Tag Archives: animal models

July 8, 2022

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A selection of some great microbiome research and I’ve highlighted some resources for spatial transcriptomics for my non-microbiome picks.

General microbiome

Host control and the evolution of cooperation in host microbiomes – Sharp & Foster. Nature Communications

Effect of Helicobacter pylori Eradication on Gastric Cancer Prevention: Updated Report From a Randomized Controlled Trial With 26.5 Years of Follow-up – Yan et al. Gastroenterology

Gut microbiome

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome – Xu et al. Microbiome

Long-Term Effects of Developmental Exposure to Oxycodone on Gut Microbiota and Relationship to Adult Behaviors and Metabolism – Lyu et al. mSystems

Biogeographic variation and functional pathways of the gut microbiota in celiac disease – Constante et al. Gastroenterology.

Animal experiments

Akkermansia muciniphila prevents cold-related atrial fibrillation in rats by modulation of TMAO induced cardiac pyroptosis – Luo et al. eBioMedicine

Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome – Machado et al. Cell Reports.

Virome

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome – Jonge et al. Nature Communications

Respiratory microbiome

Host lung microbiota promotes malaria-associated acute respiratory distress syndrome – Mukherjee et al. Nature Communications

Bioinformatics

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. BMC Bioinformatics

Non-microbiome picks

As spatial transcriptomics grows in popularity you might be interested in some recent reviews & examples of the technology in use

An introduction to spatial transcriptomics for biomedical research – Williams et al. Genome Medicine

Deciphering tissue structure and function using spatial transcriptomics – Walker et al. Communications biology

Method of the Year: spatially resolved transcriptomics – Marx. Nature Methods

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays – Chen et al. Cell (The recent famous Cell cover using Stereo-Seq)

Museum of spatial transcriptomics – Moses & Pachter. Nature Methods

July 5, 2022

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Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

June 10, 2022

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Several great microbiome papers out today including a review on rethinking healthy eating in Cell Host & Microbe, a large population study on the development of the infant gut microbiome (n=1900) in Science, and two studies showcasing metabolomics predictive value for recurrent CDI and NAFLD.  

Gut Microbiome

[REVIEW] Rethinking healthy eating in light of the gut microbiome – Armet et al. Cell Host & Microbe.

Gut metabolites predict Clostridioides difficile recurrence – Dawkins et al. Microbiome

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles – Olm et al. Science

Risk assessment with gut microbiome and metabolite markers in NAFLD development. Leung et al. Science Translational Medicine.

Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer – Bi et al. Nature Communications

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. Cell Host & Microbe

Animal experiments

Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome – Gao et al. npj Biofilms & Microbiomes

Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs – Hui et al. npj Biofilms & Microbiomes

Virome

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome – Li et al. iScience

Bioinformatics

Phylogeny-guided microbiome OTU-specific association test (POST) – Huang et al. Microbiome

May 3, 2022

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General microbiome

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Worby et al. Nature Microbiology. 2022

Human gut microbiome

Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins – Yang et al. Gut

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Button et al. Cell Host & Microbe

Gut microbial similarity in twins is driven by shared environment and aging – Vilchez-Vargas et al. eBioMedicine

Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. Kwan et al. mSystems

Human respiratory & oral microbiome

Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation – Widder et al. Microbiome

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective – Zhang et al. mBio

Animal experiments

Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats – Hu et al. mSystems

Water/Extremophile microbiome

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans – Duncan et al. Microbiome

Bioinformatics

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Martino et al. mSystems

BiomeHorizon: Visualizing Microbiome Time Series Data in R – Fink et al. mSystems

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. Yarmosh et al. mSphere

Non microbiome picks

Ancestry-inclusive dog genomics challenges popular breed stereotypes – Morrill et al. Science. 

Dietary fibre in hypertension and cardiovascular disease management: systematic review and meta-analyses – Reynolds et al. BMC Medicine

March 25, 2022

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Human gut microbiome

In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort – Wosinska et al. Microorganisms

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes – Ting et al. Gut

Human respiratory microbiome

Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza et al. Nature Communications

Probiotics

Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice – Daniel et al. Nature Communications

Animal experiments

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue – Agranyoni et al. npj biofilms and microbiomes

The microbiota restrains neurodegenerative microglia in a model of amyotrophic lateral sclerosis – Cox et al. Microbiome

Water & Extremophile microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. Microbiome

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Murakami et al. Microbiome.

Virome

Phages and their satellites encode hotspots of antiviral systems – Rousset et al. Cell Host & Microbe

Fungi

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Li et al. Cell Host & Microbe

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors – Sharma et al. npj Biofilms and microbiomes

Bioinformatics

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases – Armstrong et al. mSystems

February 21, 2022

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Today’s digest features two excellent metagenome – metabolome association studies in Nature Medicine and a great article in Genome Biology showing that the sustained software development is what you should look for in a bioinformatic software, not what journal it was published in.

Human gut microbiome

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease – Talmor-Barkan et al. Nature Medicine. 

Microbiome and metabolome features of the cardiometabolic disease spectrum – Fromentin et al. Nature Medicine

Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort – Aasmets et al. Nature Communications

Animal Microbiome

Drivers of gut microbiome variation within and between groups of a wild Malagasy primate – Rudolph et al. Microbiome

Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle – Xue et al. Microbiome

The gut microbiome and antibiotic resistome of chronic diarrhea rhesus macaques (Macaca mulatta) and its similarity to the human gut microbiome – Yang et al Microbiome

Virome

Independent host- and bacterium-based determinants protect a model symbiosis from phage predation – Lynch et al. Cell Reports

Virome characterization of game animals in China reveals a spectrum of emerging pathogens – He et al. Cell

Water and extremophile microbiome

Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal – Freudenthal et al. Microbiome

Bioinformatics

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks – Zhou et al. Microbiome

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software – Gardner et al. Genome Biology

Non-Microbiome picks

If you’ve listened to The Dropout podcast you might like this editorial.  

The post-Theranos world – Nature Biotechnology. 

December 24, 2021

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Happy Holidays from the MicrobiomeDigest Team!

Human and General Microbiome

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response – Christine N Spencer – Science 

Association of the gut microbiota and fecal short-chain fatty acids with skeletal muscle mass and strength in children – Fengyan Chen – FASEB Journal

Characteristics of Fecal Microbiota and Machine Learning Strategy for Fecal Invasive Biomarkers in Pediatric Inflammatory Bowel Disease – Xinqiong Wang – Frontiers in Cellular and Infection Microbiology

The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism – Jennifer A Buffa – Nature Microbiology

Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis – Liujing Huang – Frontiers in Cellular and Infection Microbiology

Natural selection for imprecise vertical transmission in host-microbiota systems – Marjolein Bruijning – Nature Ecology & Evolution

Comparison of the airway microbiota in children with chronic suppurative lung disease – Bushra Ahmed – BMJ Open Respiratory Research

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections – Letícia T Oliveira – Journal of Medical Microbiology

Oral Colonization by Entamoeba gingivalis and Trichomonas tenax: A PCR-Based Study in Health, Gingivitis, and Periodontitis – Alaa Yaseen – Frontiers in Cellular and Infection Microbiology

Human and General Microbiome – Reviews

Systematic Review: Probiotics Evaluation in Oncological Surgery: A Systematic Review of 36 Randomized Controlled Trials Assessing 21 Diverse Formulations – Elise Cogo – Current Oncology

Review: Untangling human milk oligosaccharides and infant gut microbiome – Andrea C Masi – iScience

Review: Periodontal Disease: The Good, The Bad, and The Unknown – Lea M Sedghi – Frontiers in Cellular and Infection Microbiology

Review: Clinical implications of preterm infant gut microbiome development – David B Healy – Nature Microbiology

COVID19 and Microbiome

Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach – Md Mizanur Rahaman – Journal of Medical Virology

Animal Microbiome

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development – Daphne Perlman – Annual Review of Animal Biosciences

Playing by their own rules: the vertebrate archaeome – Sarah M Hird – Trends in Microbiology

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii – Victoria A Ingham – PLoS Genetics

Comparative Study of Intestinal Microbiota Composition of Six Edible Fish Species – Tamir Ofek – Frontiers in Microbiology

Captivity Influences the Gut Microbiome of Rhinopithecus roxellana – Xiaochen Wang – Frontiers in Microbiology

Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease – Rodrigo Santibáñez – Veterinary Sciences

Beneficial Microbes and Compounds

Evaluation of Microbiome Alterations Following Consumption of BIOHM, a Novel Probiotic – Mahmoud A Ghannoum – Current Issues in Molecular Biology

