milk replacer treatment temporarily increased the abundance of Actinomycetes (day 25 and 45), while the relative proportion of several intestinal functional bacteria such as Parasutterella, Megasphaera, Prevotellaceae, Akkermansia, and Subdoligranulum species were significantly higher in R group than in B group. The major changes in gut microflora composition might reflect positive effect of milk replacer feeding on the development and maturation of intestine during the early stage, which was connected with substrate availability in the gut. Our study provides an effective strategy to promote the development of the gut microbiome, which is helpful for a smooth transition during the early-weaning period in YBGs.

RevDate: 2021-09-26

Turjeman S, O Koren (2021)

ARGuing the case for (or against) probiotics.

Trends in microbiology pii:S0966-842X(21)00215-8 [Epub ahead of print].

Antibiotic resistance is one of the leading medical challenges with which we are currently faced. Antibiotics, while powerful medical tools, also wreak havoc on the endogenous microbiota. Many believe that probiotics can restore the microbiota following antibiotic treatment and might even suppress the spread of antibiotic-resistance genes, but a recent study (Montassier et al.) suggests otherwise.

RevDate: 2021-09-26

Wang L, Wang X, Zhang G, et al (2021)

The impact of pelvic radiotherapy on the gut microbiome and its role in radiation-induced diarrhoea: a systematic review.

Radiation oncology (London, England), 16(1):187.

Pelvic radiotherapy is the key treatment for pelvic malignancies, usually including pelvic primary tumour lesions and lymphatic drainage areas in the pelvic region. Therefore, the intestinal tract in the radiation field is inevitably damaged, a phenomenon clinically referred to as radiation enteritis, and diarrhoea is the most common clinical symptom of radiation enteritis. Therefore, it is necessary to study the mechanism of radiation-induced diarrhoea. It has been found that the gut microbiome plays an important role in the development of diarrhoea in response to pelvic radiotherapy, and the species and distribution of intestinal microbiota are significantly altered in patients after pelvic radiotherapy. In this study, we searched for articles indexed in the Cochrane Library, Web of Science, EMBASE and PubMed databases in English and CNKI, Wanfang data and SINOMED in Chinese from their inception dates through 13 March 2020 to collect studies on the gut microbiome in pelvic radiotherapy patients. Eventually, we included eight studies: one study report on prostatic carcinoma, five studies on gynaecological carcinoma and two papers on pelvic carcinomas. All studies were designed as self-controlled studies, except for one that compared toxicity to nontoxicity. The results from all the studies showed that the diversity of intestinal flora decreased during and after pelvic radiotherapy, and the diversity of intestinal flora decreased significantly in patients with diarrhoea after radiotherapy. Five studies observed that the community composition of the gut microbiota changed at the phylum, order or genus level before, during, and after pelvic radiotherapy at different time points. In addition, the composition of the gut microbiota before radiotherapy was different between patients with postradiotherapy diarrhoea and those without diarrhoea in five studies. However, relevant studies have not reached consistent results regarding the changes in microbiota composition. Changes in the intestinal flora induced by pelvic radiotherapy and their relationship between changes in intestinal flora and the occurrence of radiation-induced diarrhoea (RID) are discussed in this study, providing a theoretical basis for the causes of RID after pelvic radiotherapy.

RevDate: 2021-09-26

Mou Z, Yang Y, Hall AB, et al (2021)

The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome.

BMC genomics, 22(1):695.

BACKGROUND: Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria.

RESULTS: To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease.

CONCLUSIONS: The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.

RevDate: 2021-09-26

Ali AH, Juran BD, Schlicht EM, et al (2021)

The PSC scientific community resource: an asset for multi-omics interrogation of primary sclerosing cholangitis.

BMC gastroenterology, 21(1):353.

BACKGROUND: Primary sclerosing cholangitis (PSC) is a rare, chronic cholestatic liver disease that often progresses to end-stage liver disease and/or the development of hepatobiliary neoplasia. Lack of prognostic tools and treatment options for PSC is driven in part by our poor understanding of its pathogenesis, which is thought to be complex, the interaction of genetic variants, environmental influences and biological response throughout the course of disease. The PSC Scientific Community Resource (PSC-SCR) seeks to overcome previous shortcomings by facilitating novel research in PSC with the ultimate goals of individualizing patient care and improving patient outcomes.

METHODS: PSC patients who receive their health care at Mayo Clinic or a collaborating site are identified by chart review and invited in person or by mail to participate. Non-Mayo patients are offered enrollment if they provide sufficient access to their medical records to evaluate inclusion/exclusion criteria. Controls without liver disease are identified with assistance of the Mayo Clinic Biobank. Participant consent is obtained at the beginning of the recruitment process by mail-in, electronic or face-to-face protocols. Clinical data is extracted from the medical record by qualified physicians and entered in a custom designed database. Participants fill out a custom-designed, comprehensive questionnaire, which collects scientifically relevant demographic and clinical information. Biospecimens are collected using mail-in kits thar are returned via overnight carrier service and processed by the biospecimen accessioning and processing facility at Mayo Clinic, which coordinates sample transfers and provides required sample preparation services. The resource is currently being utilized to perform omics-scale projects investigating the exposome, metabolome, methylome, immunome and microbiome in PSC. Datasets and residual biospecimens will be shared with researchers proposing scientifically sound PSC-focused research with approval of the appropriate review boards.

DISCUSSION: Patient-based studies leveraging the latest technologies for targeted and wide-scale interrogation of multiple omics layers offer promise to accelerate PSC research through discovery of unappreciated aspects of disease pathogenesis. However, the rarity of PSC severely limits such studies. Here we describe our effort to overcome this limitation, the PSC-SCR, a repository of patient biospecimens coupled with clinical and omics data for use by the broader PSC research community.

RevDate: 2021-09-25

Hakim JA, Green GBH, Watts SA, et al (2021)

Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics.

Current issues in molecular biology, 43(2):978-995 pii:cimb43020070.

This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.

RevDate: 2021-09-25

Cheng M, Ge X, Zhong C, et al (2021)

Micro-co-evolution of Host Genetics with Gut Microbiome in Three Chinese Ethnic Groups.

Journal of genetics and genomics = Yi chuan xue bao pii:S1673-8527(21)00304-0 [Epub ahead of print].

Understanding the micro-co-evolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical studies. To gain insight into the interactions between host genetic variation and the gut microbiome, we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in a same boarding college and representing three ethnic groups, Uyghur, Kazakh, and Han Chinese. We found that differences in gut microbiome were stronger between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition, functional composition, enterotype stratification, and microbiome genetic differentiation. We also observed considerable correlations between host genetic variants and the abundance of a subset of gut microbial species. Notably, interactions between gut microbiome species and host genetic variants might have coordinated effects on specific human phenotypes. Bacteroides ovatus, previously reported to modulate intestinal immunity, is significantly correlated with the host genetic variant rs12899811 (meta-P = 5.55 × 10-5), which regulates the VPS33B expression in the colon, acting as a tumor suppressor of colorectal cancer. These results advance our understanding of the micro-co-evolution of the human gut microbiome and their interactive effects with host genetic variation on phenotypic diversity.

RevDate: 2021-09-25

Abu Y, Tao J, Dutta R, et al (2021)

Brief Hydromorphone Exposure During Pregnancy Sufficient to Induce Maternal and Neonatal Microbial Dysbiosis.

Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology [Epub ahead of print].

Prenatal opioid exposure is associated with significantly adverse medical, developmental, and behavioral outcomes in offspring, though the underlying mechanisms driving these impairments are still unclear. Accumulating evidence implicates gut microbial dysbiosis as a potential modulator of these adverse effects. However, how opioid exposure during pregnancy alters the maternal and neonatal microbiome remain to be elucidated. Here, we utilize a murine model of brief hydromorphone exposure during pregnancy (gestation day 11-13; i.p.; 10 mg/kg) to examine its impact on the maternal and neonatal microbiome. Fecal samples were collected at various timepoints in dams (4 days post hydromorphone exposure, birth, and weaning) and offspring (2, 3, and 5 weeks) to interrogate longitudinal changes in the microbiome. Stomach contents at 2 weeks were also collected as a surrogate for breastmilk and microbial analysis was performed using 16S rRNA sequencing. Alongside alterations in the maternal gut microbial composition, offspring gut microbiota exhibited distinct communities at 2 and 3 weeks. Furthermore, functional profiling of microbial communities revealed significant differences in microbial community-level phenotypes gram-negative, gram-positive, and potentially pathogenic in maternal and/or neonatal hydromorphone exposed groups compared with controls. We also observed differences in stomach microbiota in opioid-exposed vs non-exposed offspring, which suggests breast milk may also play a role in shaping the development of the neonatal gut microbiota. Together, we provide evidence of maternal and neonatal microbial dysbiosis provoked even with brief hydromorphone exposure during pregnancy.

RevDate: 2021-09-25

Zhang Y, Qu Y, Yang J, et al (2021)

A pilot study to investigate the alteration of gut microbial profile in Dip2a knockout mice.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

Accumulating evidence has pointed out that the gut-brain axis plays important roles in the etiology of autism spectrum disorder (ASD). Gut dysbiosis was reported in both ASD human patients and animal models. Dip2a was identified as a human ASD candidate gene. Deletion of Dip2a led to dendritic spine dysfunction and autistic-like behaviors in mice. To further investigate if Dip2a deletion leads to gut dysbiosis, we used 16S rDNA sequencing to study the gut microbiota in Dip2a KO mice. In both co-housed and separated breeding conditions, deletion of Dip2a could affect the gut microbiome composition. The probiotic bacteria, Lactobacillus and Bifidobacterium, became less abundant, while some potentially harmful bacteria, Alistipes, Lachnospiraceae_NK4A136_group, Clostridium, Desulfovibrio, and Enterorhabdus, became more abundant. We further found that probiotic treatment could help to reconstitute the gut microbiome composition in Dip2a KO mice. Altogether, these data showed DIP2A is required for the proper composition of gut microbiota, and the probiotics have potential roles in rectifying the gut microbiota in Dip2a KO mice.

RevDate: 2021-09-25

Mittelstrass J, Sperone FG, MW Horton (2021)

Using transects to disentangle the environmental drivers of plant microbiome assembly.

Plant, cell & environment [Epub ahead of print].

Environmental heterogeneity is a major driver of plant microbiome assembly, but the specific climate and soil conditions that are involved remain poorly understood. To better understand plant microbiome formation, we examined the bacteria and fungi that colonize wild strawberry (Fragaria vesca) plants in North American and European populations. Using transects as replicates, we found strong overlap among the environmental conditions that best predict the overall similarity and richness of the plant microbiome, including soil nutrients that replicate across continents. Temperature is also among the main predictors of diversity for both bacteria and fungi in both the leaf and, unexpectedly, the root microbiome. Our results indicate that a small number of environmental factors, and their interactions, consistently contribute to plant microbiome formation, which has implications for predicting the contributions of microbes to plant productivity in ever-changing environments. This article is protected by copyright. All rights reserved.

RevDate: 2021-09-25

Bai YZ, Roberts SH, Kreisel D, et al (2021)

Microbiota in heart and lung transplantation: implications for innate-adaptive immune interface.

Current opinion in organ transplantation pii:00075200-900000000-98809 [Epub ahead of print].

PURPOSE OF REVIEW: Transplantation continues to be the only treatment option for end-stage organ failure when other interventions have failed. Although short-term outcomes have improved due to advances in perioperative care, long-term outcomes continue to be adversely affected by chronic rejection. Little is known about the role microbiota play in modulating alloimmune responses and potentially contributing to graft failure. Initial data have identified a correlation between specific changes of the recipient and/or donor microbiota and transplant outcomes. In this review, we will focus on recent findings concerning the complex interplay between microbiota and the innate immune system after heart and lung transplantation.

RECENT FINDINGS: Gut microbiome derangements in heart failure promote an inflammatory state and have lasting effects on the innate immune system, with an observed association between increased levels of microbiota-dependent metabolites and acute rejection after cardiac transplantation. The lung allograft microbiome interacts with components of the innate immune system, such as toll-like receptor signalling pathways, NKG2C+ natural killer cells and the NLRP3 inflammasome, to alter posttransplant outcomes, which may result in the development of chronic rejection.

SUMMARY: The innate immune system is influenced by alterations in the microbiome before and after heart and lung transplantation, thereby offering potential therapeutic targets for prolonging allograft survival.

RevDate: 2021-09-25

Anonymous (2021)

A High-Fat Diet Controls MHC Class II on ISCs via the Microbiome.

Cancer discovery pii:2159-8290.CD-RW2021-134 [Epub ahead of print].

A high-fat diet (HFD) increases tumorigenicity by reducing MHC class II on intestinal stem cells (ISC).

RevDate: 2021-09-25

Kumpitsch C, Fischmeister FPS, Mahnert A, et al (2021)

Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans.

Microbiome, 9(1):193.

BACKGROUND: Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood.

RESULTS: We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH4 breath content 5-75 ppm) and low emitters (CH4 < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis.

CONCLUSIONS: This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.

RevDate: 2021-09-25

Arostegui D, T Wallach (2021)

The Cutting Edge of Gastroenteritis: Advances in Understanding of Enteric Infection.

Journal of pediatric gastroenterology and nutrition pii:00005176-900000000-95536 [Epub ahead of print].

ABSTRACT: In recent years, multiple advances have been made in the care, diagnosis, and mechanistic understanding of acute gastroenteritis (AGE). In this review we discuss the current state of the art of diagnosis and management, as well as how changes in practice can improve care and decrease costs. We will discuss current research demonstrating the effect of AGE on the microbiome and how that may be linked to secondary effects or long-term changes. We will explore the use of novel technologies to further our capacity to understand how gastrointestinal infections occur and promulgate. Finally, will discuss advances in our understanding of how gastrointestinal infections capacitate other changes such as post-viral motility or other post viral intestinal dysfunction.

RevDate: 2021-09-26

Shah T, Shah Z, Baloch Z, et al (2021)

The role of microbiota in respiratory health and diseases, particularly in tuberculosis.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 143:112108 pii:S0753-3322(21)00892-1 [Epub ahead of print].

Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.

RevDate: 2021-09-24

Sato Y, Hamai T, Hori T, et al (2021)

Optimal start-up conditions for the efficient treatment of acid mine drainage using sulfate-reducing bioreactors based on physicochemical and microbiome analyses.

Journal of hazardous materials, 423(Pt B):127089 pii:S0304-3894(21)02057-4 [Epub ahead of print].

Typically, sulfate-reducing bioreactors used to treat acid mine drainage (AMD) undergo an initial incubation period of a few weeks to acclimatize sulfate-reducing bacteria (SRB), although necessity of this preincubation has rarely been evaluated. To reduce time and economic cost, we developed an SRB acclimatization method using the continuous flow of AMD into bioreactors fed with rice bran, and compared with the conventional acclimatization method. We found that the SRB sufficiently acclimatized without the preincubation phase. Furthermore, we examined the performance and SRB communities in bioreactors operated for >200 days under seven different conditions, in which the amount of rice bran added and hydraulic retention times (HRTs) were varied. A comparison of the various bioreactor conditions revealed that the lowest rice bran amount (50 g) and the shortest HRT (6 h) caused a deterioration in reactor performance after day 144 and 229, respectively. In both cases, relatively aerobic environments developed due to the lack of organic matter seemed to inhibit sulfate reduction. Of the conditions tested, operation of the bioreactors with 200 g of rice bran and an HRT of 12.5 h was the most effective in treating AMD, showing a sulfate reduction rate of 20.7-77.9% during days 54-242. DATA AND MATERIALS AVAILABILITY: All data needed to evaluate the conclusions of this study are presented in the paper and/or the appendix.

RevDate: 2021-09-24

Kim Y, S Oh (2021)

Machine-learning insights into nitrate-reducing communities in a full-scale municipal wastewater treatment plant.

Journal of environmental management, 300:113795 pii:S0301-4797(21)01857-0 [Epub ahead of print].

This study carried out machine-learning (ML) modeling using activated sludge microbiome data to predict the operational characteristics of biological unit processes (i.e., anaerobic, anoxic, and aerobic) in a full-scale municipal wastewater treatment plant. An ML application pipeline with optimization strategies (e.g., model selection, input data preprocessing, and hyperparameter tuning) could significantly improve prediction performance. Comparative analysis of the ML prediction performance suggested that linear models (support vector machine and logistic regression) had a high prediction performance (93% accuracy), comparable to that of non-linear models such as random forest. Feature importance analysis using the linear ML models identified the microbial taxa that were specifically associated with anoxic processes, many of which (e.g., Ferruginibacter) were found to have ecologically important genomic and phenotypic characteristics (e.g., for nitrate reduction). Time-series microbial community dynamics demonstrated that the taxa identified using ML were frequently occurring and dominating in the anoxic process over time, thus representing the core nitrate-reducing community. Despite the general dominance of the core community over time, the analysis further revealed successional seasonal patterns of distinct sub-groups, indicating differences in the functional contribution of sub-groups by season to the overall nitrate-reducing potential of the system. Overall, the results of this study suggest that ML modeling holds great promise for the predictive identification and understanding of key microbial players governing the functioning and stability of biological wastewater systems.

RevDate: 2021-09-24

Zuo T, Wu X, Wen W, et al (2021)

Gut Microbiome Alterations in COVID-19.

Genomics, proteomics & bioinformatics pii:S1672-0229(21)00206-0 [Epub ahead of print].

Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with 'long COVID' (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2 infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida, may hinder the re-assembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.

RevDate: 2021-09-24

Shan J, Qu Y, Wang S, et al (2021)

Regulation of neurotoxicity in the striatum and colon of MPTP-induced Parkinson's disease mice by gut microbiome.

Brain research bulletin pii:S0361-9230(21)00272-0 [Epub ahead of print].

Increasing evidence suggests the role of gut-microbiota-brain axis in the pathogenesis of Parkinson's disease (PD). The objective of this study was to examine whether repeated administration of MPTP (1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) can influence the neurotoxicity in the striatum and colon, and the composition of gut microbiota and short-chain fatty acids (SCFAs) in feces of adult mice. MPTP caused the reduction of dopamine transporter (DAT) and tyrosine hydroxylase (TH) in the striatum, and increases in phosphorylated α-synuclein (p-α-Syn) in the striatum and colon. There was a negative correlation between the expression of TH in the striatum and the expression of p-α-Syn in the colon, suggesting a role of gut-brain communication. MPTP caused abnormalities in the α- and β-diversity of gut microbiota in the mice. Furthermore, the relative abundance of the genus Faecalicatena in the MPTP-treated group was significantly lower than that of control group. Interestingly, there was a positive correlation between the genus Faecalicatena and the expression of TH in the striatum. Moreover, MPTP did not alter the levels of SCFAs in feces samples. However, there was a positive correlation between the relative abundance of the genus Faecalicatena and propionic acid. The data suggest that MPTP-induced increases in colonic p-α-Syn expression might be associated with dopaminergic neurotoxicity in the striatum via gut-microbiota-brain axis.

RevDate: 2021-09-24

Smith KB, Murray E, Gregory JG, et al (2021)

Pubertal Probiotics Mitigate Lipopolysaccharide-Induced Programming of the Hypothalamic-Pituitary-Adrenal axis in Male Mice only.

Brain research bulletin pii:S0361-9230(21)00288-4 [Epub ahead of print].

Puberty is a period of rapid cortical and neuronal development. Stress exposure during puberty programs the hypothalamic-pituitary-adrenal (HPA) axis responsiveness to future stressors. However, programming can result in an enduring maladaptation of the HPA axis activity and can be associated with long-term anxiety- and depression-like behaviours. Probiotic treatment mitigates the effect of stress on mental health, suggesting that the gut microbiome may mediate the programming of the HPA axis. However, the mechanism underlying this effect remains elusive. Thus, we investigated the effect of probiotic exposure on lipopolysaccharide (LPS)-induced programming of the HPA axis and glucocorticoid receptor (GR) expression in the paraventricular (PVN), basolateral amygdala (BLA), piriform cortex (PIR), and medial prefrontal cortex (mPFC). Male and female mice were exposed to either probiotics or control skim milk and were treated with either saline or LPS during puberty. Prior to euthanasia in adulthood, mice were restrained for 30minutes. The results showed that pubertal LPS treatment permanently decreased GR expression in the PVN in milk fed control males. However, pubertal probiotic treatment blocked the LPS-induced decrease in GR expression in males. Given that this effect is limited to males, further research is required to better understand sex differences in the interactions between the gut microbiome and the programming of the HPA axis during puberty. Nevertheless, our findings suggest that the gut microbiome influences the neurophysiology of the HPA axis and mediates its programming in pubertal males. The prevention of GR reduction in the male PVN and PIR using probiotics illustrates the complexity of the gut-brain communication and compels continued investigation.

RevDate: 2021-09-24

Gustin AT, Thurman AR, Chandra N, et al (2021)

Recurrent bacterial vaginosis following metronidazole treatment is associated with microbiota richness at diagnosis.

American journal of obstetrics and gynecology pii:S0002-9378(21)01046-2 [Epub ahead of print].

BACKGROUND: Bacterial vaginosis- a condition defined by a shift from Lactobacillus dominance to a polymicrobial, anaerobic bacterial community - increases the risk of acquiring sexually transmitted infections and other complications of the female reproductive tract . Antibiotic treatment frequently fails to return the microbiome to an optimal Lactobacillus-dominated state. No criteria currently exist to identify patients likely to experience treatment failure.

OBJECTIVE(S): We sought to identify pre-treatment community signatures associated with treatment failure through 16S rRNA gene analysis.

STUDY DESIGN: Twenty-eight women enrolled in an oral metronidazole treatment trial of BV were studied. Cervicovaginal lavage samples were collected prior to metronidazole treatment, and again at 7 and 30-days post-treatment. Cervicovaginal lavage DNA was amplified and sequenced using a paired-end, V4 region, 2x150 MiSeq run.

RESULTS: Of the 28 women, 25% failed to clear bacterial vaginosis, 35.7% demonstrated a transient clearance - shifting to community-type 2 (Lactobacillus iners dominant, CT2) at visit 2 only; 7.1% demonstrated delayed clearance - reaching CT2 at the final visit only; and 32.1% of patients experienced sustained bacterial vaginosis clearance. Examination of community composition and structure demonstrated that both richness and evenness were significantly lower for women who sustained clearance, while women who failed to clear bacterial vaginosis possessed the highest median levels of richness, evenness, and diversity pre-treatment. Soluble immune factors in the lower reproductive improved significantly following a shift from CT4 to a Lactobacillus-dominant microbiome, with samples categorized as CT2 possessing significantly higher levels of SLPI, GROa, and MIP3a and significantly lower levels of ICAM-1. While shifts to Lactobacillus-dominance improved markers of mucosal tissue health, these gains were only temporary amongst women who experienced recurrence.

CONCLUSIONS: Assemblies of highly diverse microbiota are associated with the enhanced resilience of bacterial vaginosis to standard metronidazole treatment. These communities may be foundational to treatment resistance or simply an indication of a well-established community made possible by canonical biofilm forming taxa. Future studies must target the transcriptional activity of these communities under the pressure of antibiotic treatment to resolve the mechanisms of their resistance.

RevDate: 2021-09-26

Bajerski F, Nagel M, J Overmann (2021)

Microbial occurrence in liquid nitrogen storage tanks: a challenge for cryobanking?.

Applied microbiology and biotechnology [Epub ahead of print].

Modern biobanks maintain valuable living materials for medical diagnostics, reproduction medicine, and conservation purposes. To guarantee high quality during long-term storage and to avoid metabolic activities, cryostorage is often conducted in the N2 vapour phase or in liquid nitrogen (LN) at temperatures below - 150 °C. One potential risk of cryostorage is microbial cross contamination in the LN storage tanks. The current review summarises data on the occurrence of microorganisms that may compromise the safety and quality of biological materials during long-term storage. We assess the potential for the microbial contamination of LN in storage tanks holding different biological materials based on the detection by culture-based and molecular approaches. The samples themselves, the LN, the human microbiome, and the surrounding environment are possible routes of contamination and can cause cross contaminations via the LN phase. In general, the results showed that LN is typically not the source of major contaminations and only a few studies provided evidence for a risk of microbial cross contamination. So far, culture-based and culture-independent techniques detected only low amounts of microbial cells, indicating that cross contamination may occur at a very low frequency. To further minimise the potential risk of microbial cross contaminations, we recommend reducing the formation of ice crystals in cryotanks that can entrap environmental microorganisms and using sealed or second sample packing. A short survey demonstrated the awareness for microbial contaminations of storage containers among different culture collections. Although most participants consider the risk of cross contaminations in LN storage tanks as low, they prevent potential contaminations by using sealed devices and - 150 °C freezers. It is concluded that the overall risk for cross contaminations in biobanks is relatively low when following standard operating procedures (SOPs). We evaluated the potential sources in detail and summarised our results in a risk assessment spreadsheet which can be used for the quality management of biobanks. KEY POINTS: • Identification of potential contaminants and their sources in LN storage tanks. • Recommendations to reduce this risk of LN storage tank contamination. • Development of a risk assessment spreadsheet to support quality management.

RevDate: 2021-09-24

Klein K, Garkov D, Rütschlin S, et al (2021)

QSDB-a graphical Quorum Sensing Database.

Database : the journal of biological databases and curation, 2021: pii:6375033.

The human microbiome is largely shaped by the chemical interactions of its microbial members, which includes cross-talk via shared signals or quenching of the signalling of other species. Quorum sensing is a process that allows microbes to coordinate their behaviour in dependence of their population density and to adjust gene expression accordingly. We present the Quorum Sensing Database (QSDB), a comprehensive database of all published sensing and quenching relations between organisms and signalling molecules of the human microbiome, as well as an interactive web interface that allows browsing the database, provides graphical depictions of sensing mechanisms as Systems Biology Graphical Notation diagrams and links to other databases. Database URL: QSDB (Quorum Sensing DataBase) is freely available via an interactive web interface and as a downloadable csv file at http://qsdb.org.

RevDate: 2021-09-24

Das S, Ge X, Han H, et al (2021)

The Integrated "Multiomics" Landscape at Peak Injury and Resolution From Alcohol-Associated Liver Disease.

Hepatology communications [Epub ahead of print].

Alcohol-associated liver disease (ALD) is a significant clinical problem for which the most effective therapy is alcohol abstinence. The two aims of this study were, first, to identify the liver transcriptome, fecal microbiome, and portal serum metabolome at peak injury and during early and late resolution from ALD; and second, to integrate their interactions and understand better the pathogenesis of ALD. To provoke alcohol-induced liver injury, female and male wild-type mice were fed the control or ethanol Lieber-DeCarli diets for 6 weeks. To study early and late resolution, alcohol was withdrawn from the diet and mice were sacrificed after 3 and 14 days, respectively. At peak injury, there was increased signal transducer and activator of transcription (Stat3), Rho-GTPases, Tec kinase and glycoprotein VI (Gp6), and decreased peroxisome proliferator-activated receptor signaling. During resolution from ALD, there was up-regulation of vitamin D receptor/retinoid X receptor, toll-like receptor, p38 and Stat3, and down-regulation of liver X receptor signaling. Females showed significant changes in catabolic pathways, whereas males increased cellular stress, injury, and immune-response pathways that decreased during resolution. The bacterial genus Alistipes and the metabolite dipeptide glycyl-L-leucine increased at peak but decreased during resolution from ALD in both genders. Hepatic induction of mitogen-activated protein kinase (Map3k1) correlated with changes in the microbiome and metabolome at peak but was restored during ALD resolution. Inhibition of MAP3K1 protected from ALD in mice. Conclusion: Alcohol abstinence restores the liver transcriptome, fecal microbiome, and portal serum metabolome in a gender-specific manner. Integration of multiomics data identified Map3k1 as a key gene driving pathogenesis and resolution from ALD.

