Category Archives: Resistome

March 18, 2024

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Today’s digest features the human gut microbiome atlas of Africa, sociobiome, a large human gut Bacteroidales culture collection, Patescibacteria in global waste water treatment plants, and more.

This month, the May 2024 contribution period of Outreachy started! Outreachy, as an internship program, supports diversity in open source & open science!

See you at #MVIF!

Gut microbiome

Expanding the human gut microbiome atlas of Africa โ€“ Dylan G Maghini โ€“ bioRxiv

Review: The individual response to antibiotics and diet โ€” insights into gut microbial resilience and host metabolism โ€“ Lars M. M. Vliex โ€“ Nature Reviews Endocrinology

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study โ€“ Leon Peto โ€“ medRxiv

Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy โ€“ Jinbing Bai โ€“ Journal of Translational Medicine

Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome โ€“ Nadia Andrea Andreani โ€“ Gut Microbes

Healthy microbiome – moving towards functional interpretation โ€“ Kinga Zieliล„ska โ€“ bioRxiv

Sociobiome – Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US โ€“ Soyoung Kwak โ€“ npj Biofilms and Microbiomes

Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans โ€“ Sarah Morais โ€“ Science

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution โ€“ Zhenrun J. Zhang โ€“ bioRxiv

Animal experiment

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects โ€“ Kertu Liis Krigul โ€“ bioRxiv

Water microbiome

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants โ€“ Huifeng Hu โ€“ Microbiome

Bioinformatics

Review: Challenges in computational discovery of bioactive peptides in โ€™omics data โ€“ Luis Pedro Coelho โ€“ Proteomics

For long-term sustainable software in bioinformatics โ€“ Luis Pedro Coelho โ€“ Plos Computational Biology

Data-driven prediction of colonization outcomes for complex microbial communities โ€“ Lu Wu โ€“ Nature Communications

February 23, 2024

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Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.

NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif

See you at #MVIF next week!

Oral microbiome

Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases โ€“ Davide Bazzani โ€“ npj Biofilms and Microbiomes

Nasal microbiome

Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability โ€“ Y Zhao โ€“ bioRxiv

Semen microbiome

Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility โ€“ Shahriar Mowla โ€“ bioRxiv

Gut microbiome

CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei โ€“ Sivan Kijner โ€“ Nature Communications

Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study โ€“ Kinga Humiล„ska-Lisowska โ€“ Plos One

The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study โ€“ Matthew VanOrmer โ€“ Plos One

Early-life exposures to specific commensal microbes prevent type 1 diabetes โ€“ Jamal Green โ€“ bioRxiv

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing โ€“ Philipp Spohr โ€“ Scientific Reports

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome โ€“ Qiyi Chen โ€“ Cell Host & Microbe

Animal experiment

The gut ileal mucosal virome is disturbed in patients with Crohnโ€™s disease and exacerbates intestinal inflammation in mice โ€“ Zhirui Cao โ€“ Nature Communications

Animal microbiome

Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog โ€“ Ji-Eun Lee โ€“ Plos One

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages โ€“ Tao Zeng โ€“ bioRxiv

Water microbiome

A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters โ€“ Francesc Corbera-Rubio – bioRxiv

Human virome

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples โ€“ Moreno Zolfo โ€“ bioRxiv

January 8, 2024

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The microbiome digest team, Juan Pablo Cardenas Astudillo, Axel Kรผnstner and Svetlana Ugarcina Perovic (it’s me), wishes you happy and healthy 2024! Also, we wish to have more members in our team in order to cover all daily microbiome science news: if you are interested in reviewing microbiome papers at your convenience (with our support!) and digest them for the community, feel free to contact us. We are happy to welcome you!

And, yes, see you at MVIF #25!