Lactobacillus rhamnosus attenuates Thai chili extracts induced gut inflammation and dysbiosis despite capsaicin bactericidal effect against the probiotics, a possible toxicity of high dose capsaicin – Wimonrat Panpetch – PloS ONE

Plant and Soil Microbiome

May the dark be with roots: A perspective on how root illumination may bias in vitro research on plant-environment interactions – Javier Cabrera – The New Phytologist

Site and land-use associations of soil bacteria and fungi define core and indicative taxa – Gschwend Florian – FEMS Microbiology Ecology

Bioinformatics

tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data – Johannes Ostner – Frontiers in Genetics

December 14, 2021

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Today’s digest contains several great recent papers, but in particular I’d like to highlight a Nature Methods paper on applying network biology approaches to the microbiome, and a Nature paper which disentangles the effects of drugs and disease on host and microbiome.

General microbiome

Fast and flexible analysis of linked microbiome data with mako – Röttjers & Faust – Nature Methods. 

Combinatorial, additive and dose-dependent drug–microbiome associations – Forslund et al. Nature 

Mammalian gut metabolomes mirror microbiome composition and host phylogeny – Gregor et al. – ISME 

Human gut microbiome

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity – Wang et al. – Genome Biology

Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM – Chen et al.  – Microbiome

Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement – Jacobs et al. – Microbiome. 

Human oral microbiome

Impact of sleep on the microbiome of oral biofilms – Sotozono et al. – PLOS One

Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine – Wigand et al. BMC Oral Health

Animal Experiments

The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiota – Blake et al. – Cell Reports Medicine

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Zhang et al. – ISME

Sexual dimorphism in glucose metabolism is shaped by androgen-driven gut microbiome – Gao et al. – Nature Communications

June 27, 2020

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Shalom from Israel and a Happy world microbiome day!

Yes, it is a true day! celebrating the huge diversity of microbes around us, above us, below us and inside us. Check the day’s official website for more information, and take the weekend to appreciate this amazing field and your own personal contribution to advancing our knowledge about microbial communities on our planet.

Personally, I did my undergrad in Ecology and Evolution, confidence that I’ll my scientific career will focus on plant ecology and distribution, or at least large animals. Microbiology classes and introduction labs bored me, and I did my best to avoid this topic. But all of a sudden, during my Master’s degree (where I worked on a pathogenicity mechanism of postharvest disease-causing bacteria), I fell in love with microbiology in general, and specific bacterial communities. The huge untapped diversity, the unbelievable functions and the amazing interactions needed to maintain a functional community of these invisible inhabitants just fascinated me. Today, as a Ph.D. student exploring secondary metabolites gene clusters in soil and root microbiome, I’m a super-fan of the bacterial world.

How did you end up being microbiome suckers? Feel free to share your stories here as a comment, on MD FB page, or directly on tweeter.

Today’s digest include several microbimoe papers of animal midels (including ‘dirty mice’), diseased tomatoes taxonomical and functional microbiome profile, AND- a sweet reminder of the pre-COVID-19 world, with an analysis of the dust microbiome of a plane (remember this vehicle?).

Human and Animal Models microbiome

**Microbial transmission in animal social networks and the social microbiome, Amar Sarkar , Nat. Eco. Evo.

Does entry to center-based childcare affect gut microbial colonization in young infants?, Gerben D. A. Hermes, Scientific Reports

Serum metabolites reflecting gut microbiome
alpha diversity predict type 2 diabetes, Cristina Menni, Gut microbes

**New Insights into the Immune System Using Dirty Mice, Sara E. Hamilton, J. Immunology.

Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics,Josefin Olausson , bioRxiv

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats, Katherine.Maki, Phys. Geno.

Animal microbiome

Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria, Hamutahl Cohen, Microbial Ecology

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet, Tahliyah S. Mims, bioRxiv

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry, Eliane Cristina Gruszka Vendruscolo, Sci. Tot. Env.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation, Zhipeng Li, FEMS Micro. Eco.

Soil and Plant microbiome

Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici, Xin Zhou, Microbial Ecology

Insights into drylands biocrust microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA, Nuttapon Pombubpa, FEMS Micro. Eco.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach, Laura Díaz-García, Microbial Ecology

Shotgun Metagenomics Of Dust Microbiome From Flight Deck And Cabin In Civil Aviation Aircraft, Yu Sun, Indoor Air

Bioinformatics

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data, D.R. Finn , FEMS Micro. Eco.

May 13, 2020

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Happy Wednesday, y’all! Before we get to today’s papers, I wanted to let everyone know about a webinar happening on June 3rd at 12:00 PM E.T. called “Unraveling the link between the gut microbiome, human health, and disease.” Tomoya Yamashita, M.D., Ph.D. from Kobe University Graduate School of Medicine and Meredith Hullar, Ph.D. from the Fred Hutchinson Cancer Research Center will both be speaking. If you’re interested you can register here.

Now onto the highlights! We have some super interesting research to share with you today including an examination of the efficacy of transplanting the human gut microbiota into mice and its impact on studying immunological responses; evidence that early-life intestinal colonizers may influence brain development; and a new tool, pepFUNK, which uses a peptide-centric approach to identify KEGG pathways in metaproteomic datasets. Enjoy!

General microbiome
Human Microbiota-Transplanted C57BL/6 Mice and Offspring Display Reduced Establishment of Key Bacteria and Reduced Immune Stimulation Compared to Mouse Microbiota-Transplantation. Lundberg, R. et al. Scientific Reports.

Review: The role of the microbiome in the neurobiology of social behaviour. Sarkar, A. et al. Biological Reviews.

Pregnancy and early life
Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Brink, L.R. et al. The American Journal of Clinical Nutrition.

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers. Lugli, A.G. et al. FEMS Microbiology Ecology.

Human respiratory microbiome
Bioorthogonal Non-Canonical Amino Acid Tagging Reveals Translationally Active Subpopulations of the Cystic Fibrosis Lung Microbiota. Valentini, T.D. et al. Nature Communications.

Human gut microbiome
Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Zhou, X. et al. Diabetes.

Berberine and Its Structural Analogs Have Differing Effects on Functional Profiles of Individual Gut Microbiomes. Li, L. et al. Gut Microbes.

Animal experiments
Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Swann, J.R. et al. Metabolites.

Bifidobacteria Shape Host Neural Circuits During Postnatal Development by Promoting Synapse Formation and Microglial Function. Luck, B. et al. Scientific Reports.

Glycerol Monolaurate, an Analogue to a Factor Secreted by Lactobacillus, Is Virucidal Against Enveloped Viruses, Including HIV-1. Welch, J.L. et al. mBio.

Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. Burgess, S.L. et al. The Journal of Clinical Investigation.

The Protective Effects of 2′-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion. Wang Y. et al. Nutrients.

Capsaicin Improves Glucose Homeostasis by Enhancing Glucagon-Like peptide-1 Secretion Through the Regulation of Bile Acid Metabolism via the Remodeling of the Gut Microbiota in Male Mice. Hui, S. et al. FASEB Journal.

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells. Schaupp L. et al. Cell.

Intratumoral Accumulation of Gut Microbiota Facilitates CD47-based Immunotherapy via STING Signaling. Shi, Y. et al. Journal of Experimental Medicine.

Animal microbiome
Housefly (Musca domestica L.) associated microbiota across different life stages. de Jonge, N. et al. Scientific Reports.

Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Deboutte, W. et al. PNAS.

Bayesian Modeling Reveals Host Genetics Associated With Rumen Microbiota Jointly Influence Methane Emission in Dairy Cows. Zhang, Q. et al. ISME Journal.

Review: The role of the gut microbiome in sustainable teleost aquaculture. Perry, W.B. et al. Proceedings of the Royal Society B.

Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Wikberg E.C. Animal Behaviour.

Plant, root, and soil microbiome
Global Warming Shifts the Composition of the Abundant Bacterial Phyllosphere Microbiota as Indicated by a Cultivation Dependent and Independent Study of the Grassland Phyllosphere of a Long-Term Warming Field-Experiment. Aydogan, E.L. et al. FEMS Microbiology Ecology.

Probiotics / prebiotics
A Human-Origin Probiotic Cocktail Ameliorates Aging-Related Leaky Gut and Inflammation via Modulating the Microbiota/Taurine/Tight Junction Axis. Ahmadi, S. et al. JCI Insight.

Bioinformatics
SHOGUN: A Modular, Accurate, and Scalable Framework for Microbiome Quantification. Hillmann, B. et al. Bioinformatics.

pepFunk: A Tool for Peptide-Centric Functional Analysis of Metaproteomic Human Gut Microbiome Studies. Simopoulos, C.M.A. et al. Bioinformatics.

Microbes in the news
Mapping the Microbiome in Saliva of COVID-19 Patients.

Inside the Belly of the Horse – Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health.