RevDate: 2021-09-24

Perofsky AC, Ancel Meyers L, Abondano LA, et al (2021)

Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes.

Molecular ecology [Epub ahead of print].

Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behavior is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux's sifaka (Propithecus verreauxi) from six social groups. Over the course of three dry seasons in a five-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among co-residing group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and individuals with less stable social ties exhibited elevated rates of microbiome turnover across seasons. Our results suggest that permanent social groupings shape the changing composition of commensal and mutualistic gut microbial communities and thus may be important drivers of health and resilience in wild primate populations.

RevDate: 2021-09-25

Harkins P, Burke E, Swales C, et al (2021)

'All disease begins in the gut'-the role of the intestinal microbiome in ankylosing spondylitis.

Rheumatology advances in practice, 5(3):rkab063.

Ankylosing spondylitis is a chronic, debilitating arthritis with a predilection for the axial skeleton. It has a strong genetic predisposition, but the precise pathogenetic mechanisms involved in its development have not yet been fully elucidated. This has implications both for early diagnosis and for effective management. Recently, alterations in the intestinal microbiome have been implicated in disease pathogenesis. In this review, we summarize studies assessing the intestinal microbiome in AS pathogenesis, in addition to synthesizing the literature exploring the postulated mechanisms by which it exerts it pathogenic potential. Finally, we review studies analysing manipulation of the microbiome as a potential therapeutic avenue in AS management.

RevDate: 2021-09-25

Murphy K, Ross RP, Ryan CA, et al (2021)

Probiotics, Prebiotics, and Synbiotics for the Prevention of Necrotizing Enterocolitis.

Frontiers in nutrition, 8:667188.

Necrotizing enterocolitis (NEC) is a major cause of morbidity and mortality in preterm infants. The exact mechanism by which NEC develops is poorly understood however there is growing evidence to suggest that perturbations in the early-life gut microbiota composition increase the risk for NEC. Modulation of the gut microbiota with probiotics, prebiotics, or in combination (synbiotics) is an area which has attracted intense interest in recent years. In this narrative review, we present an overview of the role of the gut microbiota in the pathogenesis of NEC. We also examine the evidence currently available from randomized controlled trials, observational studies, systematic reviews, and meta-analysis examining the role of probiotics, prebiotics, and synbiotics in reducing the risk of or preventing NEC. Current clinical practice guidelines with recommendations on the routine administration of probiotics to preterm infants for NEC are also explored.

RevDate: 2021-09-25

Maan H, Gilhar O, Porat Z, et al (2021)

Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production.

Frontiers in cellular and infection microbiology, 11:722778.

Beneficial and probiotic bacteria play an important role in conferring immunity of their hosts to a wide range of bacterial, viral, and fungal diseases. Bacillus subtilis is a Gram-positive bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great importance for the elimination of pathogens and establishing beneficial host-associated communities. In this work, we used B. subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and imaging flow cytometry (IFC) analysis supported the notion that Arabidopsis thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin, plipastatin, and the polyketide bacillaene. IFC was more robust in quantifying the inducing effects of A. thaliana, considering the overall heterogeneity of the population. Our results highlight IFC as a useful tool to study the effect of association with a plant host on bacterial gene expression. Furthermore, the common regulation of multiple biosynthetic clusters for antibiotic production by the plant can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.

RevDate: 2021-09-25

Liyai R, Kimita G, Masakhwe C, et al (2021)

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya.

PeerJ, 9:e12067.

Background: There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans.

Methods: Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3-V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database.

Results: cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by Anaplasma (8.0%), Methylobacterium (3.5%), Delftia (3.8%), Coxiella (2.6%), Bradyrhizobium (1.6%) and Acinetobacter (1.1%). Other less abundant (<1%) and potentially pathogenic included Ehrlichia, Rickettsia, Leptospira, Borrelia, Brucella, Chlamydia and Streptococcus. By Shannon diversity index, Acomys spleens carried more diverse bacteria (mean Shannon diversity index of 2.86, p = 0.008) compared to 1.77 for Crocidura, 1.44 for Rattus, 1.40 for Arvicathis and 0.60 for Mastomys.

Conclusion: This study examined systemic bacteria that are filtered by the spleen and the findings underscore the utility of 16S rRNA deep sequencing in characterizing complex microbiota that are potentially relevant to one health issues. An inherent problem with the V3-V4 region of 16S rRNA is the inability to classify bacteria reliably beyond the genera. Future studies should utilize the newer long read methods of 16S rRNA analysis that can delimit the species composition.

RevDate: 2021-09-25

Hinsu A, Dumadiya A, Joshi A, et al (2021)

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere.

PeerJ, 9:e12035.

Background: Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified.

Methods: In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data.

Results: In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.

RevDate: 2021-09-25

Xiang K, Wang P, Xu Z, et al (2021)

Causal Effects of Gut Microbiome on Systemic Lupus Erythematosus: A Two-Sample Mendelian Randomization Study.

Frontiers in immunology, 12:667097.

The observational association between gut microbiome and systemic lupus erythematosus (SLE) has been well documented. However, whether the association is causal remains unclear. The present study used publicly available genome-wide association study (GWAS) summary data to perform two-sample Mendelian randomization (MR), aiming to examine the causal links between gut microbiome and SLE. Two sets of MR analyses were conducted. A group of single nucleotide polymorphisms (SNPs) that less than the genome-wide statistical significance threshold (5 × 10-8) served as instrumental variables. To obtain a comprehensive conclusion, the other group where SNPs were smaller than the locus-wide significance level (1 × 10-5) were selected as instrumental variables. Based on the locus-wide significance level, the results indicated that there were causal effects of gut microbiome components on SLE risk. The inverse variance weighted (IVW) method suggested that Bacilli and Lactobacillales were positively correlated with the risk of SLE and Bacillales, Coprobacter and Lachnospira were negatively correlated with SLE risk. The results of weighted median method supported that Bacilli, Lactobacillales, and Eggerthella were risk factors for SLE and Bacillales and Coprobacter served as protective factors for SLE. The estimates of MR Egger suggested that genetically predicted Ruminiclostridium6 was negatively associated with SLE. Based on the genome-wide statistical significance threshold, the results showed that Actinobacteria might reduce the SLE risk. However, Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) detected significant horizontal pleiotropy between the instrumental variables of Ruminiclostridium6 and outcome. This study support that there are beneficial or detrimental causal effects of gut microbiome components on SLE risk.

RevDate: 2021-09-25

Xu Z, Liu Z, Chen J, et al (2021)

Effect of Direct Viral-Bacterial Interactions on the Removal of Norovirus From Lettuce.

Frontiers in microbiology, 12:731379.

Norovirus (NoV) is the main non-bacterial pathogen causing outbreaks of gastroenteritis and is considered to be the leading cause of foodborne illness. This study aims to determine whether lettuce-encapsulated bacteria can express histo-blood group antigen (HBGA)-like substances to bind to NoV and, if so, to explore its role in protecting NoV from disinfection practices. Fifteen bacterial strains (HBGA-SEBs) were isolated from the lettuce microbiome and studied as they were proved to have the ability to express HBGA-like substances through indirect ELISA detection. By using attachment assay, HBGA-SEBs showed great abilities in carrying NoVs regarding the evaluation of binding capacity, especially for the top four strains from genera Wautersiella, Sphingobacterium, and Brachybacterium, which could absorb more than 60% of free-flowing NoVs. Meanwhile, the direct viral-bacterial binding between HBGA-like substance-expressing bacteria (HBGA-SEB) and NoVs was observed by TEM. Subsequently, results of simulated environmental experiments showed that the binding of NoVs with HBGA-SEBs did have detrimental effects on NoV reduction, which were evident in short-time high-temperature treatment (90°C) and UV exposure. Finally, by considering the relative abundance of homologous microorganisms of HBGA-SEBs in the lettuce microbiome (ca. 36.49%) and the reduction of NoVs in the simulated environments, we suggested putting extra attention on the daily disinfection of foodborne-pathogen carriers to overcome the detrimental effects of direct viral-bacterial interactions on the reduction of NoVs.

RevDate: 2021-09-25

Yue C, Luo X, Ma X, et al (2021)

Contrasting Vaginal Bacterial Communities Between Estrus and Non-estrus of Giant Pandas (Ailuropoda melanoleuca).

Frontiers in microbiology, 12:707548.

Bacterial infection and imbalance of bacterial community in the genitourinary system of giant panda could affect the reproductive health. In severe cases, it can also lead to abortion. In this study, 13 of vaginal secretions in the estrue (E) group and seven of vaginal secretions in the non-estrue (NE) group were used to study the composition and diversity of vaginal bacterial communities between estrus and non-estrus by 16S rRNA gene sequencing analysis. The results showed that the vaginal microbiome in giant pandas shared the same top five abundant species between estrus and non-estrus at the phylum level. However, the vaginal microbiome changed significantly during estrus at the genus level. In top 10 genera, the abundance of Escherichia, Streptococcus, and Bacteroides in the E group was significantly higher than that in the NE group (p<0.05); Azomonas, Porphyromonas, Prevotella, Campylobacter, and Peptoniphilus in the NE group was significantly higher than that in the E group (p<0.05). The richness and diversity of vaginal microbiome in giant panda on estrus were significantly lower than those on non-estrus (p<0.05). It is noteworthy that the abundance of Streptococcus, Escherichia, and Bacteroides of vagina in giant pandas maintained low abundance in the daily. Whereas, they increased significantly during estrus period, which may play an important role in female giant pandas during estrus period. It was hypothesized that hormones may be responsible for the changes in the vaginal microbiome of giant pandas between estrus and no-estrus stages.