Vaginal microbiome

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment โ€“ Meilin Zhu โ€“ bioRxiv

Gut microbiome

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen โ€“ Brantley Hall โ€“ Nature Microbiology

Influence of feeding practices in the composition and functionality of infant gut microbiota and its relationship with health โ€“ Misael Martรญnez-Martรญnez โ€“ PlosOne

Mucin-degrading gut bacteria promote anti-parasitic immunity โ€“ Mathis Wolter โ€“ bioRxiv

Host genetic regulation of human gut microbial structural variation โ€“ Daria V. Zhernakova โ€“ Nature

Animal microbiome

Deciphering the gut microbiome of grass carp through multi-omics approach โ€“ Ming Li โ€“ Microbiome

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus โ€“ Chloe G. Shaw โ€“ BMC Microbiology

Animal experiments

Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis โ€“ Runxiang Xie โ€“ Microbiome

Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity โ€“ Erica Bonazzi โ€“ Microbiome

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice โ€“ Rachel M. Bleich โ€“ Microbiome

Environmental microbiome

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes โ€“ Victor Borin Centurion โ€“ Environmental Microbiome

Plant, root, soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet โ€“ Abdelrahman Alahmad โ€“ Microbiome

Methods

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome โ€“ Lei Cao โ€“ Nature Methods

Bioinformatics

A catalogue of small proteins from the global microbiome โ€“ Yiqian Duan โ€“ bioRxiv

December 15, 2023

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Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome โ€“ David Galeana-Cadena โ€“ Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system โ€“ Omry Koren โ€“ Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition โ€“ Matthew C. Hibberd โ€“ Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients โ€“ Zixuan Xie โ€“ Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii โ€“ Jing Yang โ€“ Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont โ€“ Peter Kuffa โ€“ Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice โ€“ Susana C. M. Ferreira โ€“ bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers โ€“ Gilles L. C. Baud โ€“ Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird โ€“ Martta Liukkonen โ€“ bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota โ€“ Nathan Vannier โ€“ Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life โ€“ Yue Clare Lou โ€“ Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities โ€“ Patrick Mรผller โ€“ Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes โ€“ James P.J. Chong โ€“ bioRxiv

November 10, 2023

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Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals โ€“ Carlos Flores โ€“ Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome โ€“ Mรกrcia Sousa โ€“ International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract โ€“ Tom Eilers โ€“ International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization โ€“ Haider S. Manzer โ€“ mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression โ€“ Atara Uzan-Yulzari โ€“ bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile โ€“ Shinya Kageyama โ€“ mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their ownerโ€™s gut and living environment โ€“ Yiwen Yang โ€“ Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk โ€“ Christopher J Dean โ€“ bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease โ€“ Lola Holcomb โ€“ mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model โ€“ Hongyu Wang โ€“ npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols โ€“ Sarah Pitell, Sarah-Jane Haig โ€“ Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants โ€“ Huifeng Hu โ€“ bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes โ€“ Christian T. Meyer โ€“ Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses โ€“ Saioa Manzano-Morales โ€“ Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool โ€“ Hoon Je Seong โ€“ Briefings in Bioinformatics


October 13, 2023

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Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science โ€“ Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics โ€“ Georgios A. Pavlopoulos โ€“ Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome โ€“ Richard J. Abdill โ€“ bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets โ€“ Anna C. Salvador โ€“ Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects โ€“ Pan Huang โ€“ bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index โ€“ Sofรญa Tesolato โ€“ PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults โ€“ Christopher H. Gu โ€“ PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy โ€“ Martin F. Laursen & Henrik M. Roager โ€“ The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments โ€“ Jessica Subirats โ€“ Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods โ€“ Sabin Khana โ€“ bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa โ€“ Claire E. Lamb & Joy E. M. Watts โ€“ Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management โ€“ Rita A. H. Hoving-Bolink โ€“ PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers โ€“ Oona L.O. Snoeyenbos-West โ€“ bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes โ€“ Daryna Zavadska โ€“ bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat โ€“ Chen Yang & MicrobiomeStat team

June 16, 2023

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Thank you for answering my question above.

Today’s digest features indigenous chicken in Ethiopia, drug effects on gut microbiome, beach water microbial risk assessment, and more. See you at #MVIF next week!

Microbial ecology

Guild and Niche Determination Enable Targeted Alteration of the Microbiome โ€“ Oriane Moyne โ€“ bioRxiv

Genital microbiome

Interaction of genital microbiota in infertile couples โ€“ David Baud โ€“ bioRxiv

Gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment โ€“ Sarela Garcia-Santamarina โ€“ bioRxiv

Skin microbiome

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons โ€“ Marcus H. Y. Leung โ€“ Microbiome

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia โ€“ Laura Glendinning โ€“ bioRxiv

Animal experiments

Effects of fenbendazole on fecal microbiome in BPH/5 mice, a model of hypertension and obesity, a brief report โ€“ Kalie F. Beckers โ€“ Plos One

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water โ€“ Chong-Su Kim and Dong-Mi Shin โ€“ Plos One

Plant microbiome

Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores โ€“ Eric W. Seabloom โ€“ Nature Communications

Methodology

Processing and Storage Methods Affect Oral and Gut Microbiome Composition โ€“ Dorothy K. Superdock โ€“ bioRxiv

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification โ€“ Yu Yang โ€“ Water Research

Bioinformatics

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics โ€“ Rรฉmi Gschwind โ€“ Nucleic Acids Research

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome โ€“ Ana Elena Pรฉrez-Cobas โ€“ Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status โ€“ Daniela Vargas-Robles โ€“ bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic โ€“ Serena Porcari โ€“ Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions โ€“ Dari Shalon โ€“ Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases โ€“ Jose Antonio Santos-Marcos โ€“ Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis โ€“ Paige Salerno โ€“ bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis โ€“ Giulia Alessandri โ€“ bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice โ€“ Paolo Manghi โ€“ Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning โ€“ Olga Mineeva โ€“ Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing โ€“ David Calderรณn-Franco โ€“ Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study โ€“ Gabriella Brigando โ€“ PlosOne

April 14, 2023

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Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions โฌ‡๏ธ

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms โ€“ Eldon Ager โ€“ bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? โ€“ Uli Klรผmper โ€“ bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites โ€“ Debby Bogaert โ€“ Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients โ€“ Justine W. Debelius โ€“ Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy โ€“ Ruben Ladeira, Julien Tap, Muriel Derrien โ€“ Microbiome Research Reports

Water microbiome

The microbial dark matter and โ€œwanted listโ€ in worldwide wastewater treatment plants โ€“ Yulin Zhang โ€“ Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems โ€“ David Calderรณn-Franco โ€“ Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and ฮฒ-cell death in streptozotocin-induced type 1 diabetic mice โ€“ Jongdee Nopparat โ€“ PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem โ€“ Madeleine Spatz โ€“ Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice โ€“ Rikeish R. Muralitharan โ€“ bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut โ€“ Shiraz A. Shah โ€“ Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria โ€“ Juntao Shen โ€“ Cell Host & Microbe

Methodology

Reducing bias in microbiome research: Comparing methods from sample collection to sequencing โ€“ Jolanda Kool โ€“ Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon โ€“ Lucie Etienne-Mesmin โ€“ Microbiology Spectrum

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes โ€“ Wojtek Bazant โ€“ Microbiome

March 9, 2023

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Today’s digest features studies on latent and established antibiotic resistance genes in microbiomes, newborn skin microbiome, drinking water microbiome after COVID-19 pandemic, and more. Listen to the science behind The Last of Us!

See you at #MVIF next week!

Antibiotic resistome

*Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes โ€“ Juan Salvador Inda-Dรญaz โ€“ Microbiome

Human skin

*The skin microbiome in the first year of life and its association with atopic dermatitis โ€“ Alexis Rapin โ€“ Allergy

Urinary tract

Review: Microbiome in urological diseases: Axis crosstalk and bladder disorders โ€“ Hae Woong Choi โ€“ Investigative and Clinical Urology

Human gut

Human microbiome variance is underestimated โ€“ Fergus Shanahan โ€“ Current Opinion in Microbiology

Population-level impacts of antibiotic usage on the human gut microbiome โ€“ Kihyun Lee โ€“ Nature Communications

Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut โ€“ Nick Bohmann โ€“ bioRxiv

Review: Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics โ€“ Aleksandr A. Arzamasov & Andrei L. Osterman โ€“ Critical Reviews in Biochemistry and Molecular Biology

Guts Imbalance Imbalances the Brain: A Review of Gut Microbiota Association With Neurological and Psychiatric Disorders โ€“ Laura Mitrea โ€“ Frontiers in Medicine

Drinking water

*Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic โ€“ Solize Vosloo โ€“ Environmental Science & Technology