April 8, 2022

Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!

Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

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

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE


An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

April 6, 2022

Today’s digest features studies on microbial genes of unknown function, oral microbiome of smokeless tobacco consumers, non-industrialized infant microbiome, and more news. Happy reading!

Microbiome Forum FOR EVERYONE
Each event is replicated shortly thereafter to reach a global audience.
ALL microbiome research & career levels welcome
Free registration.

Global microbiome

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples – Hannah-Marie Martiny – mSystems

Symposium Review: After the storm—Perspectives on the taxonomy of Lactobacillaceae – Nanzhen Qiao – JDS Communications

Oral microbiome

Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Gut microbiome

Unravelling specific diet and gut microbial contributions to inflammatory bowel disease – Gabriel Vasconcelos Pereira – bioRxiv

Effects of caloric restriction on the gut microbiome are linked with immune senescence – Julia Sbierski-Kind – Microbiome

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome – Gabriele Andrea Lugli – Environmental Microbiology

Review: Diet-gut microbiota interactions on cardiovascular disease – Xufei Zhang and Philippe Gérard – Computational and Structural Biotechnology Journal

*Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles – Matthew R Olm – bioRxiv

Animal microbiome

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Animal experiment

Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors – Yves A Millet – bioRxiv

Plant microbiome

The phyllosphere microbiome shifts toward combating melanose pathogen – Pu-Dong Li – Microbiome

Wastewater microbiome

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis – Rodolfo Palomo-Briones – bioRxiv


Review: Next-generation sequencing: insights to advance clinical investigations of the microbiome – Caroline R. Wensel – The Journal of Clinical Investigations

Metagenomics-enabled microbial surveillance – Karrie K. K. Ko – Nature Microbiology


Software testing in microbial bioinformatics: a call to action – Boas C.L. van der Putten – Microbial Genomics

Review: Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation – Alban Mathieu – Frontiers in Microbiology

*Unifying the known and unknown microbial coding sequence space – Chiara Vanni – eLife

NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the Microbiology, Immunology, and Cancer Biology Sciences.

April 04, 2022

General microbiome

[REVIEW]Types and functions of heterogeneity in mycobacteria – Chung, Johnson & Aldridge – Nature Reviews Microbiology

Human breast tissue microbiome

The breast tissue microbiome, stroma, immune cells and breast cancer – Hieken et al. – Neoplasia

Human gut microbiome

Intestinal virome in patients with alcohol use disorder and after abstinence – Hsu et al. – Hepatology Communications

Sexual Dimorphism in the Gut Microbiome: Microgenderome or Microsexome? – Mulak, Larauche & Tache – J Neurogastroenterol Motil

Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics – Papaiakovou et al. – Parasites & Vectors

[REVIEW]Connecting the Human Microbiome and Pancreatic Cancer – Sexton et al. – Cancer and Metastasis Reviews

Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota – Ostrowski et al. – Nature Microbiology

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis – Smith et al. – Scientific Reports

[PREPRINT]Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes – Merrill et al. – bioRxiv

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

Light-Sensitive Lactococcus lactis for Microbe–Gut–Brain Axis Regulating via Upconversion Optogenetic Micro-Nano System – Pan et al. – ACS Nano

Biogeography, succession, and origin of the chicken intestinal mycobiome – Robinson et al. – Microbiome

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

Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome – Plata et al. – Communications Biology

Animal microbiome (for animals in the wild)

Microplastics impact the accumulation of metals in earthworms by changing the gut bacterial communities – Yang, Xu & Yu – Science of The Total Environment

Plant, root, and soil microbiome

Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location – Okamoto et al. – Molecular Ecology

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

[REVIEW]Microbial metabolites in the marine carbon cycle – Moran et al. – Nature Microbiology


[PREPRINT]Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – bioRxiv

March 31, 2022

General microbiome

Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming – Peng et al. – PLOS Computational Biology

[PREPRINT]Superfast Evolution of Multi-drug Antibiotic Resistance – Zhang et al. – bioRxiv

