April 6, 2021

Human gut microbiome

Thousands of previously unknown phages discovered in whole-community human gut metagenomes – Benler et al. – Microbiome

*Elevated rates of horizontal gene transfer in the industrialized human microbiome – Groussin et al. – Cell

Animal microbiome

Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes – Keenum et al. – Microbiome

Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential – Muurinen et al. – Scientific Reports


Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data – Stamboulian et al. – Microbiome

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains – Zünd et al. – Microbiome

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection – Danko et al. – Microbiome

March 22


Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens – Cook et al. – Microbiome

Plant microbiome

Protists as main indicators and determinants of plant performance – Guo et al. – Microbiome

Rock metagenomes

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages – Albanese et al. – Microbiome

Mouse gut microbiome

Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota – Xiang et al. – Microbiome

Human gut microbiome

Associations between habitual diet, metabolic disease, and the gut microbiota using latent Dirichlet allocation – Breuninger et al. – Microbiome

Maternal gut microbiota reflecting poor diet quality is associated with spontaneous preterm birth in a prospective cohort study – Gershuni et al. – Am J Clin Nutr

March 5, 2021

Human microbiome

A multi-omic investigation of male lower urinary tract symptoms: Potential role for JC virus – Thomas S. et al. – PLOS ONE

Association between physical activity and changes in intestinal microbiota composition: A systematic review – Aya V. et al. – PLOS ONE

Plant microbiome

Specialized microbiomes facilitate natural rhizosphere microbiome interactions counteracting high salinity stress in plants – Santos S. et al. – Environmental and Experimental Botany


Impact of sampling depth on pathogen detection in pit latrines – Capone D. et al. – PLOS Neglected Tropical Diseases

A novel methodology to study antimicrobial properties of high-touch surfaces used for indoor hygiene applications—A study on Cu metal – Chang T. et al. – PLOS ONE

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation – Wilson R. M. et al. – PLOS ONE

Animal microbiome

Wastewater treatment works change the intestinal microbiomes of insectivorous bats – Mehl C. et al. – PLOS ONE

Microbial communities developing within bulk sediments under fish carcasses on a tidal flat – Kawamoto Y. et al. – PLOS ONE

Host-microbe interactions

Host-microbe cross-talk governs amino acid chirality to regulate survival and differentiation of B cells – Suzuki M. et al. – Science Advances


An integrated, modular approach to data science education in microbiology – Dill-McFarland, K. A. et al. – PLOS Computational biology


Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes – Salvato, F. et al. – PLOS Pathogens

August 31, 2020

Human gut microbiome

Keystone taxa indispensable for microbiome recovery – Sean M. Gibbons – Nature Microbiology

Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial – Mokkala et al. – Gut

Environmental microbiome

Preprint: Bacterial Community Assemblages in Classroom Floor Dust of 50 Public Schools in a Large City: Characterization Using 16s rRNA Sequences and Associations with Environmental Factors – Park et al.

A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis – North et al. – Science

Animal microbiome

Effect of glycerol feed-supplementation on seabass metabolism and gut microbiota – Louvado et al. – Applied Microbiology and Biotechnology

Food microbiome

Secrets of the cheese microbiome – Danilo Ercolini – Nature Food


A heterogeneous microbial consortium producing short-chain fatty acids from lignocellulose – Shahab et al. – Science

Non-microbiology pics

One Health(y) Cities: Cities are pandemic ecosystems and that’s where the action ought to happen – Evelyne de Leeuw – Cities and Health

July 22, 2020

Human microbiome

The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences – Adebayo et al. – Cell Host & Microbe

The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study – Koedooder et al. – Human reproduction

Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS) – Yang et al. – Frontiers in Microbiology

Gut microbiome

Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition – Chen et al. – Science

Prenatal stress increases IgA coating of offspring microbiota and exacerbates necrotizing enterocolitis-like injury in a sex-dependent manner – Brawner et al. – Brain, Behavior, and Immunity

General microbiome

* Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts – McLean et al. – Cell Reports

June 26, 2020


Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation – Olesen et al. – bioRxiv

Oral microbiome

Streptococcus mutans adhesion force sensing in multi-species oral biofilms – Wang et al. – npc Biofilms and Microbiomes

Skin microbiome

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction – Ianiri et al. – PNAS

Gut-brain axis

The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens – Kumar et al. – Cell Host and Microbe

May 31, 2020

Human microbiome

The interplay between immune system and microbiota in gynecological diseases: a narrative review – Villa et al. – European Review for Medical and Pharmacological Sciences

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians –  Rubel et al. – Genome Biology

Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets – Xu et al. – Gut Microbes

Dissimilarity of Airway and Lung Tissue Microbiota in Smokers undergoing Surgery for Lung Cancer – Reinhold et al. – Microorganisms

Chemotherapy-induced ileal crypt apoptosis and the ileal microbiome shape immunosurveillance and prognosis of proximal colon cancer – Roberti et al. – Nature Medicine

Animal microbiome

Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus) – Yang et al. – PeerJ

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic E. coli F18 – Li et al. – Frontiers in Microbiology

The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics – Nettles et al. – Microbial Ecology

Food microbiome

Assessment of overall microbial community shift during Cheddar cheese production from raw milk to aging – Choi et al. – Applied Microbiology and Biotechnology

Marine microbiome

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan – Sichert et al. – Nature Microbiology

Scientific communication and education

Preprint: A rapid urban biodiversity blitz using aquatic environmental DNA – Hupalo et al. – bioRxiv

Preprint: The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic – Fox – bioRxiv

May 5, 2020


The Virtual Microbiome Summit – May 19-22, 2020

Multi-site human microbiome

Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients – Yang et al. – BMC Oral Health

Human gut microbiome

Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile – Arnoriaga-Rodríguez et al. – Microbiome

Preprint: Antibiotics may influence gut microbiome signaling to the brain in preterm neonates – Russell et al. – bioRxiv

Animal experiments

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al. – Microbiome


Preprint: A study’s got to know its limitations – Gooch et al. – bioRxiv