Category Archives: Animal experiments

October 26, 2022

Posted on by

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

Posted on by

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

Posted on by

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 28, 2022

Posted on by

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 22, 2022

Posted on by

Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.

Enjoy!

Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases

Techniques

A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE

September 21, 2022

Posted on by

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 18, 2022

Posted on by

Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

August 31, 2022

Posted on by

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 10, 2022

Posted on by

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

Posted on by

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