May 05, 2021

Special Issue on Interplay of Gene Expression Regulation and Microbiome

Cells has a call for papers for a special issue about the ‘Interplay of Gene Expression Regulation and Microbiome‘. This Special Issue should serve as a platform to bring together recent advances in the understanding of the dynamic interplay between gene regulation and host-microbiome interaction.

Human oral microbiome

Anna Karenina and the subgingival microbiome associated with periodontitis – Altabtaei et al. – Microbiome

Human gut microbiome

[REVIEW]The Association Between Intestinal Bacteria and Allergic Diseases—Cause or Consequence? – Han et al. – Front. Cell. Infect. Microbiol.

[Review]Exploring the Modulatory Effects of Gut Microbiota in Anti-Cancer Therapy – Li, Deng & Chen – Front. Oncol.

[REVIEW]The interplay between Helicobacter pylori and gastrointestinal microbiota – Chen et al. Gut Microbes

Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence – Vallianou et al. – Metabploism

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

Gut microbiota contributes to the development of hypertension in a genetic mouse model of systemic lupus erythematosus – de la Visitación et al. – British Journal of Pharmacology

Infant gut microbiota modulation by human milk disaccharides in humanized microbiome mice – Rubio-Del-Campo – Gut Microbes

Animal microbiome (for animals in the wild)

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Apostolopoulos et al. PLOS One

Bioinformatics

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 – Beghini et al. – eLife

Techniques

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements – Tourlousse et al. – Microbiome

May 4, 2021

In today’s post – host-microbe marker for inflammatory bowel disease, evolution of soil bacterium along the climate gradient, how C. difficile exploits host metabolite under inflammatory conditions induced by its own toxins and differential response of commensals to alter C. difficle virulence.

Job Posting

Microbiome Scientific Researcher, Computational (Cancer Immunology) – Genentech South San Francisco, California

General Microbiome

Endothelium–gut communication: IGF‐1Rs crosstalk with microbiota – Zhen Bouman Chen – EMBO reports

Recent advances in marine algae oligosaccharides: structure, analysis, and potential prebiotic activities – Xu-Ting Xie – Critical Reviews in Food Science and Nutrition

Human Microbiome

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li – Gut

Gut Dysbiosis Associated with Antibiotics and Disease Severity and Its Relation to Mortality in Critically Ill Patients – Masahiro Ojima – Digestive Diseases and Sciences

Effects of Totum-63 on glucose homeostasis and post-prandial glycemia: a translational study – Vivien Chavanelle – American Journal of Physiology Endocrinology and Metabolism

Impact of a fermented soy beverage supplemented with acerola by-product on the gut microbiota from lean and obese subjects using an in vitro model of the human colon – Antonio Diogo Silva Vieira – Environmental biotechnology

Decoding the matrix: multiomics reveals host-microbe biomarker for inflammatory bowel disease – Monica Viladomiu – The Journal of Clinical Investigation

Animal Microbiome

C. difficile exploits a host metabolite produced during toxin-mediated disease – Kali M. Pruss – Nature

In vivo commensal control of Clostridioides difficile virulence – Brintha P. Girinathan – BioRxiv

Description and comparison of the skin and ear canal microbiota of non-allergic and allergic German shepherd dogs using next generation sequencing – Neoklis Apostolopoulos – PlosOne

Plant, root and soil microbiome

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient – Alexander B. Chase – PNAS

Soils and sediments host novel archaea with divergent monooxygenases implicated in ammonia oxidation – Spencer Diamond – BioRxiv

Water microbiome

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem – Ya-Jou Chen – ISME Journal

Techniques

Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S – Yi‐Chun Yeh – Environmental Microbiology

Bacteria

Completion of the gut microbial epi-bile acid pathway – Heidi L. Doden – Gut Microbes

Possible effects of Porphyromonas gingivalis on the blood-brain barrier in Alzheimer’s disease – Ingar Olsen – Expert Review of Anti-infective Therapy

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii – Tao Luo – Nature Communications

May 3, 2021

Water microbiome

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea – Płaza et al. – PLoS ONE

From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru – Romero et al. – PLoS ONE

Distribution and diversity of eukaryotic microalgae in Kuwait waters assessed using 18S rRNA gene sequencing – Kumar et al. – PLoS ONE

Plant microbiome

Toward understanding microbiota homeostasis in the plant kingdom – Paasch & He – PLoS Pathogens

Animal microbiome

Seasonal dynamics of diet–gut microbiota interaction in adaptation of yaks to life at high altitude – Guo et al. – npj Biofilms and Microbiomes

Low biomass microbiome

Experimental parameters defining ultra-low biomass bioaerosol analysis – Luhung et al. – npj Biofilms and Microbiomes

Human gut microbiome

A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization – Petersen et al. – Cell Reports Medicine

May 1, 2021

Have a great International Workers’ Day! Today, in this Digest: a review article about the role of butyrate (a product of microbiome activity) in the early development of microbiota. We have also: probiotics and COVID19, microbiota toxins and cardiovascular disease, microbiome studies from Indonesia, a US cohort study investigating links between the microbiome, diet, and TMAO levels; several articles about connections between the diet and the microbiome, shrimp microbiota, and more!   

Human and General Microbiome

Review: Microbial driven genetic variation in holobionts – Ilana Zilber-Rosenberg and Eugene Rosenberg – FEMS Microbiology Reviews

Review: Butyrate: A Link between Early Life Nutrition and Gut Microbiome in the Development of Food Allergy – Margherita Di Costanzo et al.,Life (MDPI)

Review: Next-Generation Probiotics and Their Metabolites in COVID-19 – Thomas Gautier et al.,Microorganisms (MDPI)

Review: Circulating bile acids as a link between the gut microbiota and cardiovascular health: Impact of Prebiotics, probiotics and polyphenol-rich foods – R.A.G. Pushpass et al., – Nutrition Research Reviews

Review: Two Gut Microbiota-Derived Toxins Are Closely Associated with Cardiovascular Diseases: A Review – Tomoya Yamashita et al., – Toxins (MDPI)

Review: Dietary Strategies for Management of Metabolic Syndrome: Role of Gut Microbiota Metabolites – Sonia Croci et al., – Nutrients (MDPI)

Review: Challenging Cosmetic Innovation: The Skin Microbiota and Probiotics Protect the Skin from UV-Induced Damage – Djouhar Souak et al., – Microorganisms (MDPI)

Perspective: Gut microbiota through an evolutionary lens – Rachel N. Carmody et al., – Science

Gut Microbiome of Indonesian Adults Associated with Obesity and Type 2 Diabetes: A Cross-Sectional Study in an Asian City, Yogyakarta – Phatthanaphong Therdtatha et al., – Microorganisms (MDPI)

Interplay between diet and gut microbiome, and circulating concentrations of trimethylamine N-oxide: findings from a longitudinal cohort of US men – Jun Li et al., – Gut (BMJ)

Isolation and identification of a human intestinal bacterium capable of daidzein conversion – Yingyu Guo et al., FEMS Microbiology Letters

Associations of fine particulate matter and its constituents with airway inflammation, lung function, and buccal mucosa microbiota in children – Yihan Wu et al., – Science of The Total Environment

Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease – Claire Healy et al., – Respiratory Research (BMC)

Gut bacterial profile in Indian children of varying nutritional status: a comparative pilot study – Chandrasekhar Balasubramaniam et al., European Journal of Nutrition

The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro – Shanthi G. Parkar et al., – Scientific Reports

Oral-Gut Microbiome Axis in Gastrointestinal Disease and Cancer – Se-Young Park et al.,cancers (MDPI)

Effects of Whole-Grain and Sugar Content in Infant Cereals on Gut Microbiota at Weaning: A Randomized Trial – Julio Plaza-Diaz et al., – Nutrients (MDPI)

Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study – Annamaria Altomare et al., – Nutrients (MPDI)

Altered Composition of Microbiota in Women with Ovarian Endometrioma: Microbiome Analyses of Extracellular Vesicles in the Peritoneal Fluid – Sa-Ra Lee et al., – International Journal of Molecular Sciences

Pathogens

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor – Jay Vornhagen et al.,PLoS Pathogens

Animal Microbiome

Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community – Quentin Lamy-Besnier et al.,Microbiology Resource Announcements

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters – Rodrigo García-López et al., – Genes (MDPI)

Plant Microbiome

Impact of pesticide/fertilizer mixtures on the rhizosphere microbial community of field-grown sugarcane – Weijuan Huang et al.,3 Biotech 

Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts – Milada Solcova et al., – Microorganisms (MDPI)

Food Microbiome

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing – Reid G. Griggs et al., – Frontiers in Microbiology

Other Microbes

Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness – Tomer Orevi and Nadav Kashtan – Frontiers in Microbiology

Draft Genome Sequences of Various Bacterial Phyla Isolated from the International Space Station – Anna C. Simpson et al.,Microbiology Resource Announcements

April 29, 2021

Good morning from Los Angeles! Today’s microbiome digest includes various interesting research and review articles. Enjoy reading.

General microbiome

The Functional Significance of Bacterial Predators – Bruce A. Hungate – mBio

Anaerobic Microbial Metabolism of Dichloroacetate – Gao Chen – mBio

Review: Recipient factors in faecal microbiota transplantation: one stool does not fit all – Camille Danne – Nature Reviews Gastroenterology and Hepatology

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition – Clarisse Marotz – mSystems

Gut microbiome

Review: Diet-Microbiota-Brain Axis in Alzheimer’s Disease – Halle J Kincaid – Annals of Nutrition and Metabolism

Review: The significance of the gut microbiome in children with functional constipation – Monika Kwiatkowska – Advances in Clinical and Experimental Medicine

Oral microbiome

Review: Focus on the cariogenic process: microbial and biochemical interactions with teeth and oral environment – G Dipalma – Journal Of Biological Regulators And Homeostatic Agents

Respiratory microbiome

Review: A scoping review of longitudinal airway microbiota studies – Tary Yin – Expert Review of Respiratory Medicine

Vaginal microbiome

Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities – Nicholas S. Rhoades – mSystems

Association of Vaginal Microbiota with Signs and Symptoms of the Genitourinary Syndrome of Menopause across Reproductive Stages – Michelle Shardell – The Journal of Gerontology

Probiotics

Targeted Delivery of Probiotics: Perspectives on Research and Commercialization – K.S. Yoha – Probiotics and Antimicrobial Proteins

Animal microbiome / Animal experiments

A Single Microbiome Gene Alters Murine Susceptibility to Acute Arsenic Exposure – Qian Wang – Toxicological Sciences

Lipocalin 2 modulates dendritic cell activity and shapes immunity to influenza in a microbiome dependent manner – Martin L Watzenboeck – PloS Pathogen

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech – Emily Ann McClure – Applied and Environmental Microbiology

Influence of Anacardium occidentale leaf supplementation in broiler chicken diet on performance, caecal microbiota, blood chemistry, immune status, carcass, and meat quality – K. Adeyemi – British Poultry Science

Effects of three different mannans on obesity and gut microbiota in high-fat diet-fed C57BL/6J mice – Yajian Song – Food & Function

The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments – Diana Luise – PLOS ONE

Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications – Kasun H. Bodawatta – Proceedings of the Royal Society B

Perturbation of gut microbiota plays an important role in micro/nanoplastics-induced gut barrier dysfunction – Jiyan Qiao – Nanoscale

Ameliorative Effect of Dietary Tryptophan on Neurodegeneration and Inflammation in d-Galactose-Induced Aging Mice with the Potential Mechanism Relying on AMPK/SIRT1/PGC-1α Pathway and Gut Microbiota – Jia Yin – Journal of Agricultural Food Chemistry

Plant, root and soil microbiome

Soybean Root Nodule and Rhizosphere Microbiome: Distribution of Rhizobial and Nonrhizobial Endophytes – Parris Mayhood – Applied and Environmental Microbiology

Hyperlocal Variation in Soil Iron and the Rhizosphere Bacterial Community Determines Dollar Spot Development in Amenity Turfgrass – Ming-Yi Chou – Applied and Environmental Microbiology

Manure-Based Amendments Influence Surface-Associated Bacteria and Markers of Antibiotic Resistance on Radishes Grown in Soils with Different Textures – Giselle K. P. Guron – Applied and Environmental Microbiology

Water microbiome

Human‐ and Infrastructure‐associated Bacteria in Greywater – M. Nagarkar – Journal of Applied Microbiology

April 28, 2021

General microbiome

Microbiota regulate innate immune signaling and protective immunity against cancer – Xing et al. – Cell Host & Microbe

Pregnancy and early life

[PREPRINT]Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants – Yan et al. – bioRxiv

[REVIEW]Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review – Zaidi, Moore & Okala – Nutrients

Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle – Seppo et al. – Allergy

Human skin microbiome

Can antibiotic‐induced changes in the composition of the hair follicle microbiome regulate human hair growth? – Lousada et al. – Experimental Dermatology

Human gut microbiome

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome – Hu et al. – Theranostics

Alteration of gut microbial profile in patients with diabetic nephropathy – Du et al. – Endocrine

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

Sargassum fusiforme fucoidan modifies gut microbiota and intestinal metabolites during alleviation of hyperglycemia in type 2 diabetic mice – Wu et al. – Food & Function

Bidirectional interaction of nobiletin and gut microbiota in mice fed with a high-fat diet – Zhang et al. – Food & Function

Reshaping of the gastrointestinal microbiome alters atherosclerotic plaque inflammation resolution in mice – Garshick et al. – Scientif Reports

Animal microbiome (for animals in the wild)

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits – Zheng et al. – PLOS One

Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone – Antwis et al. – Journal of Animal Ecology

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

[PREPRINT]A Scenic River in Rural Ohio Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy et al. – bioRxiv

[PREPRINT]Diversity of free-living prokaryotes on terrestrial and marine Antarctic habitats – Bendia et al. – bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics – Cabello-Yeves – Environmental Microbiome

Techniques

Obtaining deeper insights into microbiome diversity using a simple method to block host and non‐targets in amplicon sequencing – Mayer et al. – Molecular Ecology Resources

April 26, 2021

Greetings from Pittsburgh! Today’s digest is preprint heavy. Topics include an optimized protocol for cyanobacterial 16S rRNA analysis, a panel of Pseudomonas aeruginosa clinical isolates, and more! Happy reading!

Events and jobs

The National Summer Undergraduate Research Project is looking for microbiology or computational immunology grad trainees, postdocs, staff scientists, and group leaders to serve as mentors for their summer program. Sign up here!


General microbiome

Preprint: A panel of diverse Pseudomonas aeruginosa clinical isolates for research and development – Lebreton et al. – bioRxiv

Pregnancy and early life

Preprint: Diet potentially drives the differentiation of eating behaviours via alterations to the gut microbiome in infants – Yan et al. – bioRxiv

Multi-site human microbiome

An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer – Borchmann – Microbiome

Plant, root, and soil microbiome

Preprint: Transcription of macromolecular N degrading genes provides a window into organic nitrogen decomposition in soil – Sieradzki et al. – bioRxiv

Built environment

Preprint: Microbial biomass, composition, and functions are responsible for the differential removal of trace organic chemicals in biofiltration systems – Cao et al. – bioRxiv
Microbes in space

Food microbiology

Preprint: Fluoroquinolone-resistant Escherichia coli originating on dairy farms are an infrequent cause of bacteriuria in humans living in the same geographical region – Mounsey et al. – bioRxiv

Techniques

Preprint: Optimized protocol for Cyanobacterial 16S rRNA analysis in Danube Delta lakes – Moza & Postolache – bioRxiv

April 25th, 2021

Today’s digest shows some great papers, with two highlights. The first being the value of a ketogenic diet on treating drug-resistant epilepsy in children, suggesting gut microbial dysbiosis is responsible for the drug resistance. the second is a thorough analysis of both the developing microbiota in goats using metagenomics and metatranscriptomics by Pan et al. Enjoy!

Gut microbiome

(Preprint) Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients – Moreira-Rosário et al. Bioxriv.

HPV infection and bacterial microbiota in the semen from healthy men. – Tuomimen et al. BMC Infectious Diseases.

(Review) Gastrointestinal dysfunction in Parkinson’s disease: molecular pathology and implications of gut microbiome, probiotics, and fecal microbiota transplantation – Metta et al. Journal of Neurology.

Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets – Gong et al. Microbial pathogenesis.

Vaginal microbiome

Oral administration of Lactobacillus crispatus M247 to papillomavirus-infected women: results of a preliminary, uncontrolled, open trial – Di Pierro et al. Minerva Obstrestics and Gynecology.

Animal experiments

(Preview) Bugs R Us: Restoring sociability with microbiota in autism. – Bellone and Lüscher. Cell reports medicine.

Anti-aging effects of a functional food via the action of gut microbiota and metabolites in aging mice – Zhang et al. Aging.

Animal microbiome

Dynamics of rumen gene expression,microbiome colonization, and their interplay in goats – Pan et al. BMC Genomics.

Evolution of rumen and oral microbiota incalves is influenced by age and time of weaning – Amin et al. Animal Microbiome

Plant, root and soil microbiome

(Review) Impacts of wildfire on soil microbiome in Boreal environments – Köster et al. Current opinion in Environmental Science & Health.

April 24th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a wide range of topics to explore! I particularly recommend taking the time to read at the fascinating review listed below exploring horizontal gene transfer in environmental microbial communities. They describe how advances in the computational analysis of metagenomic data has allowed us to dive deeper in understanding these processes in microbiomes.

Among the list of very interesting research papers in this digest, you’ll find a fascinating study exploring the symbiotic microbial communities associated with deeper corals. Although extensive litterature has been published on coral microbiomes from shallow waters, this papers is the first to examine microbial communities associated with the deep photosymbiotic corals, living at more than 150 m of depth!

Today’s non-microbiology pick is a really interesting paper from Faldelmola and collaborators reporting on the development by the Pan-African H3Africa Bioinformatics Network of two data portals for African genomic medicine and African microbiomes datasets. The paper explore how they lead a very successful 6-days hackathon allowing to efficiently develop these two important scientific ressources, but also how they build a collaborative community of African researchers and experts.

Have a great Weekend!


General microbiome

Review: Examining horizontal gene transfer in microbial communities – Brito – Nature reviews microbiology

Preprint: Evidence for a billion-years arms race between viruses, virophages and eukaryotes – Barreat and Katzourakis – BioRxiV

Unifying community detection across scales from genomes to landscapes – Hudon et al. – Oikos

Human gut microbiome

Preprint: Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut – Watson et al. – BioRxiV


Animal experiments

Diversity and characteristics of raw milk microbiota from Korean dairy farms using metagenomic and culturomic analysis – Ryu et al. – Food control

Animal microbiome

Preprint: Reclassification of seven honey bee symbiont strains as Bombella apis – Smith et al. – BioRxiV

Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth) – Rouzé et al. – ISME Journal

Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes – Thongsripong et al. – Scientific reports

Water and extremophile microbiome

Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents – McAllister et al. – ISME Journal

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones – Sun et al. – ISME Journal

Morphological complexity affects the diversity of marine microbiomes – Lemay et al. – ISME Journal

Preprint: Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic – Ferreira et al. – BioRxiV


Bioinformatics

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC – Parrello et al. – Plos One

A roadmap for metagenomic enzyme discovery – Robinson et al. – Natural Product Reports

Techniques

Preprint: Synergistic effect of short- and long-read sequencing on functional meta-omics – Galata et al. – BioRxiV


My non-microbiology picks

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings – Fadlelmola et al. – Database

April 23, 2021

Good morning from New Jersey! Lots of papers to share today, particularly regarding animal microbiota and new bioinformatics tools.

General microbiome

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer, Alice Tzeng et al., Genome Medicine

Pregnancy and early life

The infant gut resistome associates with E. coli, environmental exposures, gut microbiome maturity, and asthma-associated bacterial composition, Xuanji Li et al., Cell Host & Microbe

Multi-site human microbiome

Review: Microbiome-immune interactions in tuberculosis, Giorgia Mori et al., PLOS Pathogens

Human gut microbiome

Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect, Almagul Kushugulova et al., Frontiers in Cellular and Infection Microbiology

Review: The aging gut microbiome and its impact on host immunity, Bosco and Noti, Genes & Immunity

Animal experiments

Ingestion of Bifidobacterium longum changes miRNA levels in the brains of mice, DeVries and Horstman et al., PLOS ONE

Heat-inactivated Lactobacillus plantarum nF1 promotes intestinal health in Loperamide-induced constipation rats, Seon-Ah Park et al., PLOS ONE

The pregnane X receptor drives sexually dimorphic hepatic changes in lipid and xenobiotic metabolism in response to gut microbiota in mice, Sharon Ann Barretto et al., Microbiome

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome, Arnon Gal et al., PLOS ONE

Animal microbiome

Diversity and functional landscapes in the microbiota of animals in the wild, Levin, Raab, Pinto, and Rothschild et al., Science

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history, Tyler J. Carrier et al., PNAS

Diet and gut microbiome enterotype are associated at the population level in African buffalo, Claire E. Couch et al., Nature Communications

Coral microbiome changes over the day–night cycle, Alicia M. Caughman et al., Coral Reefs

An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota, Mao and Chuang et al., PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Preprint: Genome-centric analyses of seasonal phyllosphere microbiome activities in perennial crops, Adina Howe et al., bioRxiv

Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition, Kristi Gdanetz et al., Phytobiomes Journal

Built environment

Categorisation of culturable bioaerosols in a fruit juice manufacturing facility, Shirleen M. Theisinger et al., PLOS ONE

Bioinformatics

Preprint: Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination, Senay Yitbarek et al., bioRxiv

Preprint: Extended taxonomic profiling of diverse environments with mOTUs 2.6, Hans-Joachim Ruscheweyh et al., bioRxiv

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome, Donovan H. Parks et al., Frontiers in Microbiology

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC, Bruce Parrello et al., PLOS ONE