RevDate: 2021-09-25

Ramirez JL, Ramos I, FM Gomes (2021)

Editorial: Systemic Coordination of Invertebrate Homeostasis.

Frontiers in physiology, 12:736185.

RevDate: 2021-09-25

Sun Z, Li J, Wang W, et al (2021)

Qingchang Wenzhong Decoction Accelerates Intestinal Mucosal Healing Through Modulation of Dysregulated Gut Microbiome, Intestinal Barrier and Immune Responses in Mice.

Frontiers in pharmacology, 12:738152.

Inflammatory bowel disease (IBD), a group of multifactorial and inflammatory infirmities, is closely associated with dysregulation of gut microbiota and host metabolome, but effective treatments are currently limited. Qingchang Wenzhong Decoction (QCWZD) is an effective and classical traditional herbal prescription for the treatment of IBD and has been proved to attenuate intestinal inflammation in a model of acute colitis. However, the role of QCWZD in recovery phase of colitis is unclear. Here, we demonstrated that mice treated with QCWZD showed a faster recovery from dextran sulfate sodium (DSS)-induced epithelial injury, accompanied by reduced mucosal inflammation and attenuated intestinal dysbiosis using bacterial 16S rRNA amplicon sequencing compared to those receiving sterile water. The protective effects of QCWZD are gut microbiota dependent, as demonstrated by fecal microbiome transplantation and antibiotics treatment. Gut microbes transferred from QCWZD-treated mice displayed a similar role in mucosal protection and epithelial regeneration as QCWZD on colitis in mice, and depletion of the gut microbiota through antibiotics treatments diminished the beneficial effects of QCWZD on colitis mice. Moreover, metabolomic analysis revealed metabolic profiles alternations in response to the gut microbiota reprogrammed by QCWZD intervention, especially enhanced tryptophan metabolism, which may further accelerate intestinal stem cells-mediated epithelial regeneration to protect the integrity of intestinal mucosa through activation of Wnt/β-catenin signals. Collectively, our results suggested that orally administrated QCWZD accelerates intestinal mucosal healing through the modulation of dysregulated gut microbiota and metabolism, thus regulating intestinal stem cells-mediated epithelial proliferation, and hold promise for novel microbial-based therapies in the treatment of IBD.

RevDate: 2021-09-24

Urushiyama D, Ohnishi E, Suda W, et al (2021)

Vaginal microbiome as a tool for prediction of chorioamnionitis in preterm labor: a pilot study.

Scientific reports, 11(1):18971.

Intra-amniotic infection (IAI) is a major cause of preterm birth with a poor perinatal prognosis. We aimed to determine whether analyzing vaginal microbiota can evaluate the risk of chorioamnionitis (CAM) in preterm labor cases. Vaginal discharge samples were collected from 83 pregnant women admitted for preterm labor. Based on Blanc's classification, the participants were divided into CAM (stage ≥ II; n = 46) and non-CAM (stage ≤ I; n = 37) groups. The 16S rDNA amplicons (V1-V2) from vaginal samples were sequenced and analyzed. Using a random forest algorithm, the bacterial species associated with CAM were identified, and a predictive CAM (PCAM) scoring method was developed. The α diversity was significantly higher in the CAM than in the non-CAM group (P < 0.001). The area under the curve was 0.849 (95% confidence interval 0.765-0.934) using the PCAM score. Among patients at < 35 weeks of gestation, the PCAM group (n = 22) had a significantly shorter extended gestational period than the non-PCAM group (n = 25; P = 0.022). Multivariate analysis revealed a significant difference in the frequency of developmental disorders in 3-year-old infants (PCAM, 28%, non-PCAM, 4%; P = 0.022). Analyzing vaginal microbiota can evaluate the risk of IAI. Future studies should establish appropriate interventions for IAI high-risk patients to improve perinatal prognosis.

RevDate: 2021-09-23

Zafar H, MH Saier (Jr) (2021)

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species.

Microbial physiology pii:000518954 [Epub ahead of print].

The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.

RevDate: 2021-09-23

Kampouris ID, Alygizakis N, Klümper U, et al (2021)

Elevated levels of antibiotic resistance in groundwater during treated wastewater irrigation associated with infiltration and accumulation of antibiotic residues.

Journal of hazardous materials, 423(Pt B):127155 pii:S0304-3894(21)02123-3 [Epub ahead of print].

Treated wastewater irrigation (TWW) releases antibiotics and antibiotic resistance genes (ARGs) into the environment and might thus promote the dissemination of antibiotic resistance in groundwater (GW). We hypothesized that TWW irrigation increases ARG abundance in GW through two potential mechanisms: the contamination of GW with resistant bacteria and the accumulation of antibiotics in GW. To test this, the GW below a real-scale TWW-irrigated field was sampled for six months. Sampling took place before, during and after high-intensity TWW irrigation. Samples were analysed with 16S rRNA amplicon sequencing, qPCR of six ARGs and the class 1 integron-integrase gene intI1, while liquid chromatography tandem mass spectrometry was performed to detect antibiotic and pharmaceutical residues. Absolute abundance of 16S rRNA in GW decreased rather than increased during long-term irrigation. Also, the relative abundance of TWW-related bacteria did not increase in GW during long-term irrigation. In contrast, long-term TWW irrigation increased the relative abundance of sul1 and intI1 in the GW microbiome. Furthermore, GW contained elevated concentrations of sulfonamide antibiotics, especially sulfamethoxazole, to which sul1 confers resistance. Total sulfonamide concentrations in GW correlated with sul1 relative abundance. Consequently, TWW irrigation promoted sul1 and intI1 dissemination in the GW microbiome, most likely due to the accumulation of drug residues.

RevDate: 2021-09-23

McDaniel EA, Wahl SA, Ishii S, et al (2021)

Prospects for multi-omics in the microbial ecology of water engineering.

Water research, 205:117608 pii:S0043-1354(21)00803-4 [Epub ahead of print].

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.

RevDate: 2021-09-26

Lin X, Zhang W, He L, et al (2021)

Understanding the hepatoxicity of inorganic mercury through guts: Perturbance to gut microbiota, alteration of gut-liver axis related metabolites and damage to gut integrity.

Ecotoxicology and environmental safety, 225:112791 pii:S0147-6513(21)00903-9 [Epub ahead of print].

Mercury (Hg) brings adverse effects to the environment and human beings and inorganic mercury (IHg) is a typical hepatic toxin. This work studied the impacts of IHg on gut microbes and metabolome together with its damage to liver and gut in rats through gut microbiome, metabolomics and metallomics. Sprague Dawley (SD) rats were orally exposed to 0.4 μg/mL IHg and sacrificed after 24 h. It was found that IHg perturbed greatly on the gut microbiota, such as increased pathogenic bacteria like G. bacillus. In addition, IHg also changed gut-liver axis related metabolites, which was confirmed by the secretion of a large number of inflammatory factors in both the gut and the liver. The changed gut-liver axis related metabolites correlated well to the changes of gut microbiome. In all, besides the direct deposition in liver of Hg, the perturbance to gut microbiome and alteration of gut-liver axis related metabolites by IHg also contributed to its hepatoxicity, which provides new insights about the hepatoxicity of chemicals. The strategy applied in this work may also be used to understand the hepatoxicity of other chemicals.

RevDate: 2021-09-23

de Oliveira BFR, Lopes IR, Canellas ALB, et al (2021)

Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11.

International journal of biological macromolecules pii:S0141-8130(21)01997-8 [Epub ahead of print].

Active heterotrophic metabolism is a critical metabolic role performed by sponge-associated microorganisms, but little is known about their capacity to metabolize marine polysaccharides (MP). Here, we investigated the genome of the sponge-derived Pseudoalteromonas sp. strain PA2MD11 focusing on its macroalgal carbohydrate-degrading potential. Carbohydrate-active enzymes (CAZymes) for the depolymerization of agar and alginate were found in PA2MD11's genome, including glycoside hydrolases (GHs) and polysaccharide lyases (PLs) belonging to families GH16, GH50 and GH117, and PL6 and PL17, respectively. A gene potentially encoding a sulfatase was also identified, which may play a role in the strain's ability to consume carrageenans. The complete metabolism of agar and alginate by PA2MD11 could also be predicted and was consistent with the results obtained in physiological assays. Despite the polysaccharide utilization locus (PUL) potentially involved in the metabolism of agarose contained mobile genetic elements from other marine Gammaproteobacteria, its unusual larger size might be due to gene duplication events. Homology modelling and structural protein analyses of the agarases, alginate lyases and sulfatase depicted clear conservation of catalytic machinery and protein folding together with suitable industrially-relevant features. Pseudoalteromonas sp. PA2MD11 is therefore a source of potential MP-degrading biocatalysts for biorefinery applications and in the preparation of pharmacologically-active oligosaccharides.

RevDate: 2021-09-23

Shan Y, Lee M, EB Chang (2021)

The Gut Microbiome and Inflammatory Bowel Diseases.

Annual review of medicine [Epub ahead of print].

Inflammatory bowel diseases (IBD) arise from a convergence of genetic risk, environmental factors, and gut microbiota, where each is necessary but not sufficient to cause disease. Emerging evidence supports a bidirectional relationship between disease progression and changes in microbiota membership and function. Thus, the study of the gut microbiome and host-microbe interactions should provide critical insights into disease pathogenesis as well as leads for developing microbiome-based diagnostics and interventions for IBD. In this article, we review the most recent advances in understanding the relationship between the gut microbiota and IBD and highlight the importance of going beyond establishing description and association to gain mechanistic insights into causes and consequences of IBD. The review aims to contextualize recent findings to form conceptional frameworks for understanding the etiopathogenesis of IBD and for the future development of microbiome-based diagnostics and interventions. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RevDate: 2021-09-23

Miele L, Napodano C, Cesario A, et al (2021)

COVID-19, adaptative immune response and metabolic associated liver disease.

Liver international : official journal of the International Association for the Study of the Liver [Epub ahead of print].

Metabolic diseases are associated with a higher risk of a severer coronavirus disease 2019 (COVID-19) course, since fatty liver is commonly associated to metabolic disorders, fatty liver itself is considered as a major contributor to low grade inflammation in obesity and diabetes. Recently a comprehensive term, metabolic (dysfunction) associated fatty liver disease (MAFLD), has been proposed. The hepatic inflammatory status observed in MAFLD patients is amplified in presence of severe acute respiratory syndrome coronavirus 2 infection. Intestinal dysbiosis is a powerful activator of inflammatory mediator production of liver macrophages. The intestinal microbiome plays a key role in MAFLD progression, which results in nonalcoholic steatohepatitis and liver fibrosis. Therefore, patients with metabolic disorders and COVID-19 can have a worse outcome of COVID-19. This literature review attempts to disentangle the mechanistic link of MAFLD from COVID-19 complexity and to improve knowledge on its pathophysiology.

RevDate: 2021-09-26

Devrim-Lanpir A, İlktaç HY, Wirnitzer K, et al (2021)

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design.

PloS one, 16(9):e0255952.

BACKGROUND: The effect of vegan diets on metabolic processes in the body is still controversial in ultra endurance athletes. The study aims to determine gut microbiome adaptation to extreme exercise according to vegan or omnivore diet consumed in ultra-marathoners. We also seek to evaluate long-term vegan diets' effects on redox homeostasis, and muscle fatigue, and assess energy availability.

METHODS: Seventy participants will be assigned to the study, including 35 vegan ultra-marathoners and 35 omnivores competing in the Sri-Chinmoy ultra marathon race. Research data will be collected from the participants at four steps (three visits to the research laboratory and the race day) throughout the study. At the first visit (seven days before the race), fecal samples, and anthropometric measurements will be collected. Body composition will be measured using DXA. Participants will be informed about keeping detailed food records and will be asked to record their diet data and activity logs during the entire study period. At second visit, maximum oxygen consumption will be measured on treadmill. On race day, blood samples will be collected immediately before, and 0. min, 2 hours, and 24 hours after the race. Body weight will be measured before and after the race. The blood and fecal samples will be stored at -80 C until analysis. Plasma malondialdehyde, reactive oxygen metabolites, total antioxidant capacity, Heatshockprotein-70, and serum Orosomucoid-1 will be analyzed in blood samples. Fecal samples will be analyzed with shotgun metagenomic analysis and interpreted using bioinformatics pipeline (HumanN2). Statistical tests will be analyzed using SPSS version 23.0 and R Software.

DISCUSSION: Study findings will determine the effects of the vegan diet on sports performance, revealing the multiple interactions between host and gut microbiome at the whole metagenomic level. Additionally, results will show the possible adaptation throughout the race by analyzing blood and fecal samples. Furthermore, by assessing energy availability and determining host-metabolite crosstalk for ultra-endurance athletes, possible nutritional deficiencies can be identified. Thus, advanced nutritional strategies can be developed based on metabolic needs.

TRIAL REGISTRATION: Current controlled trials, ISRCTN registry 69541705. Registered on 8 December 2019.

RevDate: 2021-09-23

Singh S, Pragman AA, LN Segal (2021)

Balancing Benefits and Risks: Do ICS Modify the Lung Microbiome?.

American journal of respiratory and critical care medicine [Epub ahead of print].

RevDate: 2021-09-24

Fung C, Rusling M, Lampeter T, et al (2021)

Automation of QIIME2 Metagenomic Analysis Platform.

Current protocols, 1(9):e254.

QIIME is a widely used, open-source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2.org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparing files and folders Support Protocol 1: Preparing your data for QAP Support Protocol 2: Understanding automated options Basic Protocol 2: Importing into QIIME Basic Protocol 3: DADA2: Filtering, trimming, merging pairs Basic Protocol 4: Performing core metrics Basic Protocol 5: Sample filtering by metadata Basic Protocol 6: Alpha diversity metrics Basic Protocol 7: Cross-sectional beta diversity Basic Protocol 8: Longitudinal feature volatility Basic Protocol 9: Sample classification.

RevDate: 2021-09-25

Paul D, Mondal SK, SM Mandal (2021)

Biologia Futura: use of biocides during COVID-19-global reshuffling of the microbiota.

Biologia futura, 72(3):273-280.

Aim The article reviews the current usage of biocides during this lockdown period for sanitizing our living areas due to the pandemic and discusses the pros and cons. Subject COVID-19 spread like wildfire to over 200 countries of the world across all continents. The causative agent, novel coronavirus (SARS-CoV-2) is being counter attacked by a thorough application of disinfectants and sterilants. However, the virus mutated over 30 times during this global pandemic, creating panic and leading to enhanced pathogenicity and consequently to more stringent sanitation measures for controlling it. However, excessive use of different types of biocides for disinfecting surfaces is highly alarming in several cases. Extensive application of biocides affects the microbial flora, leading to an abrupt decrease in the number and diversity of beneficial microbes that may directly affect the functioning of nutrient cycles. Results The increased concentration of biocides in agricultural land via surface water or pond water indirectly affect the soil and water ecosystem, soil aggregation and fertility. This will also lead to the flourishing of resistant strains due to loss of competition from the other species, which fail to persist after prolonged use of biocides. Conclusion It is necessary to realize the environmental impacts of biocides and sterilants. It is the right time to stop their entry into the agricultural ecosystem by following adequate management strategies and complete neutralization.

RevDate: 2021-09-23

Huang X, Li L, Ling Z, et al (2021)

Gut microbiome diversity mediates the association between right dorsolateral prefrontal cortex and anxiety level.

Brain imaging and behavior [Epub ahead of print].

Despite the fast growing interest in the impact of microbiome-gut-brain interaction on regulating emotional behavior in animals, the underlying mechanisms on how brain anatomy together with gut microbiotic condition jointly influence emotional state in healthy human volunteers remain largely unknown and hypothetic. Here, high-resolution structural magnetic resonance imaging data, stool samples, and psychological assessment results on anxiety level were collected from 61 healthy adults. Voxel-based morphometry was used to assess gray matter (GM) volumes, whereas 16s rRNA gene sequencing was used for bacterial classification. Correlation and mediation analysis were conducted to quantify the relationships among regional GM volume, gut microbiome diversity, and anxiety level. We observed that anxiety level was negatively correlated with GM volume in the right dorsolateral prefrontal cortex and alpha diversity index of gut microbiome. Additional mediation analysis revealed the indirect effect of dorsolateral prefrontal cortex GM volume on anxiety level via gut microbiome diversity. Our findings provide potential evidence of the microbiome-gut-brain interactions and their association with anxiety, highlighting gut microbiome diversity as a mediator that influences the relationship between brain morphometry and anxiety level.

RevDate: 2021-09-23

Wu H, Zhang Z, Wang J, et al (2021)

Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome.

Microbial ecology [Epub ahead of print].

Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.

RevDate: 2021-09-23

Wang T, Ling W, Plantinga AM, et al (2021)

Testing microbiome association using integrated quantile regression models.

Bioinformatics (Oxford, England) pii:6374494 [Epub ahead of print].

MOTIVATION: Most existing microbiome association analyses focus on the association between microbiome and conditional mean of health or disease-related outcomes, and within this vein, vast computational tools and methods have been devised for standard binary or continuous outcomes. However, these methods tend to be limited either when the underlying microbiome-outcome association occurs somewhere other than the mean level, or when distribution of the outcome variable is irregular (e.g., zero-inflated or mixtures) such that conditional outcome mean is less meaningful. We address this gap by investigating association analysis between microbiome compositions and conditional outcome quantiles.

RESULTS: We introduce a new association analysis tool named MiRKAT-IQ within the Microbiome Regression-based Kernel Association Test framework using Integrated Quantile regression models to examine the association between microbiome and the distribution of outcome. For an individual quantile, we utilize the existing kernel machine regression framework to examine the association between that conditional outcome quantile and a group of microbial features (e.g., microbiome community compositions). Then, the goal of examining microbiome association with the whole outcome distribution is achieved by integrating all outcome conditional quantiles over a process, and thus our new MiRKAT-IQ test is robust to both the location of association signals (e.g.,mean, variance, median) and the heterogeneous distribution of the outcome. Extensive numerical simulation studies have been conducted to show the validity of the new MiRKAT-IQ test. We demonstrate the potential usefulness of MiRKAT-IQ with applications to actual biological data collected from a previous microbiome study.

AVAILABILITY: R codes to implement the proposed methodology is provided in the MiRKAT package, which is available on CRAN.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2021-09-23

Bodein A, Scott-Boyer MP, Perin O, et al (2021)

timeOmics: an R package for longitudinal multi-omics data integration.

Bioinformatics (Oxford, England) pii:6374493 [Epub ahead of print].

MOTIVATION: Multi-omics data integration enables the global analysis of biological systems and discovery of new biological insights. Multi-omics experimental designs have been further extended with a longitudinal dimension to study dynamic relationships between molecules. However, methods that integrate longitudinal multi-omics data are still in their infancy.

RESULTS: We introduce the R package timeOmics, a generic analytical framework for the integration of longitudinal multi-omics data. The framework includes pre-processing, modelling and clustering to identify molecular features strongly associated with time. We illustrate this framework in a case study to detect seasonal patterns of mRNA, metabolites, gut taxa, and clinical variables in patients with diabetes mellitus from the integrative Human Microbiome Project.

AVAILABILITY: timeOmics is available on Bioconductor and github.com/abodein/timeOmics.

RevDate: 2021-09-23

Iyer V, Raut J, A Dasgupta (2021)

Impact of pH on growth of Staphylococcus epidermidis and Staphylococcus aureus in vitro.

Journal of medical microbiology, 70(9):.

The pH of skin is critical for skin health and resilience and plays a key role in controlling the skin microbiome. It has been well reported that under dysbiotic conditions such as atopic dermatitis (AD), eczema, etc. there are significant aberrations of skin pH, along with a higher level of Staphylococcus aureus compared to the commensal Staphylococcus epidermidis on skin. To understand the effect of pH on the relative growth of S. epidermidis and S. aureus, we carried out simple in vitro growth kinetic studies of the individual microbes under varying pH conditions. We demonstrated that the growth kinetics of S. epidermidis is relatively insensitive to pH within the range of 5-7, while S. aureus shows a stronger pH dependence in that range. Gompertz's model was used to fit the pH dependence of the growth kinetics of the two bacteria and showed that the equilibrium bacterial count of S. aureus was the more sensitive parameter. The switch in growth rate happens at a pH of 6.5-7. Our studies are in line with the general hypothesis that keeping the skin pH within an acidic range is advantageous in terms of keeping the skin microbiome in balance and maintaining healthy skin.

RevDate: 2021-09-23

Sawant S, Dugad J, Parikh D, et al (2021)

Identification & correlation of bacterial diversity in oral cancer and long-term tobacco chewers- A case-control pilot study.

Journal of medical microbiology, 70(9):.

Introduction. Squamous cell carcinoma is a highly aggressive type of oral cancer (OC). It is the most common cancer among men, and accounts for almost 90 % of all oral cancers in India. Consumption of tobacco is a leading factor contributing to maximum oral cancer incidences as per the WHO.Hypothesis/Gap statement. Researchers reported a direct association of microorganisms with dysbiosis in various oral lesions including oral cancer. However, there is a dearth of information related to compositional changes in the oral microbiome in long-term tobacco chewers and the Indian oral cancer population.Aim. The aim of this study was to identify and correlate the bacterial diversity in the oral cavity of tobacco chewers, patients with oral cancer and healthy subjects in the Indian population.Methods. Oral rinse samples were collected for ten subjects in each group followed by DNA extraction. The variable regions of the bacterial 16S rRNA gene (V6-V8) were amplified, sequenced, processed, and analysed using QIIME2 platform to assess alpha and beta diversity between the study groups.Results. This pilot study showed genus Streptococcus dominated the control group (18.54 %), and the abundance decreased in tobacco and OC group (9.63 and 5.45% respectively); whereas genus Prevotella dominated the tobacco and OC group (21.01 and 26.03% respectively). A shift in abundance of microbiome was observed from control population to oral cancer via the tobacco chewing population. Maximum alpha diversity of oral microbiome was found in Indian tobacco chewers. Beta diversity of tobacco chewers was similar to both the healthy population as well as oral cancer patients suggesting transitioning of the oral microbiome from healthy to oral cancer microbiome via the tobacco chewers microbiome.Conclusion. The data provides evidence of oral bacterial dysbiosis due to tobacco chewing habits that can further lead to progression towards cancer.

RevDate: 2021-09-25

Hirano R, Sakanaka M, Yoshimi K, et al (2021)

Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile.

Gut microbes, 13(1):1973835.

Certain existing prebiotics meant to facilitate the growth of beneficial bacteria in the intestine also promote the growth of other prominent bacteria. Therefore, the growth-promoting effects of β-galactosides on intestinal bacteria were analyzed. Galactosyl-β1,4-l-rhamnose (Gal-β1,4-Rha) selectively promoted the growth of Bifidobacterium. Bifidobacterium longum subsp. longum 105-A (JCM 31944) has multiple solute-binding proteins belonging to ATP-binding cassette transporters for sugars. Each strain in the library of 11 B. longum subsp. longum mutants, in which each gene of the solute-binding protein was disrupted, was cultured in a medium containing Gal-β1,4-Rha as the sole carbon source, and only the BL105A_0502 gene-disruption mutant showed delayed and reduced growth compared to the wild-type strain. BL105A_0502 homolog is highly conserved in bifidobacteria. In a Gal-β1,4-Rha-containing medium, Bifidobacterium longum subsp. infantis JCM 1222T, which possesses BLIJ_2090, a homologous protein to BL105A_0502, suppressed the growth of enteric pathogen Clostridioides difficile, whereas the BLIJ_2090 gene-disrupted mutant did not. In vivo, administration of B. infantis and Gal-β1,4-Rha alleviated C. difficile infection-related weight loss in mice. We have successfully screened Gal-β1,4-Rha as a next-generation prebiotic candidate that specifically promotes the growth of beneficial bacteria without promoting the growth of prominent bacteria and pathogens.

RevDate: 2021-09-23

Karunatillaka I, Jaroszewski L, A Godzik (2021)

Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome.

Proteins [Epub ahead of print].

Several plastic degrading enzymes have been described in the literature, most notably PETases that are capable of hydrolyzing polyethylene terephthalate (PET) plastic. One of them, the PETase from Ideonella sakaiensis, a bacterium isolated from environmental samples within a PET bottle recycling site, was a subject of extensive studies. To test how widespread PETase functionality is in other bacterial communities, we used a cascade of BLAST searches in the JGI metagenomic datasets and showed that close homologs of I. sakaiensis PETase can also be found in other metagenomic environmental samples from both human-affected and relatively pristine sites. To confirm their classification as putative PETases, we verified that the newly identified proteins have the PETase sequence signatures common to known PETases and that phylogenetic analyses group them with the experimentally characterized PETases. Additionally, docking analysis was performed in order to further confirm the functional assignment of the putative environmental PETases.

RevDate: 2021-09-23

von Schassen H, Andresen V, P Layer (2021)

[The new guideline on irritable bowel syndrome: what is new?].

Deutsche medizinische Wochenschrift (1946), 146(19):1243-1248.

IRRITABLE BOWEL SYNDROME: WHAT IS NEW?: The following refers only to irritable bowel syndrome (IBS) in adults. The new guideline includes a separate section on IBS for paediatric patients. Irritable bowel syndrome (IBS) presents as a heterogeneous picture with chronic abdominal complaints related to the bowel. These are usually accompanied by changes in bowel movements and lead to impaired quality of life. The genesis is multifactorial and there are complex underlying pathophysiological mechanisms associated with IBS. Thus, disturbances in various components of the gut-brain axis and the increasing importance of the microbiome can be identified. Various psychological comorbidities also play a role.

DIAGNOSTICS: The diagnosis is made by a thorough anamnesis and symptom-oriented exclusion of important differential diagnoses. A subdivision into different subtypes depending on the main symptoms is beneficial for the further management of IBS patients. The diagnosis of IBS should be made as early as possible after reliable exclusion of the important differential diagnoses. If diarrhoea dominates as a symptom, a detailed differential diagnosis and functional diagnosis should be carried out.

THERAPY: There is no proven causal and no established standard therapy. Due to the variable genesis and symptom manifestation of IBS, a broad spectrum of therapy options results, whereby there is no individual prediction regarding effectiveness and therefore every therapy is initially probationary. Symptom-independent general therapies that can be used for all subtypes include dietary methods (e. g. the low-FODMAP diet), probiotics, psychotherapy methods and complementary medicine. The choice of symptom-dependent drug treatments is made according to the subtype/main symptom. In the case of diarrhoea, bile acid binders, the non-absorbable antibiotic rifaximin or, in individual cases, 5-HT3-antagonists can be used in addition to loperamide. In constipation, prucalopride and linaclotide have value in addition to the use of soluble fibre and macrogol/other laxatives. For abdominal pain/cramps, studies show good results for spasmolytics, especially peppermint oil, and for tricyclic-type antidepressants. For the main symptom of flatulence, probiotics, rifaximin and especially the low-FODMAP diet can show positive results in studies.

RevDate: 2021-09-23

Shokoohi E, Mashela PW, RAR Machado (2021)

Bacterial communities associated with Zeldia punctata, a bacterivorous soil-borne nematode.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

Soil inhabiting organisms are important determinants of agroecosystem productivity. Understanding the composition, the abundance, and the type of interactions established by soil microorganisms is therefore crucial to design strategies to improve agricultural practices and agroecosystem management. In this study, we collected Zeldia punctata nematodes in maize fields in South Africa and profiled their associated bacterial communities using next-generation sequencing. We observed that Z. punctata nematodes establish associations with ecologically diverse bacterial species. The most abundant species observed are Pseudomonas syringae, a phytopathogenic bacterial complex; Lactobacillus paraplantarum, a broadly distributed bacterial species that is present in soils, water bodies, and animal intestinal tracts and has certain probiotic and antimicrobial properties; and Melissococcus plutonius, a serious pathogenic bacterial species that causes brood disease in honeybees. Our study contributes to a better understanding of the soil bacterial communities associated with nematodes in maize agricultural soils in South Africa and unravels the presence of diverse detrimental and beneficial nematode-associated bacteria.

RevDate: 2021-09-25

Wong KR, Sgro M, Yamakawa GR, et al (2021)

Gut microbiome depletion and repetitive mild traumatic brain injury differentially modify bone development in male and female adolescent rats.

Bone reports, 15:101123.

Dysregulation of the gut microbiome has been shown to disrupt both bone formation and bone resorption in several preclinical and clinical models. However, the role of microbiome in adolescent bone development remains poorly understood. This effect of disrupted bone development may be more pronounced during adolescence, when bone development is vulnerable to environmental stimuli and external insults (e.g., antibiotic treatment and traumatic brain injury), as this is a critical window of development. Therefore, in this study, we sought to investigate the effect of repetitive mild traumatic brain injury (RmTBI) and gut microbiome depletion by antibiotic treatment on femur length and bone density in male and female adolescent Sprague Dawley rats. Rats were randomly assigned to receive standard or antibiotic autoclaved drinking water and to receive sham or RmTBIs injuries. Using micro-computed tomography (μCT), we found sexually dimorphic changes in adolescent bone development in response to microbiome depletion and RmTBI. Specifically, gut microbiome depletion stunted femur growth in males and altered cross sectional bone area (CSA), bone area fraction, and the bone volume of low and mid density bone in the distal metaphyseal region of the femur. Conversely, RmTBI and antibiotic treatment individually disrupted bone growth, bone area fraction, and bone volume of high-density bone within the distal metaphyseal region of the femur in females, but not when combined. Therefore, findings from this study indicate that gut microbiome and RmTBI may alter bone development in a sex-dependent manner during adolescence.

RevDate: 2021-09-25

Wang J, Mason CJ, Ju X, et al (2021)

Parasitoid Causes Cascading Effects on Plant-Induced Defenses Mediated Through the Gut Bacteria of Host Caterpillars.

Frontiers in microbiology, 12:708990.

Koinobiont endoparasitoid wasps whose larvae develop inside a host insect alter several important facets of host physiology, potentially causing cascading effects across multiple trophic levels. For instance, the hijacking of the host immune responses may have effects on how insects interact with host plants and microbial associates. However, the parasitoid regulation of insect-plant-microbiome interactions is still understudied. In this study, we used the fall armyworm (FAW), Spodoptera frugiperda, and the braconid parasitoid Cotesia marginiventris to evaluate impacts of parasitism on the gut microbiome of FAW larvae, and respective maize plant defense responses. The level of reactive oxygen species and the microbial community in larval gut underwent significant changes in response to parasitism, leading to a significant reduction of Enterococcus, while elevating the relative abundance of Pseudomonas. FAW with parasitism had lower glucose oxidase (GOX) activity in salivary glands and triggered lower defense responses in maize plants. These changes corresponded to effects on plants, as Pseudomonas inoculated larvae had lower activity of salivary GOX and triggered lower defense responses in maize plants. Our results demonstrated that parasitism had cascading effects on microbial associates across trophic levels and also highlighted that insect gut bacteria may contribute to complex interrelationships among parasitoids, herbivores, and plants.

RevDate: 2021-09-25

Jiang F, Gao H, Qin W, et al (2021)

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer.

Frontiers in microbiology, 12:699797.

Musk deer (Moschus spp.) is a globally endangered species due to excessive hunting and habitat fragmentation. Captive breeding of musk deer can efficiently relieve the hunting pressure and contribute to the conservation of the wild population and musk supply. However, its effect on the gut microbiota of musk deer is unclear. Recent studies have indicated that gut microbiota is associated with host health and its environmental adaption, influenced by many factors. Herein, high-throughput sequencing of the 16S rRNA gene was used based on 262 fecal samples from forest musk deer (M. berezovskii) (FMD) and 90 samples from alpine musk deer (M. chrysogaster) (AMD). We sought to determine whether seasonal variation can affect the structure and function of gut microbiota in musk deer. The results demonstrated that FMD and AMD had higher α-diversity of gut microbiota in the cold season than in the warm season, suggesting that season change can affect gut microbiota diversity in musk deer. Principal coordinate analysis (PCoA) also revealed significant seasonal differences in the structure and function of gut microbiota in AMD and FMD. Particularly, phyla Firmicutes and Bacteroidetes significantly dominated the 352 fecal samples from captive FMD and AMD. The relative abundance of Firmicutes and the ratio of Firmicutes to Bacteroidetes were significantly decreased in summer than in spring and substantially increased in winter than in summer. In contrast, the relative abundance of Bacteroidetes showed opposite results. Furthermore, dominant bacterial genera and main metabolic functions of gut microbiota in musk deer showed significant seasonal differences. Overall, the abundance of main gut microbiota metabolic functions in FMD was significantly higher in the cold season. WGCNA analysis indicated that OTU6606, OTU5027, OTU7522, and OTU3787 were at the core of the network and significantly related with the seasonal variation. These results indicated that the structure and function in the gut microbiota of captive musk deer vary with seasons, which is beneficial to the environmental adaptation and the digestion and metabolism of food. This study provides valuable insights into the healthy captive breeding of musk deer and future reintroduction programs to recover wild populations.

RevDate: 2021-09-25

Yang X, Zhang X, Yang W, et al (2021)

Gut Microbiota in Adipose Tissue Dysfunction Induced Cardiovascular Disease: Role as a Metabolic Organ.

Frontiers in endocrinology, 12:749125.

The gut microbiome has emerged as a key regulator of host metabolism. Accumulating evidence has indicated that the gut microbiota is involved in the development of various human diseases. This association relies on the structure and metabolites of the gut microbiota. The gut microbiota metabolizes the diet ingested by the host into a series of metabolites, including short chain fatty acids, secondary bile acids, trimethylamine N-oxide, and branched-chain amino acids, which affects the physiological processes of the host by activating numerous signaling pathways. In this review, we first summarize the various mechanisms through which the gut microbiota influences adipose tissue dysfunction and metabolic processes that subsequently cause cardiovascular diseases, highlighting the complex interactions between gut microbes, their metabolites, and the metabolic activity of the host. Furthermore, we investigated the current status of clinical therapies for adipose tissue dysfunction directed at the gut microbiota. Finally, we discuss the challenges that remain to be addressed before this field of research can be translated to everyday clinical practice.

RevDate: 2021-09-23

Schneider KM, Candels LS, Hov JR, et al (2021)

Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling.

Nature metabolism, 3(9):1228-1241.

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology for which there are no approved therapeutic options. Patients with PSC display changes in gut microbiota and in bile acid (BA) composition; however, the contribution of these alterations to disease pathogenesis remains controversial. Here we identify a role for microbiota-dependent changes in BA synthesis that modulates PSC pathophysiology. In a genetic mouse model of PSC, we show that loss of microbiota-mediated negative feedback control of BA synthesis results in increased hepatic BA concentrations, disruption of bile duct barrier function and, consequently, fatal liver injury. We further show that these changes are dependent on decreased BA signalling to the farnesoid X receptor, which modulates the activity of the rate-limiting enzyme in BA synthesis, CYP7A1. Moreover, patients with advanced stages of PSC show suppressed BA synthesis as measured by serum C4 levels, which is associated with poor disease prognosis. Our preclinical data highlight the microbiota-dependent dynamics of BA metabolism in cholestatic liver disease, which could be important for future therapies targeting BA and gut microbiome interactions, and identify C4 as a potential biomarker to functionally stratify patients with PSC and predict disease outcomes.

RevDate: 2021-09-23

Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, et al (2021)

Mass spectrometry-based metabolomics in microbiome investigations.

Nature reviews. Microbiology [Epub ahead of print].

Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.

RevDate: 2021-09-24

Chaudhari SN, McCurry MD, AS Devlin (2021)

Chains of evidence from correlations to causal molecules in microbiome-linked diseases.

Nature chemical biology, 17(10):1046-1056.

Human-associated microorganisms play a vital role in human health, and microbial imbalance has been linked to a wide range of disease states. In this Review, we explore recent efforts to progress from correlative studies that identify microorganisms associated with human disease to experiments that establish causal relationships between microbial products and host phenotypes. We propose that successful efforts to uncover phenotypes often follow a chain of evidence that proceeds from (1) association studies; to (2) observations in germ-free animals and antibiotic-treated animals and humans; to (3) fecal microbiota transplants (FMTs); to (4) identification of strains; and then (5) molecules that elicit a phenotype. Using this experimental 'funnel' as our guide, we explore how the microbiota contributes to metabolic disorders and hypertension, infections, and neurological conditions. We discuss the potential to use FMTs and microbiota-inspired therapies to treat human disease as well as the limitations of these approaches.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )