June 8, 2022

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Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum

Techniques

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 15, 2022

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General microbiome

[PREPRINT]Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica – Escudero-Leyva et al. – bioRxiv

Pregnancy and early life

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life – Wells et al. – Annual Review of Nutrition

Multi-site human microbiome

A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao – Han et al. – Clinical and Translational Medicine

Human oral microbiome

The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine – Herremans et al. – Microbiome

Human skin microbiome

Altered skin fungal and bacterial community compositions in tinea capitis – Rong et al. – Mycoses

Effects of short chain fructo-oligosaccharides on selected skin bacteria – Le Bourgot et al. – Scientific Reports

Human vaginal microbiome

Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome – Ruotsalainen et al. – Medical Microbiology and Immunology

Human gut microbiome

Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients – Hoang et al. – BMC Cancer

Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study – Miao et al. – BMC Medicine

[REVIEW]The role of virome in the gastrointestinal tract and beyond – Tiamani et al. – FEMS Microbiology Reviews

[REVIEW]Time-limited diets and the gut microbiota in cardiometabolic disease – Ratiner et al. – Journal of Diabetes

Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial – Huang et al. – Journal of Autoimmunity

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer – Fu et al. – Cell

Pharmacokinetic and gut microbiota analyses revealed the effect of Lactobacillus acidophilus on the metabolism of Olsalazine in ulcerative colitis rats – Li et al.

Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis – Forster et al. – Nature Microbiology

Plant, root, and soil microbiome

The plant host environment influences competitive interactions between bacterial pathogens – Ehau-Taumaunu & Hockett – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data – Darcy et al. – bioRxiv

June 13, 2022

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Today’s digest features metagenomics for clinical UTI diagnostics, microbial diversity in kombucha tea, microbial source tracking using single nucleotide variants, and more. Happy reading!

Neonatal microbiome

Editorial: More data needed on neonatal microbiome seeding – W. Florian Fricke & Jacques Ravel – Microbiome

Urinary microbiome

The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis – Cara Joyce – Frontiers in Cellular and Infection Microbiology

*Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study – Victoria A Janes – The Lancet Microbe

Gut microbiome

Perspective: Tiny Gatekeepers: Microbial Control of Host Drug Transporters – Than S. Kyaw and Peter J. Turnbaugh – Clinical Pharmacology & Therapeutics

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids – Henry H. Le – Cell Host & Microbe

Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in paediatric haematopoietic stem cell transplantation – Gintare Vaitkute – Microbiome

Animal microbiome

Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis – Vittorio Boscaro – Nature Microbiology

Water microbiome

Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB) – Han Gao – Water Research

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster – Irmarie Cotto – bioRxiv

Soil microbiome

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies – Ying Wang – Frontiers in Microbiology

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra – Igor S. Pessi – bioRxiv

Food

*Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations – Elizabeth A. Landis – mSystems

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods – Irina Spacova, Sarah Ahannach – Frontiers in Nutrition

Bioinformatics

coda4microbiome: compositional data analysis for microbiome studies – M.Luz Calle & Antoni Susin – bioRxiv

GeneToList: A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist – Joshua D. Breidenbach – bioRxiv

*Microbiome source tracking using single nucleotide variants – Leah Briscoe – bioRxiv

June 11, 2022

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Have a nice weekend! In this digest: An interesting study about the effect of various dietary fibers (e.g., arabinoxylan, inulin) on the human microbiome (Lancaster, Cell Host & Microbe). Additionally, this digest includes more papers about maternal IgG interplay with neonatal microbiome. 

Human and General Microbiome

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans – Samuel M. Lancaster – Cell Host & Microbe

–> A preview for the paper: Stitching together a healthy gut microbiome with fiber – Thomas M Schmidt – Cell Host & Microbe

Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity – Katherine Z Sanidad – Science Immunology

Altered Metabolomics in Bipolar Depression With Gastrointestinal Symptoms – Xiang-Jie Guo – Frontiers in Psychiatry

Meta-analysis of mucosal microbiota reveals universal microbial signatures and dysbiosis in gastric carcinogenesis – Changan Liu – Oncogene

Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D Gerson – Journal of Reproductive Immunology

Beneficial Microbes and Compounds

Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity – Raquel Alonso-Roman – Nature Communications

Honeys with anti-inflammatory capacity can alter the elderly gut microbiota in an ex vivo gut model – Daoyan Wu – Food Chemistry

Model Animal Microbiome

Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice – Julia L Drewes – Cancer Discovery

Non-Model Animal Microbiome

Variation in gut microbiome structure across the annual hibernation cycle in a wild primate – Lydia K Greene – FEMS Microbiology Ecology

A high-throughput DNA sequencing study of fecal bacteria of seven Mexican horse breeds – Fernando Hernández-Quiroz – Archives of Microbiology

Species- and site-specific circulating bacterial DNA in Subantarctic sentinel mussels Aulacomya atra and Mytilus platensis – Sophia Ferchiou – Scientific Reports

Plant Microbiome

Review: The unsung roles of microbial secondary metabolite effectors in the plant disease cacophony – Lorena I Rangel – Current Opinion in Plant Biology

Plant-microbe interactions in the rhizosphere via a circular metabolic economy – Elisa Korenblum – The Plant Cell

Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest – Mengjiao Li – Environmental Microbiome

Nitrogen availability determines plant growth promotion and the induction of root branching by the probiotic fungus Trichoderma atroviride in Arabidopsis seedlings – José López-Bucio – Archives of Microbiology

Environmental Microbiome

Review: Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies – Shengnan Li – The Science of the Total Environment

More Microbes

Perspective: Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation – Mariana O Barcoto – Frontiers in Microbiology

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials – Jiarui Sun – Microbial Genomics

Bioinformatics and Experimental Microbiome Analysis

DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization – Anna M Forsman – Integrative and Comparative Biology

Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies – Jacqueline Rehner – Genomics, Proteomics & Bioinformatics

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

June 08, 2022

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General microbiome

Tet2 deficiency drives liver microbiome dysbiosis triggering Tc1 cell autoimmune hepatitis – Pandey et al. – Cell Host & Microbe

Human gut microbiome

[PREPRINT]Mucosal host–microbe interactions associate with clinical phenotypes in inflammatory bowel disease – Hu et al. – bioRxiv

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Gut microbiome mediates the protective effects of exercise after myocardial infarction – Zhou et al. – Microbiome

Animal microbiome (for animals in the wild)

Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny – Bechade et al. – FEMS Microbiology Ecology

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT]Summer dynamics of microbial diversity on a mountain glacier – Hotaling, Price & Hamilton – bioRxiv

Bioinformatics

MIAOME: Human microbiome affect the host epigenome – Wang et al. – Computational and Structural Biotechnology Journal

Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates – By IMPACTT investigators – Computational and Structural Biotechnology Journal

phyloMDA: an R package for phylogeny-aware microbiome data analysis – Liu et al. – BMC Bioinformatics

MeShClust v3.0: high-quality clustering of DNA sequences using the mean shift algorithm and alignment-free identity scores – Girgis – BMC Genomics

June 6, 2022

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Have a nice Monday! Today, in this Digest we have some pendant papers from last week.

Human and General Microbiome

The role of immune cells in the liver tumor microenvironment: an involvement of gut microbiota-derived factors – Tomonori Kamiya – International Immunology

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention – Stephanie B Orchanian – Advanced Biology

Short chain fatty acids-producing and mucin-degrading intestinal bacteria predict the progression of early Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Intestinal inflammation alters the antigen-specific immune response to a skin commensal – Geil R Merana – Cell Reports

Characterization of resistome in Lactobacillus genomic sequences from the human gut – Jale Moradi – Journal of Global Antimicrobial Resistance

Clustering Analysis of the Multi-Microbial Consortium by Lactobacillus Species Against Vaginal Dysbiosis Among Ecuadorian Women – David Pacha-Herrera – Frontiers in Cellular and Infection Microbiology

Nutritional Intake and Gut Microbiome Composition Predict Parkinson’s Disease – Michal Lubomski – Frontiers in Aging Neuroscience

Beneficial Microbes and Compounds

Review: Bacteriocin-Producing Probiotic Lactic Acid Bacteria in Controlling Dysbiosis of the Gut Microbiota –  Anjana – Frontiers in Cellular and Infection Microbiology

Review: Relationship between gut microbiota and colorectal cancer: Probiotics as a potential strategy for prevention – Seung Yun Lee – Food Research International 

Review: Health benefits of microalgae and their microbiomes – Ines Krohn – Microbial Biotechnology

Lactobacillus reuteri J1 prevents obesity by altering the gut microbiota and regulating bile acid metabolism in obese mice – Chenxi Zhang – Food & Function

Non-Model Animal Microbiome 

16S rRNA Gene Sequencing Reveals Specific Gut Microbes Common to Medicinal Insects – Jin Geng – Frontiers in Microbiology

Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets – Leli Wang – Microbiome

Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa – Meiqi Ma – Microbial Ecology

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection – Zhiyuan He – Microbiome

Plant Microbiome

Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes – Pin Su – Scientific Data

Environmental Microbiome

Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies – Qiang Pu – Journal of Hazardous Materials

The sanitary indoor environment-a potential source for intact human-associated anaerobes – Manuela-Raluca Pausan – NPJ Biofilms and Microbiomes

More Microbes

Review: Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications – Pranami Goswami – NPJ Biofilms and Microbiomes

Bioinformatic and Experimental Microbiome Analysis

Review: Emerging technologies in the study of the virome – Sophie E Smith – Current Opinion in Virology

EasyMap – An Interactive Web Tool for Evaluating and Comparing Associations of Clinical Variables and Microbiome Composition – Ehud Dahan – Frontiers in Cellular and Infection Microbiology

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples – Anaïs Biclot – Microbiome

BiGAMi: Bi-Objective Genetic Algorithm Fitness Function for Feature Selection on Microbiome Datasets – Mike Leske – Methods and Protocols

June 4, 2022

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Highlights!

Review: Translating Microbiome Research From and To the Clinic – Zhenrun J Zhang – Annual Review of Microbiology → An exploration of different experimental studies associating the gut microbiota with certain human diseases, highlighting translational advances 

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Wenshan Zheng – Science → A powerful technique to obtain single amplified genomes (SAG) from human microbiome samples 

Human and General Microbiome

Review: Gut microbiota and atopic dermatitis in children: a scoping review – Yue Liu – BMC Pediatrics

Review: Gut microbiome and autoimmune disorders – Walaa Abdelaty Shaheen – Clinical and Experimental Immunology

Altered Vaginal Microbiota Composition Correlates With Human Papillomavirus and Mucosal Immune Responses in Women With Symptomatic Cervical Ectopy – Mariana López-Filloy – Frontiers in Cellular and Infection Microbiology

Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients – Ornella la Fortune Tchoupou Saha – Frontiers in Microbiology

Machine learning aided construction of the quorum sensing communication network for human gut microbiota – Shengbo Wu – Nature Communications

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts – S R Stockdale – Scientific Reports

Gut microbial metabolites in Parkinson’s disease: Association with lifestyle, disease characteristics, and treatment status – Robin M Voigt – Neurobiology of Disease

Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids – Sujeet S Bhoite – The Journal of Biological Chemistry

Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death – Yun Teng – Cell Host & Microbe

Beneficial Microbes and Compounds

Review: A Review: Cereals on Modulating the Microbiota/Metabolome for Metabolic Health – Jayani Kulathunga – Current Nutrition Reports

Anti-Diabetic Potential of Chlorella pyrenoidosa-Based Mixture and its Regulation of Gut Microbiota – Wenyu Xiong – Plant Foods for Human Nutrition

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment – Chiara Argentini – Applied and Environmental Microbiology

Animal Microbiome

Synchrony and idiosyncrasy in the gut microbiome of wild baboons – Johannes R Björk – Nature Ecology & Evolution

Environmental Microbiome

A synergistic bacterial pool decomposes tebuthiuron in soil – Edivaldo Wilson de Lima – Scientific Reports

The microbiome of cryospheric ecosystems – Massimo Bourquin – Nature Communications

Extremophiles

Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil – Sabrina Behairi – Extremophiles

Bioinformatics and Microbiome Analysis

Multiscale analysis of count data through topic alignment – Julia Fukuyama – Biostatistics

SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling – Yongqiang Luo – Small Methods

June 3, 2022

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Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.

Events

Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.

COVID-19

Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv

Bioinformatics

backbone: An R package to extract network backbones – Neal – PLOS ONE


June 01, 2022

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General microbiome

[REVIEW]Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms – Cani et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Role of Microbiota in Viral Infections and Pathological Progression – Mizutani et al. – Viruses

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Newbury et al. – PNAS

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales – Martinez-Gutierrez & Aylward – PLOS Genetics

Interspecies commensal interactions have nonlinear impacts on host immunity – Rice et al. – Cell Host & Microbe

Human skin myco-/microbiome

Distinct skin microbiome community structures in congenital ichthyosis – Tham et al. – British Journal of Dermatology

Biodiversity of mycobial communities in health and onychomycosis – Olbrich et al. – Scientific Reports

Human gut microbiome

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study – Jiang et al. – Genome Medicine

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

Discovery of bioactive microbial gene products in inflammatory bowel disease – Zhang et al. – Nature

Animal microbiome (for animals in the wild)

The functional evolution of termite gut microbiota – Arora et al. – Microbiome

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods – Oba et al. – Journal of Animal Science

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth – Zhang et al. – Front. Microbiol.

Plant, root, and soil microbiome

Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships – Schäfer et al. – Nature Microbiology

Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis – Mehlferber et al. – Current Biology