Category Archives: Animal microbiome

December 7, 2020

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Today we have some excellent review articles in Science, and Gut as well as several interesting research articles.

COVID-19 

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms – Gordon et al. Science

Robust neutralizing antibodies to SARS-CoV-2 infection persist for months – Wajnberg et al. Science

General Microbiome

[REVIEW] The role of the microbiota in human genetic adaptation – Suzuki and Ley – Science 

Gut microbiome

Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism – Penney et al. mSystems

[REVIEW] Gut microbiota-derived metabolites as central regulators in metabolic disorders – Agus et al. Gut

Human respiratory microbiome

[REVIEW]  Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways. Khanolkar et al. mSystems

Animal microbiome

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen – Gharechahi et al. ISME

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks – Fan et al. BMC Microbiology

Bioinformatics

[REVIEW]  Analysis of microbial compositions: a review of normalization and differential abundance analysis – Lin and Peddada. Npj Biofilms and Microbiomes. 

Non-microbiome pick 

A comparative genomics multitool for scientific discovery and conservation – Zoonomia Consortium. Nature

December 04, 2020

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General microbiome

Highly multiplexed spatial mapping of microbial communities – Shi et al. – Nature

Human respiratory microbiome

Comparison of the human microbiome in adults and children with chronic rhinosinusitis – Park et al. – PLOS One

Human gut microbiome/mycobiome

Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy – Jayasudha et al. – PLOS One

Mucosa-Associated Microbiota in Patients with Irritable Bowel Syndrome: A Comparison of Subtypes – Matsumoto et al. – Digestion

[REVIEW]The Role of the Gut Microbiota and the Immune System in the Development of Autism – Lungba et al. – Cureus Journal of Medical Science

Animal microbiome

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows – Ekman et al. – PLOS One

Gut microbiota is associated with protection against Marek’s disease virus infection in chickens – Bavananthasivam – Virology

Stingless bees and microbial interactions – de Paula et al. – Current Opinion in Insect Science

Bioinformatics

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis – Hupfauf et al. – PLOS One

December 02, 2020

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General microbiome

The Interplay of Sex Steroids, the Immune Response, and the Intestinal Microbiota – Pace & Watnick – Trends in Microbiology

[REVIEW]Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome? – Ricci et al. – Int. J. Mol. Sci.

[REVIEW]Microbiota and Obesity: Where Are We Now? – Ballini et al. – Biology

Human vaginal microbiome

Vaginal Microbiome-Based Bacterial Signatures for Predicting the Severity of Cervical Intraepithelial Neoplasia – Lee et al. – Diagnostics

Human gut microbiome

A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches – Li et al. – Computational and Structural Biotechnology Journal

[REVIEW]Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives – Vandeputte – Nutrion Reviews

[REVIEW]Harnessing the gut microbiota to promote metabolic health – Zmora – Nutrion Reviews

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

Cage bedding modifies metabolic and gut microbiota profiles in mouse studies applying dietary restriction – Gregor et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Influence of Environmental Stressors on the Microbiota of Zebra Mussels (Dreissena polymorpha) – Mathai et al. – Invertebrate Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks – Wang et al. – Journal of Hazardous Materials

Plant, root, and soil microbiome

Variable characteristics of microbial communities on the surface of sweet cherries under different storage conditions – Zhang et al. – Postharvest Biology and Technology

Biodiversity of pesticides degrading microbial communities and their environmental impact – Kumar et al. – Biocatalysis and Agricultural Biotechnology

Bioinformatics

[REVIEW]Evaluating and minimizing batch effects in metabolomics – Han & Li – Mass Spectrometry Reviews

November 30, 2020

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Hello from Luebeck! Today we selected among others maternal obesity and neurodevelopment, infant growth, breastfeeding and c-section, dental microbiome, gut microbiome and diseases/cancer, a couple of animal and plant microbiome studies. Of particular interest is a study diet and problem solving in a bird species (Parus major).

