July 5, 2022

Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

June 22, 2022

General microbiome

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection – Long et al. – Communications Biology

Pregnancy and early life

[PREPRINT]Strong pathogen competition in neonatal gut colonisation – Mäklin et al. – bioRxiv

Human skin microbiome

Dysbiosis of Skin Microbiota with Increased Fungal Diversity is Associated with Severity of Disease in Atopic Dermatitis – Schmid et al. – JEADV

Human gut microbiome

Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China – Sun et al. – mSystems

A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer – Yuan et al. – Investigational New Drugs

[REVIEW]Vegetarianism, Microbiota and Cardiovascular health: Looking back, and forward – Kumar et al. – European Journal of Preventive Cardiology

[REVIEW]Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis – So, Loughman & Staudacher – The American Journal of Clinical Nutrition

Profiling gut microbiota and bile acid metabolism in critically ill children – Kean et al. – Scientific Reports

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. – BMC Bioinformatics

The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease – Xu et al. – Gut Pathogenes

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

Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota – Hu et al. – PNAS

Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems – Weinert-Nelson, Biddle & Williams – Animal Microbiome

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

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States – LaMartina, Schmoldt & Newton – Microbiology Resource Announcements

Techniques

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level – Ge et al. – PNAS

June 15, 2022

General microbiome

[PREPRINT]Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica – Escudero-Leyva et al. – bioRxiv

Pregnancy and early life

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life – Wells et al. – Annual Review of Nutrition

Multi-site human microbiome

A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao – Han et al. – Clinical and Translational Medicine

Human oral microbiome

The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine – Herremans et al. – Microbiome

Human skin microbiome

Altered skin fungal and bacterial community compositions in tinea capitis – Rong et al. – Mycoses

Effects of short chain fructo-oligosaccharides on selected skin bacteria – Le Bourgot et al. – Scientific Reports

Human vaginal microbiome

Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome – Ruotsalainen et al. – Medical Microbiology and Immunology

Human gut microbiome

Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients – Hoang et al. – BMC Cancer

Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study – Miao et al. – BMC Medicine

[REVIEW]The role of virome in the gastrointestinal tract and beyond – Tiamani et al. – FEMS Microbiology Reviews

[REVIEW]Time-limited diets and the gut microbiota in cardiometabolic disease – Ratiner et al. – Journal of Diabetes

Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial – Huang et al. – Journal of Autoimmunity

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

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer – Fu et al. – Cell

Pharmacokinetic and gut microbiota analyses revealed the effect of Lactobacillus acidophilus on the metabolism of Olsalazine in ulcerative colitis rats – Li et al.

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

Plant, root, and soil microbiome

The plant host environment influences competitive interactions between bacterial pathogens – Ehau-Taumaunu & Hockett – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data – Darcy et al. – bioRxiv

June 01, 2022

General microbiome

[REVIEW]Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms – Cani et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Role of Microbiota in Viral Infections and Pathological Progression – Mizutani et al. – Viruses

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Newbury et al. – PNAS

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales – Martinez-Gutierrez & Aylward – PLOS Genetics

Interspecies commensal interactions have nonlinear impacts on host immunity – Rice et al. – Cell Host & Microbe

Human skin myco-/microbiome

Distinct skin microbiome community structures in congenital ichthyosis – Tham et al. – British Journal of Dermatology

Biodiversity of mycobial communities in health and onychomycosis – Olbrich et al. – Scientific Reports

Human gut microbiome

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study – Jiang et al. – Genome Medicine

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. – Cell Host & Microbe

Discovery of bioactive microbial gene products in inflammatory bowel disease – Zhang et al. – Nature

Animal microbiome (for animals in the wild)

The functional evolution of termite gut microbiota – Arora et al. – Microbiome

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods – Oba et al. – Journal of Animal Science

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth – Zhang et al. – Front. Microbiol.

Plant, root, and soil microbiome

Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships – Schäfer et al. – Nature Microbiology

Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis – Mehlferber et al. – Current Biology

May 25, 2022

General microbiome

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness – Ørsted et al. – PLOS Genetics

Human skin microbiome/virome

[PREPRINT]Diversity, abundance, and host specificity of the human skin associated circular and single stranded DNA virome – Graham et al. – bioRxiv

[REVIEW]Climate change, the cutaneous microbiome and skin disease: implications for a warming world – Isler et al. – International Journal of Dermatology

Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects – Benitez-Paez et al. – Gut Microbes

Human gut microbiome

[PREPRINT]Greater alteration of gut microbiota occurs in childhood obesity than adulthood obesity – Yu et al. – bioRxiv

Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet – Dahlin et al. – eBioMedicine

Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome – Liu et al. – Front. Microbiol.

Animal microbiome (for animals in the wild)

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing – Que et al. – Front. Cell. Infect. Microbiol.

Bacterial Adaptation to Venom in Snakes and Arachnida – Esmaeilishirazifard et al. – Microbiology Spectrum

Plant, root, and soil microbiome

Recent advances in understanding of fungal and oomycete effectors – Wilson & McDowell – Current Opinion in Plant Biology

Fungi associated with the potato taste defect in coffee beans from Rwanda – Hale et al. – Botanical Studies

Delineating the Bacteriome of Packaged and Loose Smokeless Tobacco Products Available in North India – Srivastava et al. – Applied Microbiology and Biotechnology

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

Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding – de Souza et al. – Scientific Reports

May 20, 2022

General microbiome

[Review]Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Liu et al. Microbiome

Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter – Hoarfost et al. – Nature Communications

Covid19 and Metabolome

Sex differences in global metabolomic profiles of COVID-19 patients – Escarcega et al. – Cell Death & Disease

Pregnancy and early life

Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures? – Keburiya et al. – BMC Women’s Health

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies – Lebeaux et al. – Pediatric Research

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

Human respiratory microbiome

The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Shimizu et al. – Thoacic Cancer

Human skin microbiome

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata – Agostinetto et al. – Databases

Human gut microbiome

Dynamic microbiome and metabolome analyses reveal the interaction between gut microbiota and anti-PD-1 based immunotherapy in hepatocellular carcinoma – Wu et al. – International Journal of Cancer

[Review]Exploring the multifactorial aspects of Gut Microbiome in Parkinson’s Disease – Pavan et al. – Folia Microbiologica

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

[Preprint]Gut microbiota of homing pigeons shows summer-winter variation under constant diet indicating a substantial effect of temperature – Dietz et al. – bioRxiv

Animal microbiome (for animals in the wild)

[Review]Bumblebees with the socially transmitted microbiome: A novel model organism for gut microbiota research – Zhang & Zheng – Insect Science

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats – Xiao et al. – The ISME Journal

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses – Li et al. – Front. Vet. Sci.

Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates – Microbiology Spectrum

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

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats – Liu et al. – Microbiome

Bioinformatics

CBEA: Competitive balances for taxonomic enrichment analysis – Nguyen, Hoen & Frost – PLOS Computational Biology

Clustering compositional data using Dirichlet mixture model – Pal & Heumann – PLOS One

Techniques

Generation and application of pseudo–long reads for metagenome assembly – Sim et al. – Giga Science

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

[Preprint]Estimating Microbial Population Data from Optical Density – Mira, Yeh & Hall – bioRxiv

May 11, 2022

General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

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

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv

Bioinformatics

Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment

April 23, 2022

Human and General Microbiome

Review: Fecal microbiota transplantation for people living with HIV: A scoping review – Brenda Caira-Chuquineyra – AIDS Research and Human Retroviruses

Review: Microbiota-derived tryptophan metabolites in vascular inflammation and cardiovascular disease – Nadja Paeslack – Amino Acids

Review: Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders – J Horn – Translational Psychiatry

Short Communication: Longitudinal analysis of the impact of oral contraceptive use on the gut microbiome – Xinwei Hua – Journal of Medical Microbiology

Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants – Emily A Kaelin – Nature Microbiology

Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups – Rachel Hurst – European Urology Oncology

Alterations of mucosa-attached microbiome and epithelial cell numbers in the cystic fibrosis small intestine with implications for intestinal disease – Jennifer Kelly – Scientific Reports

Peptidoglycan from Akkermansia muciniphila MucT: chemical structure and immunostimulatory properties of muropeptides – Pilar Garcia-Vello – Glycobiology

Impact of Food Origin Lactiplantibacillus plantarum Strains on the Human Intestinal Microbiota in an in vitro System – Natalia Garcia-Gonzalez – Frontiers in Microbiology

Plasma branched-chain and aromatic amino acids correlate with the gut microbiota and severity of Parkinson’s disease – Yi Zhang – NPJ Parkinson’s Disease

Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and influence the host response – Evgeniya V Shmeleva – PLoS Pathogens

Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome – Zlatan Mujagic – Gut Microbes

Multi-omics analyses of serum metabolome, gut microbiome and brain function reveal dysregulated microbiota-gut-brain axis in bipolar depression – Zhiming Li – Molecular Psychiatry

Abnormal gut microbiota and bile acids in patients with first-episode major depressive disorder and the correlation analysis – Ning Sun – Psychiatry and Clinical Neurosciences

Analysis of the Vulvar Skin Microbiota in Asymptomatic Women and Patients With Vulvar Lichen Sclerosus Based on 16S rRNA Sequencing – Xiaoxiao Liu – Frontiers in Cell and Developmental Biology

A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation – Mustafa Özçam – Cell Host & Microbe

Animal Microbiome

Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques – Nicholas S Rhoades – Cell Reports

Characterisation of the symbionts in the Mediterranean fruit fly gut – Mike Darrington – Microbial Genomics

Stability of the Microbiome of the Sponge Mycale (Oxymycale) acerata in the Western Antarctic Peninsula – Lea Happel – Frontiers in Microbiology

Gut Microbiota-Testis Axis: FMT Mitigates High-Fat Diet-Diminished Male Fertility via Improving Systemic and Testicular Metabolome – Yanan Hao – Microbiology Spectrum

Gut Microbiota of Wild Fish as Reporters of Compromised Aquatic Environments Sleuthed through Machine Learning – John Turner – Physiological Genomics

Plant Microbiome

Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes – Anchittha Satjarak – Scientific Reports

Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiome – Lucas Schmitz – The ISME Journal

Environmental Microbiology

Chemotaxis shapes the microscale organization of the ocean’s microbiome – Jean-Baptiste Raina – Nature

Catabolism of sialic acids in an environmental microbial community – Sergio Tomás-Martínez – FEMS Microbiology Ecology

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams – Susheel Bhanu Busi – Nature Communications

Bioinformatics

Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa – Renato Giliberti – PLoS Computational Biology

Metagenomic signatures of balancing selection in the human gut – Andrew H Moeller – Molecular Ecology

Techniques

Method for absolute quantification of short chain fatty acids via reverse phase chromatography mass spectrometry – Dominique G Bihan – PloS One

April 20, 2022

General microbiome

How the gut talks to the brain – Adamantidis – Science

Pregnancy and early life

Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus – Chen et al. – PLOS One

Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding – Grant-Beurmann et al. – Microbiome

Human respiratory microbiome

The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections – Li et al. – PLOS One

Human skin microbiome

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes – Verbanic, Deacon & Chen – Microbiology Spectrum

Human vaginal microbiome

Vaginal microbiota as an unusual cause of spondylodiscitis – Kolakowska et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

Environmental factors shaping the gut microbiome in a Dutch population – Gacesa et al. – Nature

Predictive Role of Gut Microbiota in Weight Loss Achievement after Bariatric Surgery – Gutierrez-Repiso et al. – Journal of the American College of Surgeons

Intestinal Blautia may protect against neutropenic fever in allogeneic transplant patients by augmenting the intestinal epithelium – Rashidi et al. – Clinical Infectious Diseases

Clinical Observation of the Effects of Oral Opioid on Inflammatory Cytokines and Gut Microbiota in Patients with Moderate to Severe Cancer Pain: A Retrospective Cohort Study – Wang et al. – Pain and Therapy

The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass – Debedat et al. – Gut Microbes

The gut microbial metabolite formate exacerbates colorectal cancer progression – Ternes et al. – Nature Metabolism

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children – Nadimpalli et al. – Nature Microbiology

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

The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids – Xiao et al. – Microbiome

Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination – Kihl et al. – PLOS One

Hawk tea prevents high-fat diet-induced obesity in mice by activating the AMPK/ACC/SREBP1c signaling pathways and regulating the gut microbiota – Tao et al. – Food & Function

Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy – Guo et al. – Journal of Applied Microbiology

The gut microbiome influences host diet selection behavior – Trevelline & Kohl – PNAS

High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction – Frazier et al. – Cell Host & Microbe

Animal microbiome (for animals in the wild)

Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome – Trujillo et al. – PLOS One

Effects of Schyzocotyle acheilognathi (Yamaguti, 1934) infection on the intestinal microbiota, growth and immune reactions of grass carp (Ctenopharyngodon idella) – Fu et al. – PLOS One

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses – Shan et al. – Microbiome

Interspecies microbiome transplantation recapitulates microbial acquisition in mosquitoes – Coon, Hedge & Hughes

Gut microbiota promote biotransformation and bioaccumulation of arsenic in tilapia – Environmental Pollution

Plant, root, and soil microbiome

Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species – Vandepol et al. – PLOS One

Bacterial and fungal microbiota of total mixed ration silage stored at various temperatures – Wali et al. – Journal of Applied Microbiology

Bioinformatics

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina – PLOS One

Techniques

THOR’s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community – Hurley et al. – mBio

Microbes in the news

Bacteria generate electricity from methane

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

Bioinformatics

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

Techniques

[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