Pregnancy and early life

Identification of the specific microbial community compositions in saliva associated with periodontitis during pregnancy – Narita & Kodama – Clinical Oral Investigations

Vaginal microbiome

Impact of Topical Interventions on the Vaginal Microbiota and Metabolome in Postmenopausal Women – Srinivasan et al. – JAMA Network Open

Human gut microbiome

[REVIEW]The interplay between anticancer challenges and the microbial communities from the gut – Hobson et al. – European Journal of Clinical Microbiology & Infectious Diseases

[EDITORIAL]Unraveling disease pathways involving the gut microbiota: the need for deep phenotyping and longitudinal data – Meyer et al. – The American Journal of Clinical Nutrition

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

The Effects of Stevia Consumption on Gut Bacteria: Friend or Foe? – Kasti et al. – Microorganisms

Jejunoileal mucosal growth in mice with a limited microbiome – Shaughnessy – PLOS One

Plant, root, and soil microbiome

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation – Causevic et al. – mSystems

Built environment (subways, indoor surfaces)

A quantitative microbial risk assessment for touchscreen user interfaces using an asymmetric transfer gradient transmission mode – di Battista – PLOS One


Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains – Emmons et al. – mSystems


Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence – Seol et al. – Microbiology Spectrum


Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria – Jaffe et al. – mSystems

March 30, 2022

General microbiome

[REVIEW]Glycan processing in gut microbiomes – La Rosa et al. – Current Opinion in Microbiology

Multi-site human microbiome

[REVIEW]The Oral-Microbiome-Brain Axis and Neuropsychiatric Disorders: An Anthropological Perspective – Bowland & Weyrich – Frontiers in Psychiatry

Human oral microbiome

Microbial and molecular differences according to the location of head and neck cancers – Kim et al. – Cancer Cell International

Microbial differences between active and remission peri-implantitis – Hashimoto et al. – Scientific Reports

Human gut microbiome

Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden – Olsson et al. – Cell Host & Microbe

Microbiota-microglia connections in age-related cognition decline – Zhou et al. – Aging Cell

Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota – Todberg – British Journal of Dermatology

[PREPRINT]Distinct Colon Mucosa Microbiomes associated with Tubular Adenomas and Serrated Polyps – Avelar-Barragan et al. – bioRxiv

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting – Liu et al. – Cell Metabolism

Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth – Testerman et al. – Hepatology Commonications

Dietary Patterns and Gut Microbiota: the Crucial Actors in Inflammatory Bowel Disease – He et al. – Advances in Nutrition

A Guide to Dietary Pattern–Microbiome Data Integration – Choi et al. – The Journal of Nutrition

Functional Significance of Different Milk Constituents in Modulating the Gut Microbiome and Infant Health – Yadav et al. – J. Agric. Food Chem.

The gut microbiome as mediator between diet and its impact on immune function – Shi et al. – Scientific Reports

Differences in the intestinal microbiome associated with diarrhea during lenvatinib treatment for hepatocellular carcinoma – Inuai et al. – Digestive Diseases

16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation – Mingjun et al. – Bioengineered

[REVIEW]Profile of Gut Microbiota of Adults with Diabetes Mellitus Type 1: A Systematic Review – Moreira et al. – Current Diabetes Reviews

Association between systemic lupus erythematosus and disruption of gut microbiota: a meta-analysis – Xiang et al. – Immunology and Inflammation

[REVIEW]The Bridge Between Ischemic Stroke and Gut Microbes: Short-Chain Fatty Acids – Fang et al. – Cellular and Molecular Neurobiology

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

Prophylactic effects of hyperforin on anhedonia-like phenotype in chronic restrain stress model: A role of gut microbiota – Zhang et al. – Letters in Applied Microbiology

Metabolome and microbiome multi-omics integration from a murine lung inflammation model of bronchopulmonary dysplasia – Saie et al. – Pediatric Research

Microbiome applications for laying hen performance and egg production – Ricke, Dittoe & Olson – Poultry Science

Animal microbiome (for animals in the wild)

[PREPRINT]The connection between the gut mycobiome community of natural black soldier fly populations and their environment – Vitenberg, Goldway & Opatovsky – bioRxiv

Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection – Jimenez et al. – Applied and Environmental Microbiology

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs – Söder et al. – Acta Veterinaria Scandinavica

Alterations in common marmoset gut microbiome associated with duodenal strictures – Sheh et al. – Scientific Reports

Plant, root, and soil microbiome

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

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

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

Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau – Ren et al. – Envionmental Microbiome

Built environment (subways, indoor surfaces)

Multikingdom interactions govern the microbiome in subterranean cultural heritage sites – Liu et al. – PNAS

Indoor green can modify the indoor dust microbial communities – Dockx et al. – Indoor Air


Microbial community succession of submerged bones in an aquatic habitat – Kaszubinski et al . – Journal of Forensic Sciences


Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation – Podlesny et al. – Microbiome

[PREPRINT]Detection of Parasites in Microbiomes using Metagenomics – Kirstagler, Aarestrup & Pamp – bioRxiv


Tryptophan Supplementation Increases the Production of Microbial-Derived AhR Agonists in an In Vitro Simulator of Intestinal Microbial Ecosystem – Koper et al. – J. Agric. Food Chem.

March 23, 2022

General microbiome

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance – Yu et al. – Nature Microbiology

Human skin microbiome

Skin microbiota diversity among genetically unrelated individuals of Indian origin – Pothbhare et al. – PeerJ

Human gut microbiome

[REVIEW]Gut microbiota and allergic diseases in children – Akagawa & Kaneko – Allergology International

[REVIEW]Gut microbiome: New biomarkers in early screening of colorectal cancer – Zhou et al. – Journal of Clinical Laboratory Analysis

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? – Eckermann et al. – Developmental Psychobiology

[PREPRINT]Meta-analysis of the autism gut microbiome identifies factors influencing study discrepancies and machine learning classification – Chavira, Wang & Mills – bioRxiv

Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy – Huang et al. – Computational and Mathematical Methods in Medicine

Animal microbiome

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation – Dallas & Warne – Microbial Ecology

Changes in gut microbiota composition with age and correlations with gut inflammation in rats – Meng et al. – PLOS One

[REVIEW]Translational multi-omics microbiome research for strategies to improve cattle production and health – Wang & Guan – Emerging Topics in Lefe Sciences

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine – Zhang et al. – Food & Function

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice – Zhou et al. – Environmental Microbiology

Microbiome-metabolomics deciphers the effects of Cistanche deserticola polysaccharides on agedconstipated rats – Liu et al. – Food & Function

Plant, root, and soil microbiome

[PREPRINT]Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts – Wu et al. – bioRxiv

Waste microbiome

[PREPRINT]Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste – Huang, Liu & Zong – bioRxiv

Food microbiology

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses – Li et al. – PLOS One


MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Gregory et al. – Microbiome

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Kalmar et al. – PLOS Genetics


[PREPRINT]Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Mahajan et al. – bioRxiv

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

Florence tomb by Michelangelo restored with aid of bacteria – The Guardian

March 16, 2022

General microbiome

Two-for-one: Dual host-microbe functions of S. epidermidis Sph – Swaney & Kalan – Cell Host & Microbe

Multi-omics strategies for investigating the microbiome in toxicology research – Morgan, Perdew & Patterson – Toxicological Sciences

Human vaginal microbiome

Vaginal microbiome and cervical cancer – Kyrgiou & Moscicki – Seminars in Cancer Biology

Human gut microbiome

Multi-omic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host-Microbe Associations – Chang et al . – JID Innovations

Impact of Nutritional Profile on Gut Microbiota Diversity in Patients with Celiac Disease – Soheilian-Khorzoghi et al. – Current Microbiology

[REVIEW]Roles of the gut virome and mycobiome in faecal microbiota transplantation – MPhil et al. – The Lancet Gastroenterology & Hepatology

The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial – Rinott et al. – Genome Medicine

Animal microbiome

Analysis of the gut microbiota composition of myostatin mutant cattle prepared using CRISPR/Cas9 – Wen, Mao & Gao – PLOS One

Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets – Cremonesi et al. – PLOS One

Microbiome function predicts amphibian chytridiomycosis disease dynamics – Bates et al. – Microbiome


MetaDecoder: a novel method for clustering metagenomic contigs – Liu et al. – Microbiome

[PREPRINT]Testing microbiome associations with censored survival outcomes at both the community and individual taxon levels – Hu et al. – bioRxiv

March 09, 2022

General microbiome

Public human microbiome data are dominated by highly developed countries – Abdill, Adamowicz & Blekhman – PLOS Biology

Beyond the Microbiome: Germ-ganism? An Integrative Idea for Microbial Existence, Organization, Growth, Pathogenicity, and Therapeutics – Kambouris et al. – OMICS

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes – Modha et al. – mSystems

Human respiratory microbiome

Alterations of lung microbiota in patients with non-small cell lung cancer – Zeng et al. – Bioengineered

Human vaginal microbiome

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing – Marquet et al. – Scientific Reports

Human gut microbiome

[REVIEW]Personal diet–microbiota interactions and weight loss – Roager & Christensen

Integrated analysis of gut microbiome and host immune responses in COVID-19 – Xu et al. – Frontiers in Medicine

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

Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets – Cremonesi et al. – PLOS One

Complete Genome Sequences of Three Staphylococcus haemolyticus Strains Isolated from the Lung of a TGFβ1 Transgenic Mouse with Lung Fibrosis – Abdel-Hamid et al. – Microbiology Resource Announcements

Colitis-associated microbiota drives changes in behaviour in male mice in the absence of inflammation – Vicentini et al. – Brain, Behaviour, and Immunity

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart – Kieser, Zdobnov & Trajkovski – PLOS Comp Biol

Plant, root, and soil microbiome

The microbiome and resistome of apple fruits alter in the post-harvest period – Wassermann et al. – Environmental Microbiome

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

Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome – Maire et al. – Integrative and Comparative Biology


[PREPRINT]A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities – Shaffer et al. – bioRxiv

[PREPRINT]A comparison of hard and soft direct methods for DNA extraction from soil – Hill et al. – bioRxiv

March 7, 2022

hard to do science

Originally tweeted by Peter Fabian (@PeterFabianLab) on March 4, 2022.

General microbiome

Microbial invasion of a toxic medium is facilitated by a resident community but inhibited as the community co-evolves – Philippe Piccardi – bioRxiv

Could a Focus on the “Why” of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society? – Leighton Pritchard – Preprints

Vaginal microbiome

Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation – Seth M. Bloom – Nature Microbiology

Citizen-science map of the vaginal microbiome – Sarah Lebeer – Research Square

Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – Michael T France – Genome Biology

Urinary microbiome

Review: The gut, vaginal, and urine microbiome in overactive bladder: a systematic review – Christina Sze – International Urogynecology Journal

Gut microbiome

Identification of antimicrobial peptides from the human gut microbiome using deep learning – Yue Ma – Nature Biotechnology

Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders – Amira Metwaly – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Temporal variations shape the gut microbiome ecology of the moth Brithys crini – Jesús Marín-Miret – Environmental Microbiology


Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Braden T. Tierney – PlosBiology

MultiBaC: An R package to remove batch effects in multi-omic experiments – Manuel Ugidos – Bioinformatics

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps – Yuxuan Du & Fengzhu Sun – Genome Biology

TOMORROW MVIF #7 and the latest microbiome science!

Hey #microbiome people! 🦠
In MARCH there is #MVIF #7!

You can register for free here:

⭐️Keynote Speaker: prof Willem De Vos ⭐️

📅Check out day and time in your city here:

See you there! 😎

Originally tweeted by Microbiome Virtual International Forum (@MicrobiomeVIF) on February 17, 2022.

March 3, 2022

Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!

Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv


Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv