Category Archives: Plant Root Soil microbiome

November 4, 2022

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Today’s digest features a 30-color colorblind friendly color palette and functions for mapping color to hierarchical/nested data, ecosystem-specific reference databases, stoma samples for a very effective way of small intestinal microbiome characterization, and a reminder that 16S rRNA gene sequencing is NOT metagenomics. Happy Friday!

Join the next #MVIF when Sarah Lebeer will talk about citizen science and vaginal microbiome!!

Global resistome

Sharing of Antimicrobial Resistance Genes between Humans and Food Animals – Huiluo Cao – mSystems

Gut microbiome

Host-microbiome interactions: Gut-Liver axis and its connection with other organs – Swadha Anand & Sharmila S. Mande – npj Biofilms and Microbiomes

Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment – Alice Chen-Liaw – bioRxiv

Effects of different amoxicillin treatment durations on microbiome diversity and composition in the gut – Katrine Lekang – Plos One

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons – Joseph J. Bruckner – Plos Biology

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants – Lauren C. Beck – Nature Microbiology

*Plasticity of the adult human small intestinal stoma microbiota – Bahtiyar Yilmaz – Cell Host & Microbe


Bioinformatics

MIDAS2: Metagenomic Intra-species Diversity Analysis System – Chunyu Zhao – Bioinformatics

Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data – Matteo Ciciani – Nature Communications

*microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data – Erin M. Dahl – Microbiology Resource Announcements

*Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling – Christina Karmisholt Overgaard – Frontiers in Microbiology


November 02, 2022

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General microbiome

[RETRACTION]Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Pregnancy and early life

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning – Vatanen et al. – Clee

Multi-site human microbiome

[REVIEW]Recent advances in systemic lupus erythematosus and microbiota: from bench to bedside – Zhan et al. –

Human vaginal microbiome

Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics – France et al. – PLOS One

Human gut microbiome

Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia – Bernard-Raichon et al. – Nature Communications

Gut microbiota and myocardial fibrosis – Xu, Yang & Bao – European Journal of Pharmacology

Assessing the relationship between physical activity and the gut microbiome in a large, population-based sample of Wisconsin adults – Holzhausen et al. – PLOS One

Challenges and costs of donor screening for fecal microbiota transplantations – Bernard et al. – PLOS One

Animal microbiome

Gut colonization by Proteobacteria alters host metabolism and modulates cocaine neurobehavioral responses – Cuesta et al. – Cell Host & Microbe

Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals – Koziol et al. – Microbiology Open

Understanding the Dynamic of POMS Infection and the Role of Microbiota Composition in the Survival of Pacific Oysters, Crassostrea gigas – Delisle et al. – Microbiology Spectrum

Changes in Gut Microbiota Structure: A Potential Pathway for Silver Nanoparticles to Affect the Host Metabolism – Wang et al. – ACS Nano

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model – Mäenpää et al. – PLOS One

Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves – Slanzon et al. – PLOS One

Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes – Gil & Hird – Microbiology Spectrum

Uropygial gland microbiota differ between free-living and captive songbirds – Grieves et al. – Scientific Reports

Plant, root, and soil microbiome

Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere – Muscatt et al. – Microbiome

Bioinformatics

CRAMdb: a comprehensive database for composition and roles of microbiome in animals – Lei et al. – NAR

Techniques

DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes – Brauer & Bengtsson – Microbiology Open

synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing – Zaramela et al. – mSystems

October 26, 2022

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General microbiome

[BOOK]Human Microbiome in Health and Disease – Part B – Progress in Molecular Biology and Translational Science

Pregnancy and early life

Relationships of the very low birth weight infant microbiome with neurodevelopment at 2 and 4 years of age – Sarkar et al. – Developmental Psychobiology

Human respiratory microbiome

The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis – Knudsen et al. – Microbiome

Human gut microbiome

Profiling the fungal microbiome after FMT for graft-versus-host disease: insights from a phase 1 interventional study – van Lier et al. – Transplantation and Cellular Therapy

Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients – Bellerba et al. – Neoplasia

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome – Piancone et al. – Scientific Reports

Animal microbiome

[DATA]Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages – Feng et al. – Scientific data

Tick transmission of Borrelia burgdorferi to the murine host is not influenced by environmentally acquired midgut microbiota – Narasimhan et al. – Microbiome

Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis – Bianchimano et al. – Microbiome

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds – Navine et al. – Molecular Ecology

Impact of Germinated Brown Rice and Brown Rice on Metabolism, Inflammation, and Gut Microbiome in High Fat Diet-Induced Insulin Resistant Mice – Zhao et al. – J. Agric. Food Chem.

Dietary Lactobacillus reuteri prevent from inflammation mediated apoptosis of liver via improving intestinal microbiota and bile acid metabolism – Lin et al. – Food Chemistry

Plant, root, and soil microbiome

Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin – Wen et al. – Microbiome

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction – Tom et al. – Microbiome

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

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary – Guo et al. – Science of The Total Environment

Bioinformatics

LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis – Özkurt et al. – Microbiome

Techniques

[PREPRINT]Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes – McCully et al. – bioRxiv

A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening – Han et al. – Scientif Reports

October 12, 2022

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General microbiome

Global airborne bacterial community—interactions with Earth’s microbiomes and anthropogenic activities – Zhao et al. – PNAS

Tumor microbiome links cellular programs and immunity in pancreatic cancer – Cancer Cell – Ghaddar et al. – Cancer Cell

Human wound microbiome

The Wound Microbiome – White & Grice – Cold Spring Harbor Perspectives in Biology

Human gut microbiome

Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke – Zhou et al. – Journal of Translational Medicine volume

Gut-Testis Axis: Microbiota Prime Metabolome To Increase Sperm Quality in Young Type 2 Diabetes – Yan et al. – Microbiology Spectrum

Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups – West et al. – Scientific Reports

[REVIEW]The role of the gut microbiota in health and cardiovascular diseases – Wang et al. – Molecular Biomedicine

Animal microbiome

Airborne polystyrene microplastics and nanoplastics induce nasal and lung microbial dysbiosis in mice – Zha et al. – Chemosphere

Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling – Yi et al. – Science of The Total Environment

Lactococcus lactis’ Effect on the Intestinal Microbiota of Streptococcus agalactiae-Infected Zebrafish (Danio rerio) – Tan et al. – Microbiology Spectrum

Exploring AI-2-mediated interspecies communications within rumen microbial communities – Liu et al. – Microbiome

Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions – Martinez-Alvaro et al. – Microbiome

Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I – Yin et al. – Microbiome

Plant, root, and soil microbiome

[CORRESONDENCE]Functionally-explicit sampling can answer key questions about the specificity of plant–microbe interactions – Fleishman et al. – Environmental Microbiome

Dissecting the cotranscriptome landscape of plants and their microbiota – Nobori et al. – EMBO Reports

Bioinformatics

MiMeDB: the Human Microbial Metabolome Database – Wishart et al. – NAR

gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions – Qi et al. – NAR

October 05, 2022

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Pregnancy and early life

Multi-omic factors associated with future wheezing in infants – Beheshti et al. – Pediatric Research

Multi-site human microbiome

Race is a key determinant of the human intratumor microbiome – Lua et al. – Cancer Cell

Human respiratory microbiome

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance – Merenstein, Bushman & Collman – Microbiome

Human milk microbiome

Maternal weight status and the composition of the human milk microbiome: A scoping review – Daiy et al. – PLOS One

Human oral microbiome

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study – Carda-Dieguez, Mazzez & Mira – Microbiome

Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection – Austin et al. – Communications Biology

Human gut microbiome

[REVIEW]SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis – Mozaffari et al. – Pathology – Research and Practice

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin – Ma et al. – Genome Biology

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Kawano et al. – Cell

Rural environment reduces allergic inflammation by modulating the gut microbiota – Yang et al. – Gut Microbes

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

Six types of tea extracts attenuated high-fat diet-induced metabolic syndrome via modulating gut microbiota in rats – Zhou et al. – Food Research International

Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity – Connor et al. – The Journal of Nutritional Biochemistry

Animal microbiome (for animals in the wild)

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle – Teseo et al. – Microbiome

Comparative multiomics study of the effects of Ellagic acid on the gut environment in young and adult mice – Duan et al. – Food Research International

[REVIEW]Crosstalk between the microbiota and insect postembryonic development – Girard et al. – Trends in Microbiology

Culturomic, metagenomic, and transcriptomic-based characterization of commensal lactic acid bacteria isolated from domestic dogs using Caenorhabditis elegans as a model for aging – Kang et al. – Journal of Animal Science

Plant, root, sponge and soil microbiome

Recruitment of specific microbes through exudates affects cadmium activation and accumulation in Brassica napus – Wu et al. – Journal of Hazardous Materials

Novel trends of genome evolution in highly complex tropical sponge microbiomes – Kelly et al. – Microbiome

[Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities](Ecotoxicology and Environmental Safety) – Li et al. –

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

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics – Seong et al. – Microbiome

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China – Chen et al. – Water Research

Bioinformatics/Software

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics – Weissman et al. – mSystems

[SOFTWARE]PhyloDM is a high-performance library that converts a phylogenetic tree into a pairwise distance matrix. – Aaron Mussig – github

September 21, 2022

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Human respiratory microbiome

The Microbiota of Human Lung of Pulmonary Tuberculosis and the Alteration Caused by Anti-tuberculosis Drugs – Zhang et al. – Current Microbiology

Human urinary microbiome

Mechanisms of the intestinal and urinary microbiome in kidney stone disease – Miller et al. – Nature Reviews Urology

Human oral microbiome

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma – Zhang et al. – Medicine

Human gut microbiome

Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients – Thompson et al. – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis – Singh et al. – Indian Journal of Gastroenterology

[REVIEW]Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis – Roessler et al. – Atherosclerosis

Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population – Bai et al. – Microbiome

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

Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – PLOS Biology

Inhibitory effects of antibiotic-induced gut microbiota depletion on acute itch behavior in mice – Zhang et al. – Brain Research Bulletin

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Yang et al. – Microbiome

Animal microbiome (for animals in the wild)

Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance – Perez-Marron et al. – Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia – Brinker et al. – Molecular Ecology

Plant, root, and soil microbiome

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds – Loiola et al. – Science of The Total Environment

[REVIEW]Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture – Diwan, Rashid & Vaishnav – Microbiological Research

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability – Phour & Sindhu – Planta

[OPINION]Plant microbiota dysbiosis and the Anna Karenina Principle – Arnault, Money & Vandenkoornhuyse

Food microbiology

Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure – Aydin et al. – Current Microbiology

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance – Calabrese et al. – Microbiome

September 9, 2022

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The #MVIF Season 2 is starting NEXT WEEK!

With the new starting time to better accommodate extra time zones &
highlights will be hosted by @gather_town for more engaging personal interaction & networking (from October).

Resistome

Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation – Allison K. Guitor – Microbiome

Review: Soil microbiomes and one health – Samiran Banerjee & Marcel G. A. van der Heijden – Nature Reviews Microbiology

Oral microbiome

Corncob structures in dental plaque reveal microhabitat taxon specificity – Viviana Morillo-Lopez – Microbiome

Vaginal microbiome

Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy – Kathryn E.McCauley – Cell Reports Medicine

Gut virome/microbiome

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort – Suguru Nishijima – Nature Communications

Review: Mutualistic interplay between bacteriophages and bacteria in the human gut – Andrey N. Shkoporov – Nature Reviews Microbiology

Identification of trypsin-degrading commensals in the large intestine – Youxian Li – Nature

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Yoshinaga Kawano – Cell

Design, construction, and in vivo augmentation of a complex gut microbiome – Alice G. Cheng – Cell

Plant, root and soil microbiome

Source and acquisition of rhizosphere microbes in Antarctic vascular plants – Sergio Guajardo-Leiva – Frontiers in Microbiology

Animal microbiome

Individual variation in the avian gut microbiota: the influence of host state and environmental heterogeneity – Shane E. Somers – bioRxiv

Animal experiment

From germ-free to wild: modulating microbiome complexity to understand mucosal immunology – Carolyn A. Thomson – Mucosal Immunology

September 8, 2022

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Today’s microbiome digest includes ten rules for teaching yourself R, food safety profiles of ready-to-eat raw minced meat, teaching that addresses eco-anxiety, as well as both pathogenic and entomopathogenic fungi!

Human gut microbiome

Meals, Microbiota and Mental Health in Children and Adolescents (MMM-Study): A protocol for an observational longitudinal case-control study – Asbjornsdottir et al. – PLOS One

Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients – Hai et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Mycoparasitism capability and growth inhibition activity of Clonostachys rosea isolates against fungal pathogens of grapevine trunk diseases suggest potential for biocontrol – Geiger et al. – PLOS One

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae – Wilberts et al. – PLOS One

Food microbiology

Bacteriological quality and antimicrobial susceptibility profiles of isolates of ready-to-eat raw minced meat from hotels and restaurants in Arba Minch, Ethiopia – Tonjo et al. – PLOS One

Bioinformatics

Ten simple rules for teaching yourself R – Lawlor et al. – PLOS Computational Biology

Techniques

Laboratory evaluation of RealStar Yellow Fever Virus RT-PCR kit 1.0 for potential use in the global yellow fever laboratory network – Basile et al. – PLOS Neglected Tropical Diseases

Science, publishing, and career )

Insufficient yet improving involvement of the global south in top sustainability science publications – Dangles et al. – PLOS One

Adapt conservation biology teaching to address eco-anxiety in students – São Pedro et al. – PLOS Biology

September 7, 2022

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General microbiome

Impact of environmental conditions and gut microbiota on the in vitro germination and growth of Clostridioides difficile – Martinez et al. – FEMS Microbiology Letters

[FORUM]Polymorphic microbes: a new emerging hallmark of cancer – Lythgoe et al. – Trends in Microbiology

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter – Hitch et al. – Systematic and Applied Microbiology

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome – Martiny et al. – PLOS Biology

Pregnancy and early life

Alterations in Vaginal Microbiota among Pregnant Women with COVID-19 – Velik et al. – Journal of Medical Virology

The Global Incidence of Adverse Events Associated with Fecal Microbiota Transplantation in Children over the Past 20 Years: A Systematic Review and Meta-Analysis – Wang et al. – Journal of Gastroenterology and Hepatology

Multi-site human microbiome

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes – Ke, Weiss & Liu – Nature Communications

Human salivary microbiome

Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity? – Liu et al. – Journal of Translational Medicine volume

Human vaginal microbiome

Does exposure to different types of menstrual protections affect the vaginal environment? – Tessandier et al. – Molecular Ecology

Human gut microbiome

High-altitude exposure decreases bone mineral density and its relationship with gut microbiota: Results from the China multi-ethnic cohort (CMEC) study – Zuo et al. – Environmental Research

Animal microbiome

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony – Uchiyama et al. – Letters of Applied Microbiology

Probiotics or synbiotics addition to sows’ diets alters colonic microbiome composition and metabolome profiles of offspring pigs – Zhu et al. – Front. Microbiol.

Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy – Laia et al. – PLOS One

Plant, root, and soil microbiome

Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance – Luo et al. – Environ. Sci. Technol.

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

Global contribution of pelagic fungi to protein degradation in the ocean -Breyer et al. – Microbiome

August 31, 2022

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Human skin microbiome

[REVIEW]Staphylococcus epidermidis and its dual lifestyle in skin health and infection – Severn & Horswill – Nature Reviews Microbiology

Human oral microbiome

Effect of chewing gum containing Xylitol and blackberry powder on oral bacteria: A randomized controlled crossover trial – Miller et al. – Archives of Oral Biology

Human gut microbiome

Antimicrobial peptide production in response to gut microbiota imbalance – Cardoso et al. – Peptides

ROLE OF GUT MICROBIOTA IN DEPRESSION: UNDERSTANDING MOLECULAR PATHWAYS, RECENT RESEARCH, AND FUTURE DIRECTION – Rathour et al. – Behavioural Brain Research

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

Gut-derived metabolites influence neurodevelopmental gene expression and Wnt signaling events in a germ-free zebrafish model – Rea et al. – Microbiome

Animal microbiome (for animals in the wild)

Age as a primary driver of the gut microbial composition and function in wild harbor seals – Pacheco-Sandoval et al. – Scientific Reports

Plant, root, and soil microbiome

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes – Cowan et al. – Microbiome

Soil fungal communities show more specificity than bacteria for plant species composition in a temperate forest in China – Chen et al. – BMC Microbiology

Microbes in space

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome – Madrigal et al. – Microbiome

Food microbiology

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities – Somerville et al. – Microbiome

Bioinformatics

Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge – Poussin et al. – BMC Genomics

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Newly Renamed Prokaryote Phyla Cause Uproar – Dan Robitzski – The Scientist