General microbiome

[REVIEW]The dynamic wound microbiome – Liu et al. – BMC Medicine

[REVIEW]Microbiome and Cervical Cancer – Castanheira et al. – Pathobiology

Pregnancy and early life

[REVIEW]The impact of maternal obesity on childhood neurodevelopment – Tong & Kalish – Journal of Perinatology

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function – Selma-Royo et al. – Microbiome

Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life – Guo et al. BMC Pediatrics

Human oral microbiome

Dental plaque microbiota profiles of children with caries-free and caries-active dentition – Qudeimat et al. – Journal of Dentistry

[REVIEW]Microbiomics: Were we all wrong before? – Kumar – Periodontology 2000

[REVIEW]Metaproteome and metabolome of oral microbial communities – Bostanci et al. – Periodontology 2000

Human gut microbiome

Gutmicrobiota, immunity and pain – Santoni, Miccini & Batelli – Immunology Letters

The Healthy Microbiome (What is the definition of a healthy gut microbiome?) – Shanahan, Ghosh & O’Toole – Gastroenterology

Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus – Wang et al. – Gut Microbes

Animal microbiome (for animals in the wild)

Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird – Davidson et al. Scientific Reports

Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon – Gillman, McKenney & Lafferty – Scientific Reports

Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life – Reese et al. – Current Biology

Plant, root, and soil microbiome

Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream – Piazzon et al. – Microbiome

A comparison of the functional diversity of microbial communities in maize rhizosphere soils in the North West Province of South Africa – Chinenyenwa Fortune Chukwuneme, Ayansina Segun Ayangbenro, Olubukola Oluranti Babalola – Rhizosphere

[REVIEW]Beyond the extremes: Rocks as ultimate refuge for fungi in drylands – Coleine et al. – Mycologia

Bioinformatics

[REVIEW]Emerging computational tools and models for studying gut microbiota composition and function – Park et al. – Current Opinion in Biotechnology

November 27, 2020

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Hello from Luebeck!

Today’s digest covers the connection between human diseases and gut microbiome, the gut feeling, secrets about plant growth and vertical stratification in urban spaces. Happy reading and happy black Friday!

General microbiome

Human microbiome and allergy – Montecchiani & Fanos – Pediatric Allergy and Immunology

Early life and childhood

Early Gut Fungal and Bacterial Microbiota and Childhood Growth – Schei et al. – Frontiers in Pediatrics

Oral human microbiome

Characterization of Lactobacilli isolated from carious dentin after selective caries removal and cavity sealing – Damé-Teixeira et al. – Archives of Oral Biology

Human gut microbiome

A Pilot Study: Changes of Intestinal Microbiota of Patients With Non-small Cell Lung Cancer in Response to Osimertinib Therapy – Cong et al. – Frontiers in Microbiology

What connection is there between intestinal microbiota and heart disease? – Poli – European Heart Journal Supplements

The Student-Centered Classroom: The New Gut Feeling – Lyles & Oli – FEMS Microbiology Letters

Animal microbiome

Comparison of the fecal microbiota composition between the blue Sheep (Pseudois nayaur) fed with Lolium perenne and Sorghum sudanense – Wu, Yuan & Pan – Canadian Journal of Microbiology

Plant, root, and soil microbiome

[REVIEW]The plant microbiome: The dark and dirty secrets of plant growth – Tkacz & Poole – Pants People Plant

Water and extremophile microbiome

[PREPRINT]Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica – Rojas-Gätjens et al. – bioRxiv

Environment

Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al. – Environmental Health Perspectives

Techniques

Power calculations for detecting differences in efficacy of fecal microbiota donors – Olesen – Contemporary Clinical Trials Communications

November 25, 2020

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Human respiratory microbiome

[PREPRINT] Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis – Watts et al. – bioRxiv

Human vaginal microbiome

VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition – France et al. – Microbiome

Human gut microbiome

Diet influences the functions of the human intestinal microbiome – De Angelis et al. – Scientific Reports

Dietary probiotic and metabolites improve intestinal homeostasis and prevent colorectal cancer – Peng et al. – Food & Function

Animal microbiome

The synergistic tumor growth-inhibitory effect of probiotic Lactobacillus on transgenic mouse model of pancreatic cancer treated with gemcitabine – Chen et al. – Scientific Reports

16S rRNA sequence data of Bombyx mori gut bacteriome after spermidine supplementation – Rajan et al. – BMC Research Notes

Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly – Näsvall et al. – Molecular Ecology

Effect of sterilization on the canine vaginal microbiota: a pilot study – Rota et al. – BMC Veterinary Research

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters – Stothart et al. – Molecular Ecology

Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic – Stewart et al. – Equine Veterinary Journal

Microbiome‐Metabolomic Analyses of the Impacts of Dietary Stachyose on Fecal Microbiota and Metabolites in Infants Intestinal Microbiota‐associated Mice – Xi et al. – Science of Food and Agriculture

Bioinformatics

MetaGeneHunt for protein domain annotation in short-read metagenomes – Berlemont et al. – Scientific Reports

SuRF: A new method for sparse variable selection, with application in microbiome data analysis – Liu – et al. – Statistics in Medicine

November 20, 2020

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Today’s digest features a systematic assessment of best practices for the sequencing-based characterization of the human vaginal microbiome, studies on link between the plaque microbiome and peri-implantitis, cutimycin [a Cutibacterium acnes-produced antibiotic that affects niche competition among the human skin microbiota] and antibiotic resistance genes in shower drains, washing machines, and dishwashers. There is a new Micro Binfie Podcast episode about moving from the wet lab into the dry lab to become a bioinformatician. Also, check out a list of interesting (freely available) events. Happy reading/listening!

Oral microbiome

*Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics – Paolo Ghensi – npj Biofilms and Microbiomes

Skin microbiome

*A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles – Jan Claesen – Science Translational Medicine

Review: Staphylococcus epidermidis—Skin friend or foe? – Morgan M. Brown and Alexander R. Horswill – Plos Pathogen

Gut microbiome

Preterm Infants Harbour a Rapidly Changing Mycobiota That Includes Candida Pathobionts – Stephen A. James – Journal of Fungi

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology – Antonio Molinaro – Nature Communications

Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers – Allyson L. Byrd – Journal of experimental medicine

Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements – Rupasri Mandal – Metabolomics

Minireview: Communal Living: Glycan Utilization by the Human Gut Microbiota – Jonathon A. Briggs – Environmental Microbiology

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut – Leszek Michalak – Nature Communications

Vaginal microbiome

*Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome – Luisa W. Hugerth – mSphere

Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily – npj Biofilms and Microbiomes

Intercepting genomic variability of Gardnerella vaginalis species through comparative genomics analyses: evolutionary and ecological implications – Chiara Tarracchini – Applied and Environmental Microbiology

Engineered phage endolysin eliminates Gardnerella in bacterial vaginosis without damaging the healthy vaginal microbiome – Christine Landlinger – medRxiv

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid – Katelyn Brandt & Rodolphe Barrangou – BMC Microbiology

Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species – Wendy Li and Zhanshan Sam Ma – Computational and Structural Biotechnology Journal

Animal microbiome

The haybiome: Characterising the viable bacterial community profile of four different hays for horses following different pre-feeding regimens – Simon Daniels – Plos One

Review: Value of Probiotics in Canine and Feline Gastroenterology – Silke Salavati Schmitz – Veterinary Clinics of North America: Small Animal Practice

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel – Marco Gerdol – Genome Biology

Technique

Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach – Shaktheeshwari Silvaraju – Applied and Environmental Microbiology

Metagenomics

Metagenomic assessment of the global distribution of bacteria and fungi – Mohammad Bahram – Environmental Microbiology

Bioinformatics

On the complexity of haplotyping a microbial community – Samuel M Nicholls – Bioinformatics

Challenges in Benchmarking Metagenomic Profilers – Zheng Sun – bioRxiv

Unifying the global coding sequence space enables the study of genes with unknown function across biomes – Chiara Vanni – bioRxiv

Nucleotide-resolution bacterial pan-genomics with reference graphs – Rachel M Colquhoun – bioRxiv

Efficient storage and analysis of quantitative genomics data with the Dense Depth Data Dump (D4) format and d4tools – Hao Hou – bioRxiv

An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome – Nicolas Nalpas – bioRxiv

The misuse of colour in science communication – Fabio Crameri – Nature Communications

Antimicrobial Resistance

*The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering – Laura Schages – Applied and Environmental Microbiology

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm – Shireen M Kotay – bioRxiv

fosM, a new family of fosfomycin resistance gene identified in bacterial species isolated from human microbiota – Sami Khabthani – Antimicrobial Agents and Chemotherapy

Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile – Ilse M. Boekhoud – bioRxiv

Events

Black In Immuno Week – Black in Immuno – 22-28 November 2020
*A collective of scientists to celebrating, amplifying, and promoting the work of Black Immunologists across the globe.

Webinar: Antibiotic Resistance in the Environment – Organizer: Resistomap – Date: Tuesday, 24 November 2020

Webinar: Microbiology Webinars – FEMS – webinar recordings available

Virtual course and symposium: Harnessing Our Inner Ecology To Track and Treat Disease – Institute for Systems Biology – October 15 and 16, 2020
*all course materials/tutorials and talks are available for free on the website

Virtual Conference on Prokaryotic Small Proteins – Organizers: Todd Gray, Kai Papenfort, Gigi Storz and Joe Wade – January 12-14, 2021

Podcast

*Moving from wet to dry with Phil Ashton – Hosts: Andrew Page, Nabil-Fareed Alikhan and Lee Katz – Micro Binfie Podcast

Real-time quantitative proteomics with Devin Schweppe – Host: Jacob Schreiber – The Bioinformatics Chat

Interspecies collaborations with Mindaugas Gapševičius – Host: Aga Pokrywka – Ferment Radio

Microbiome as Organ: Researcher Colin Hill Talks Bacteria and Bacteriophages in Human Body with Colin Hill – Host: Richard Jacobs – The Finding Genius Podcast

What Does Your Microbiome Say About You? with Colin Hill – Host: Andrea Hardy – Let’s Gut Real

Colouring booklet

Microbes, diet and beyond by Microbiome Support EU project; Illustrations by Maria Pock

Boardgame

Drugs vs Bugs, a free and exciting Print’n’Play boardgame developed by Célia Souque

November 14, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find great papers, in particular in soil and water microbiology but also in bioinformatics! As an example, Mara and collaborators are exploring the viruses found in the oxygen-deficient water column of the Cariaco basin. Interestingly, a large diversity of viral Auxilliary Metabolic Genes (AMGs) were found and give new insights in how phages may interact with their bacterial hosts in this understudied ecosystem.

In the bioinformatics section, I recommend anyone interested in phage metagenomics to take a look at the paper from Ren and collaborators. The authors have developed a reference-free and alignment-free deep learning tool, called DeepVirFinder, allowing the retrieval of viral sequences in metagenomes.

Today’s non-microbiology digest is a paper announcing the last update of the Genome Online Database (GOLD), a manually curated collection of genome projects and their metadata from around the world, which now contains more than a million entries! Great news for bioinformaticians!

Have a great Saturday!

Human gut microbiome

The bacterial association with oral cavity and intra-abdominal abscess after gastrectomy – Nishikawa et al. – PlosOne

Animal microbiome

Loss of symbiont infectivity following thermal stress can be a factor limiting recovery from bleaching in cnidarians – Kishimoto et al. – ISME Journal

Plant, root, and soil microbiome

A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases – Tian et al. – ISME Journal

Air microbiome

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait – Al Salameen et al. – PlosOne

Water and extremophile microbiome

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system – Huber et al. – ISME Journal

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities – Kraemer et al. – ISME Journal

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline – Mara et al. – ISME Journal

Phages and Viruses

Metagenomic Analysis of the Enteric RNA Virome ofInfants from the Oukasie Clinic, North West Province,South Africa, Reveals Diverse Eukaryotic Viruses – Mogotsi et al. – Viruses

Bioinformatics

Identifying viruses from metagenomic data using deep learning – Ren et al. – Quantitative Biology

Review: Reconstructing organisms in silico: genome-scale models and their emerging applications – Fang et al. – Nature Reviews Microbiology

Zero-Inflated gaussian mixed models for analyzing longitudinal microbiome data – Zhang et al. – PlosOne

Evaluating the number of different genomes in a metagenome by means of the compositional spectra approach – Kirzhner et al. – PlosOne

Survey of metaproteomics software tools for functional microbiome analysis – Sajulga et al. – PlosOne

Techniques

Sample pooling methods for efficient pathogen screening: Practical implications – Furstenau et al. – PlosOne

My non-microbiology picks

Genomes OnLine Database (GOLD) v.8: overview and updates – Mukherjee et al. – Nucleic Acids Research

November 12, 2020

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Good morning! There’s a really exciting collection of papers to share with you this morning. Among them, a study of gut archaea across multiple host domains, a link between F. nucleatum and esophageal cancer, and two new databases of shotgun metagenomic data. (There’s also a fun paper about environmental transmission of microbes aboard the International Space Station.)

General microbiome

Preprint – Strong influence of vertebrate host phylogeny on gut archaeal diversity, Nicholas D Youngblut et al., bioRxiv

A genomic catalog of Earth’s microbiomes, Stephen Nayfach et al., Nature Biotechnology

Human vaginal microbiome

Review – Vaginal microbiota and the potential of Lactobacillus derivatives in maintaining vaginal health, Wallace Jeng Yang Chee, Microbial Cell Factories

Human gut microbiome

Preprint – Fusobacterium Nucleatum Predicts a Risk for Esophageal Squamous Cell Carcinoma, Chao Shi et al., Research Square

Preprint – Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes, Kim and Lee et al., bioRxiv

Preprint – Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut, David C. Danko et al., bioRxiv

Review: An infectious diseases perspective on the microbiome and allogeneic stem cell transplant, Olivia C. Smibert et al., Current Opinion in Infectious Diseases

Animal experiments

Preprint – Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes, Sally L. Bornbusch et al., bioRxiv

Pinto beans modulate the gut microbiome, augment MHC II protein, and antimicrobial peptide gene expression in mice fed a normal or western-style diet, Babajide A. Ojo et al., Journal of Nutritional Biochemistry

Preprint – Contagious Antibiotic Resistance: Plasmid Transfer Among Bacterial Residents of the Zebrafish Gut, Wesley Loftie-Eaton et al., bioRxiv

Animal microbiome

Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys, Anna J. Jasinska et al., Microbiome

A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo, Narat and Amato et al., Scientific Reports

Bioinformatics

Preprint – AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities, Almut Heinken et al., bioRxiv

Techniques

Preprint – Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., bioRxiv

November 9, 2020

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Happy Monday morning from San Francisco, California! Hope everyone had a restful weekend. For those who aren’t quite ready for the working week, how about easing in to things with a warm beverage and some great microbiome reads?

Today’s digest includes two papers that blew my mind. The first is a paper by van Tatenhove-Pel et al. which looks at how cell-to-cell distance in 3D space impacts the metabolic interactions between bacteria. The second, by Nowosad et al., examines the role of the gut microbiota on B cell selection and antibody affinity maturation in gut-associated germinal centers. Other fascinating papers include: a pilot study profiling the gut microbiomes of South Africans in an urban cohort and a transitioning rural cohort which was designed collaboratively with community leaders (Oduaran et al.); a review paper about using brachyuran crabs as a model for studying how animal-microbiome symbioses evolve when aquatic organisms transition to land (Cannicci et al.); and a paper that used shotgun metagenomics to identify current and historical microbiomes in lake sediment which could help our understanding of how humans impact lake ecosystems over time (Garner et al.). Happy reading, y’all!

General Microbiome
Microbial competition reduces metabolic interaction distances to the low µm-range. – van Tatenhove-Pel, R.J. et al., The ISME Journal

Human Respiratory Microbiome
Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. – Tang, H.H.F, et al., Journal of Allergy and Clinical Immunology

Human Gut Microbiome
Distinct Fecal and Plasma Metabolites in Children with Autism Spectrum Disorders and Their Modulation after Microbiota Transfer Therapy. – Kang, D-W et al., mSphere

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. – Sánchez-Quinto, A. et al., Microorganisms

Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. – Oduaran, O.H. et al., BMC Microbiology

Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma. – Depber, M. et al., Nature Medicine

Fecal Microbiota Changes in Patients With Postpartum Depressive Disorder. – Zhou, Y. et al., Frontiers in Cellular and Infection Microbiology

Animal Experiments
Tunable dynamics of B cell selection in gut germinal centres. – Nowosad, C.R. et al., Nature

Acute liver failure is regulated by MYC- and microbiome-dependent programs. – Kolodziejczyk, A.A. et al., Nature Medicine

Epithelial TLR4 signaling activates DUOX2 to induce microbiota-driven tumorigenesis. – Burgueño, J.F. et al., Gastroenterology

Gut Microbiome Alters the Activity of Liver Cytochromes P450 in Mice With Sex-Dependent Differences. – Jourová, L. et al., Frontiers in Pharmacology

Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp. – Gálvez, E.J.C. et al., Cell Host & Microbe

FXR in the dorsal vagal complex is sufficient and necessary for upper small intestinal microbiome-mediated changes of TCDCA to alter insulin action in rats. – Zhang, S-Y et al., Gut

Animal Microbiome
Review: To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. – Cannicci, S. et al., Frontiers in Microbiology

Insect Microbiome
The direct and indirect effects of environmental toxicants on the health of bumblebees and their microbiomes. – Rothman, J.A. et al., Proceedings of the Royal Society B, Biological Sciences

A Very Hungry Caterpillar: Polyethylene Metabolism and Lipid Homeostasis in Larvae of the Greater Wax Moth ( Galleria mellonella). – LeMoine, C.M. et al., Environmental Science and Technology

Plant, Root, and Soil Microbiome
Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds. – Liao, S. et al., mSystems

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems. – Allard, S.M. et al., mSystems

Water and Extremophile Microbiome
The water chemistry and microbiome of household wells in Medawachchiya, Sri Lanka, an area with high prevalence of chronic kidney disease of unknown origin (CKDu). McDonough, L.K. et al., Scientific Reports

Sediment Metagenomes as Time Capsules of Lake Microbiomes. – Garner, R.E. et al., mSphere

Built Environment
Bioaerosols in the Athens Metro: Metagenetic insights into the PM 10 microbiome in a naturally ventilated subway station. – Grydaki, N. et al., Environment International

Probiotics
Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions. – Albright, M.B.N. et al., mBio

Microbiological, immunological, and histological changes in the gut of Salmonella Enteritidis-challenged rats fed goat cheese containing Lactobacillus rhamnosus EM1107. – Rolim, F.R.L. et al., Journal of Dairy Science

Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics. – Duar, R.M. et al., Nutrients

Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU. – Yousuf, E.I. et al., Frontiers in Microbiology

Bioinformatics
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. – Lam, T.J. et al., PLoS Computational Biology

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. – Berglund, F. et al., Microbial Genomics

Review: Naught all zeros in sequence count data are the same. – Silverman, J.S. et al., Computational and Structural Biotechnology Journal

Techniques
Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. – Saladié, M. et al., Frontiers in Microbiology

Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research. – Víquez-R, L. et al., Ecology and Evolution