September 28, 2022

General microbiome

[Personal View]Causal discovery for the microbiome – Corander, Hanage & Pensar – The Lancet Microbe

Integrative functional analysis uncovers metabolic differences between Candida species – Begum et al. – Communications Biology

Human skin microbiome

Evolution of the facial skin microbiome during puberty in normal and acne skin – Schneider et al. – JEADV

Human gut microbiome

[REVIEW]Harnessing Microbiota to Improve Immunotherapy for Gastrointestinal Cancers – Goc & Sonnenberg – Cancer Immunol Res

[REVIEW]Gut microbiome in multiple sclerosis-related cognitive impairment – Ghadiri et al. – Multiple Sclerosis and Related Disorders

[REVIEW]The Microbiome in Gastrointestinal Cancers – White & Wargo – Gastroenterology Clinics of North America

Human gut microbiota and its metabolites impact immune responses in COVID-19 and its complications – Nagata et al. – Gastroenterology

Gut microbial fermentation promotes the intestinal anti-inflammatory activity of Chinese yam polysaccharides – Bai et al. – Food Chemistry

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

The preventive effects of probiotic Akkermansia muciniphila on D-galactose/AlCl3 mediated Alzheimer’s disease-like rats – He et al. – Experimental Gerontology

Characterizing the chicken gut colonization ability of a diverse group of bacteria – Poudel et al. – Poultry Science

Obesity induced gut dysbiosis contributes to disease severity in an animal model of multiple sclerosis – Shahi et al. – Front. Immunol.

Animal microbiome (for animals in the wild)

Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii) – Zhang et al. – Science of The Total Environment

Network analysis reveals significant joint effects of microplastics and tetracycline on the gut than the gill microbiome of marine medaka – Liao et al. – Journal of Hazardous Materials

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American Alligators (Alligator mississippiensis) – Murphy et al. – Environmental Microbiology

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards – Williams et al. – Applied and Environmental Microbiology

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

Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication – Weingarten & Jackson – Microbial Ecology

Built environment (subways, indoor surfaces)

Microbial community regulation and performance enhancement in gas biofilters by interrupting bacterial communication – Wang et al. – Microbiome

Bioinformatics

Identification of microbial features in multivariate regression under false discovery rate control – Srinivasan, Xue and Zhan – Computational Statistics & Data Analysis

Techniques

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oyewole et al. – Microbiome

September 21, 2022

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 14, 2022

General microbiome

[PREPRINT]Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity – Puente-Sánchez et al. – bioRiv

Human airway microbiome

[PREPRINT]Genomic and ecologic characteristics of the airway microbial-mucosal complex – Cuthbertson et al. – bioRxiv

Animal microbiome (for animals in the wild)

[DATA ]A global dataset of microbial community in ticks from metagenome study – Liu et al. – Scientific Data

Highland adaptation of birds on the Qinghai-Tibet Plateau via gut microbiota – Liu et al. – Applied Microbiology and Biotechnology

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

[PREPRINT][Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway](Microbial community dynamics during a harmful Chrysochromulina leadbeateri bloom in northern Norway) – Aalto et al. – bioRxiv

September 7, 2022

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

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

August 24, 2022

General microbiome

[REVIEW]Detecting bacterial adaptation within individual microbiomes – Liebermann – Phil. Trans. R. Soc. B

[REVIEW]Soil microbiomes and one health – Banerjee & van der Heijden – Nature Reviews Microbiology

Pregnancy and early life

Microbial Analysis of Umbilical Cord Blood Reveals Novel Pathogens Associated with Stillbirth and Early Preterm Birth – Vander Haar et al. – mBio

Human respiratory microbiome

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis – Avalos-Fernandez et al. – Respiratory Research

Human saliva microbiome

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students – Ahrens et al. – Scientific Reports

Human gut microbiome

The gut microbiota is associated with immune cell dynamics in humans – Schluter et al. – Nature

The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces – Vujkovic-Cvijin et al. – Science Translational Medicine

Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling – Kim et al. – ISME Communications

Correlation of inflammatory biomarkers with the diversity of Bacteroidaceae, Bifidobacteriaceae, Prevotellaceae and Lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease – Asgharian et al. – Advances in Medical Sciences

Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective – Stefanetti & Kasper – Biochemistry

Location-specific signatures of Crohn’s disease at a multi-omics scale – Gonzalez et al. – Microbiome

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample – Mohr et al. – Scientific Reports

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

The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes – Miranda et al. – mSystems

Microbes in space

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

Bioinformatics

[PREPRINT]Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 – Blanco-Miguez et al. – bioRxiv

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data – Lin, Eggesbø & Peddada – Nature Communications

Techniques

Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing – Wiemann et al. – Gut Microbes

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples – Baker et al. – mSystems

August 17, 2022

Pregnancy and early life

[REVIEW]Special Diets in Infants and Children and Impact on Gut Microbioma – Di Profio et al. – Nutrients

Cervicovaginal Complement Activation and Microbiota During Pregnancy and in Parturition – Livson et al. – Frontiers in Immunology

Human gut microbiome

[REVIEW]Interaction between microbiota and immunity and its implication in colorectal cancer – Xing et al. – Frontiers in Immunology

Mapping the human gut mycobiome in middle-aged and elderly adults: multiomics insights and implications for host metabolic health – Shuai et al. – Gut

Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease – Hellmann et al. – IBD

Pan-cancer analysis of microbiome quantitative trait loci – Chen et al. – Cancer Research

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

A Comparison of the Impact of Restrictive Diets on the Gastrointestinal Tract of Mice – Gregor et al. – Nutirents

High fat diets induce early changes in gut microbiota that may serve as markers of ulterior altered physiological and biochemical parameters related to metabolic syndrome. Effect of virgin olive oil in comparison to butter – Andújar-Tenorio et al. – PLOS One

Animal microbiome (for animals in the wild)

Host-Specific Larval Lepidopteran Mortality to Pathogenic Serratia Mediated by Poor Diet – Mason et al. – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Chemical and microbial characterization of sugarcane mill mud for soil applications – Uchimiya, Hay & LeBlanc – PLOS One

August 10, 2022

General microbiome

Microbiome-associated human genetic variants impact phenome-wide disease risk – Markowitz et al. – PNAS

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk – Wang et al. – Microbiome

[REVIEW]A framework for testing the impact of co-infections on host gut microbiomes – Schmid et al. – Animal Microbiome

Human vaginal microbiome

Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? – Yang et al. – PLOS One

Human gut microbiome

[REVIEW]The role of the gut microbiota in multiple sclerosis – Correale, Hohlfeld & Baranzini

Specific gut microbiota alterations in essential tremor and its difference from Parkinson’s disease – Zhang et al. – NPJ Parkinson’s Disease

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics – Podlesny et al. – Cell Reports Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Cheung et al. – Journal of Gastroenterology and Hepatology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Animal microbiome

Camel milk microbiota: A culture-independent assessment – Rahmeh et al. – Food Research International

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity – Weikart et al. – The Journal of Nutritional Biochemistry

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs – Gaire et al. – Microbiome

Plant, root, and soil microbiome

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation – Fox, Widmer & Lüscher – Environmental Research

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

The streamwater microbiome encodes hydrologic data across scales – URycki et al. – Science of The Total Environment

Bioinformatics / Data

[PREPRINT]Lake iTag measurements over nineteen years, introducing the limony dataset – Rohwer & McMahon – bioRxiv

August 03, 2022

Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

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

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology

Bioinformatics

Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

June 29, 2022

General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

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

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

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

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv