March 26, 2021

Good morning from New Jersey! Tons of papers to share with you today, including three about the role of the microbiome in COVID-19 and multiple new analysis tools and techniques.

Human respiratory microbiome

Functional profiling of COVID-19 respiratory tract microbiomes, Niina Haiminen et al., Scientific Reports

[Preprint] Mild CF Lung Disease is Associated with Bacterial Community Stability, Thomas H. Hampton et al., bioRxiv

Human skin microbiome

[Preprint] On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity, Felix M. Key et al., bioRxiv

Human gut microbiome

[Mini-Review] The Unique Impact of COVID-19 on Human Gut Microbiome Research, Ella Burchill et al., Frontiers in Medicine

Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome, Koester and Li et al., PLOS ONE

[Review] Towards a mechanistic understanding of reciprocal drug–microbiome interactions, Michael Zimmermann et al., Molecular Systems Biology

[Review] The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices, Celia Fuentes‐Chust et al., Advanced Materials

[Preprint] The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome, Domenick J Braccia et al., bioRxiv

Model experiments

[Preprint] Species richness determines C. difficile invasion outcome in synthetic human gut communities, Susan Hromada et al., bioRxiv

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue, Oryan Agranyoni et al., npj Biofilms and Microbiomes

Improvement of loperamide-induced slow transit constipation by Bifidobacterium bifidum G9-1 is mediated by the correction of butyrate production and neurotransmitter profile due to improvement in dysbiosis, Yutaka Makizaki et al., PLOS ONE

Animal microbiome

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales, Stefanie P. Glaeser et al., Microbial Ecology

Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations, Courtney M. Dunphy et al., Journal of Animal Ecology

Fish predation on corals promotes the dispersal of coral symbionts, Carsten G. B. Grupstra et al., Animal Microbiome

Plant, root, and soil microbiome

Global analysis of the apple fruit microbiome: Are all apples the same?, Ahmed Abdelfattah et al., Environmental Microbiology

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome, Wipf and Coleman-Derr, PLOS ONE

Water and extremophile microbiome

[Preprint] Uncharted biosynthetic potential of the ocean microbiome, Lucas Paoli et al., bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics, Pedro J. Cabello-Yeves et al., Environmental Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics, Yuan Lin et al., Microbiome

Bioinformatics

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing, Singh and Clarke et al., Frontiers in Microbiology

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries, Liangliang Zhang et al., BMC Bioinformatics

Model-Based Microbiome Data Ordination: A Variational Approximation Approach, Yanyan Zeng et al., Journal of Computational and Graphical Statistics

Techniques

Blue poo: impact of gut transit time on the gut microbiome using a novel marker, Francesco Asnicar et al., Gut

Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., Scientific Reports

Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli, Julie Haendiges et al., PLOS ONE

February 19, 2021

Good morning from New Jersey! There’s an amazing batch of microbiome papers to share with you today, including studies that use skin microbes to fight cancer, gut microbes to fight rotavirus, and evidence that the bird microbiome may harbor a mechanism that protects them from malaria. There’s also a fun story about dogs training a computer to detect prostate cancer.

General microbiome

Feasibility of integrating canine olfaction with chemical and microbial profiling of urine to detect lethal prostate cancer, Guest, Harris and Sfanos et al., PLOS ONE

Human skin microbiome

Preprint: Eliciting a potent antitumor immune response by expressing tumor antigens in a skin commensal, Yiyin Erin Chen et al., bioRxiv

Human nearly-sterile sites

Preprint: Fetal gut colonization: meconium does not have a detectable microbiota before birth, Katherine M. Kennedy et al., bioRxiv

Human gut microbiome

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk, Dong D. Wang et al., Nature Medicine

Gut microbiome pattern reflects healthy ageing and predicts survival in humans, Tomasz Wilmanski et al., Nature Metabolism

The composition of the gut microbiome differs among community dwelling older people with good and poor appetite, Cox and Bowyer et al., Journal of Cachexia, Sarcopenia and Muscle

Animal microbiome

The uropygial gland microbiome of house sparrows with malaria infection, Elin Videvall et al., Journal of Avian Biology

The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance, Andrea J. Jani et al., The ISME Journal

Plant, root and soil microbiome

Carbon Fluxes and Microbial Activities from Boreal Peatlands Experiencing Permafrost Thaw, M.P. Waldrop et al., JGR Biogeosciences

Probiotics/prebiotics

Escherichia coli Nissle 1917 administered as a dextranomar microsphere biofilm enhances immune responses against human rotavirus in a neonatal malnourished pig model colonized with human infant fecal microbiota, Husheem Michael et al., PLOS ONE

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation, Marielle Nguyen et al., Frontiers in Pediatrics

January 22, 2021

Good morning from New Jersey! A wide range of microbiome research to share with you today. Highlights include fecal microbiota transplantation in horses with colitis and a review on the foggy relationship between microbes and plastics. There are also a couple papers on metabolic modeling and an examination of how much black soldier flies like human food waste (hint: a lot).

Jobs

New postdoctoral positions were just announced at the University of Minnesota for “research at the interface of microbiome + human genomics” in the lab of Dr. Ran Blekhman (disclosure: my Ph.D. advisor).

Human skin microbiome

Potential role of the skin and gut microbiota in premenarchal vulvar lichen sclerosus: A pilot case-control study, Chattopadhyay and Arnold et al., PLOS ONE

Human gut microbiome

Degradation of complex arabinoxylans by human colonic Bacteroidetes, Gabriel V. Pereira et al., Nature Communications

Review – The complexities of the diet-microbiome relationship: advances and perspectives, Emily R. Leeming et al., Genome Medicine

Review – Understanding the host-microbe interactions using metabolic modeling, Jansma and El Aidy, Microbiome

Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime, Li and Nelson, Microbial Ecology

Animal experiments

Preprint – The Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster, Nana Ankrah et al, bioRxiv

Animal microbiome

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea, Caroline A. McKinney et al., PLOS ONE

Climate change alters the haemolymph microbiome of oysters, Elliot Scanes et al., Marine Pollution Bulletin

Functional screening of a Caatinga goat (Capra hircus) rumen metagenomic library reveals a novel GH3 β-xylosidase, Betulia de Morais Souto et al., PLOS ONE

Built environment

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions, Thomas Klammsteiner et al., Frontiers in Microbiology

Review – Plastics and the microbiome: impacts and solutions, G. Lear et al., Environmental Microbiome

Bioinformatics

Real-time resolution of short-read assembly graph using ONT long reads, Son Hoang Nguyen et al., PLOS Computational Biology

Covariance matrix filtering with bootstrapped hierarchies, Bongiorno and Challet, PLOS ONE

December 10, 2020

Good morning from New Jersey! Only a few new research articles to share with you today, but FOUR new reviews on the microbiome’s role in cancers and periodontal disease. And if you’re feeling adventurous, PLOS ONE just published an article on human postmortem decomposition that includes a brief evaluation of the buried corpse microbiome.

Jobs

A new postdoctoral position was just posted at the University of Minnesota for research on new methods of fecal microbiota transplantation.

General microbiome

Review – Unexpected guests in the tumor microenvironment: microbiome in cancer, Abigail Wong-Rolle et al., Protein Cell

Review – Understanding the microbial components of periodontal diseases and periodontal treatment-induced microbiological shifts, Ioannis Fragkioudakis et al., Journal of Medical Microbiology

Human gut microbiome

Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila, Kenny C. Mok et al., mBio

Interpretable Machine Learning Framework Reveals Robust Gut Microbiome Features Associated With Type 2 Diabetes, Wanglong Gou et al., Diabetes Care

Gut microbial ecosystem in Parkinson’s disease: New clinico‐biological insights from multi‐omics, Ai Huey Tan et al., Annals of Neurology

Review – Intervention on Gut Microbiota May Change the Strategy for Management of Colorectal Cancer, Sedigheh Taghinezhad‐S et al., Gastroenterology and Hepatology

Short-Chain Fatty Acid-Producing Gut Microbiota Is Decreased in Parkinson’s Disease but Not in Rapid-Eye-Movement Sleep Behavior Disorder, Hiroshi Nishiwaki et al., mSystems

Animal experiments

Respiratory tissue-associated commensal bacteria offer therapeutic potential against pneumococcal colonization, Soner Yildiz et al., eLife

Effects of Pinus massoniana pollen polysaccharides on intestinal microenvironment and colitis in mice, Niu and Shang et al., Food & Function

A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes, Zhigang Liu et al., mSystems

Plant, root, and soil microbiome

Preprint – Rapid evolution of bacterial mutualism in the plant rhizosphere, Erqin Li et al., bioRxiv

Review – Coffee Microbiota and Its Potential Use in Sustainable Crop Management, Benoit Duong et al., Frontiers in Sustainable Food Systems

Bioinformatics

Review – Tissue-associated microbial detection in cancer using human sequencing data, Rebecca M. Rodriguez et al., BMC Bioinformatics

Techniques

Preprint – BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery, Embriette R. Hyde et al., bioRxiv

November 12, 2020

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

October 22, 2020

Good morning! A relatively short collection of articles to share with you today—highlights include a human microbiome study that evaluated disease markers in more than 3,000 subjects, a study of emerging antibiotic resistance in melting Alaskan permafrost, and a preprint that found multiple immune responses typically associated with the microbiome may actually be more closely linked to viruses.

Human gut microbiome

Health and disease markers correlate with gut microbiome composition across thousands of people, Ohad Manor et al., Nature Communications

Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease, Francesca De Filippis et al., Current Biology

Preprint: Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli, Boas CL van der Putten et al., bioRxiv

Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities, Fredrick M Mobegi et al., eLife

Animal experiments

A longitudinal study reveals the alterations of the Microtus fortis colonic microbiota during the natural resistance to Schistosoma japonicum infection, Du Zhang et al., Experimental Parasitology

Animal microbiome

Seasonal variation in the gut microbiota of rhesus macaques inhabiting limestone forests of southwest Guangxi, China, Yuhui Li et al., Archives of Microbiology

Preprint: Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation, Anita Silver et al., bioRxiv

Plant, root, and soil microbiome

Preprint: Unearthing the Boreal Soil Resistome Associated with Permafrost Thaw, Haan and Drown, bioRxiv

Phages and viruses

Preprint: Enteric viruses evoke broad host immune responses resembling bacterial microbiome, Simone Dallari et al., bioRxiv

September 17, 2020

Another broad selection of microbiome papers for you this morning. Several papers today show how microbial communities are influenced by pollution, water depth, and El Niño, plus a study that found ants use signals from soil microbes to decide where to nest.

Human gut microbiome

Lactobacillus strains vary in their ability to interact with human endometrial stromal cells, Shiroda and Manning, PLOS ONE

A predictive index for health status using species-level gut microbiome profiling, Vinod K. Gupta et al., Nature Communications

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease, Sarah Vascellari et al., mSystems

Human nearly sterile sites

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics, Lee and Choi et al., Scientific Reports

Animal microbiome

The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil, Hongmei Huang et al., PLOS Pathogens

Influence of host genetics in shaping the rumen bacterial community in beef cattle, Abbas and Howard et al., Scientific Reports

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System, Charlotte B. Francoeur et al., mBio

Plant, root, and soil microbiome

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts, Shawn M. Higdon et al., PLOS ONE

Water and extremophile microbiome

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa, Angel Valverde et al., Archives of Microbiology

Persistent El Niño driven shifts in marine cyanobacteria populations, Alyse A. Larkin et al., PLOS ONE

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands, Phoma and Makhalanyane, Environmental Microbiology

Bioinformatics

Preprint: Tracking strains predicts personal microbiomes and reveals recent adaptive evolution, Shijie Zhao et al., bioRxiv

August 6, 2020

Good morning from Minnesota! A broad selection of papers to share with you today: Immune responses in lung transplant patients, an examination of how hurricanes can alter the soil microbiome, and a cool preprint on host–microbe interactions in stickleback, plus 10 more—

Human respiratory microbiome

(Preprint) Nasal commensal, Staphylococcus epidermidis shapes the mucosal environment to prevent influenza virus invasion through Serpine1 induction, Ara Jo et al., bioRxiv

Cystic Fibrosis Lung Transplant Recipients Have Suppressed Airway Interferon Responses during Pseudomonas Infection, Daniel T. Dugger et al., Cell Reports Medicine

Human gut microbiome

The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients, Qianqian Zeng et al., Scientific Reports

Home, Sweet Home: How Mucus Accommodates our Microbiota, Benjamin X Wang et al., The FEBS Journal

Animal experiments

Preprint: Immune gene expression covaries with gut microbiome composition in stickleback, Lauren E Fuess et al., bioRxiv

Transient neonatal antibiotic exposure increases susceptibility to late-onset sepsis driven by microbiota-dependent suppression of type 3 innate lymphoid cells, Xinying Niu et al., Scientific Reports

Animal microbiome

Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire, Robert Pieper et al., The ISME Journal

Plant, root, and soil microbiome

Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease, Emilie Bruez et al., Environmental Microbiology

Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica, William D. Eaton et al., PLOS ONE

Water and extremophile microbiome

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data, Alise J Ponsero et al., Nucleic Acids Research

Microbial communities can predict the ecological condition of headwater streams, Robert H. Hilderbrand et al., PLOS ONE

Bioinformatics

(Preprint) Snipe: Highly sensitive pathogen detection from metagenomic sequencing data, Lihong Huang et al., bioRxiv

Techniques

Impact of time and temperature on gut microbiota and SCFA composition in stool samples, Janet L. Cunningham et al., PLOS ONE

July 8, 2020

Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

May 7, 2020

Good morning! There’s a particularly broad collection of microbiome papers to share with you today, from the bacteria that hang onto wounds after debridement to the biofilms that form in the ancient ruins of a town buried by the eruption of Mount Vesuvius. A few unusual highlights include the sexually transmitted microbiome of bedbugs and the gut microbes that colonize a sea cucumber after it grows up, remove its own digestive tract and grows a new one. Some interesting new software tools are hiding in the “Bioinformatics” section at the bottom as well.

General microbiome

Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Frédéric Peyrusson et al., Nature Communications

Human respiratory microbiome

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment, Md Zohorul Islam et al., PLOS ONE

Human skin microbiome

Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds, Samuel Verbanic et al., npj Biofilms and Microbiomes

Human gut microbiome

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer, Clélia Coutzac et al., Nature Communications

Functional and phylogenetic alterations in gut microbiome are linked to graft-versus-host disease severity, Mathilde Payen et al., Blood Advances

Animal experiments

Preprint: Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model, Miyoshi and Lee et al., bioRxiv

Dietary Fiber Protects against Diabetic Nephropathy through Short-Chain Fatty Acid–Mediated Activation of G Protein–Coupled Receptors GPR43 and GPR109A, Yan Jun Li et al., Journal of the American Society of Nephrology

Probiotic strain Lactobacillus plantarum YYC-3 prevents colon cancer in mice by regulating the tumour microenvironment, Yuanchun Yue et al., Biomedicine & Pharmacotherapy

Effect of stevia on the gut microbiota and glucose tolerance in a murine model of diet-induced obesity, Sarah L. Becker et al., FEMS Microbiology Ecology

Animal microbiome

Sea cucumber intestinal regeneration reveals deterministic assembly of the gut microbiome, Brooke L. Weigel, Applied and Environmental Microbiology

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations, Sara Bellinvia et al., Proceedings of the Royal Society B

Plant, root, and soil microbiome

Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model, John W. Schroeder et al., Nature Communications

Preprint: Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments, Julia B. Gontijo et al., bioRxiv

Preprint: Community succession of the grapevine fungal microbiome in the annual growth cycle, Liu and Howell, bioRxiv

Characterizing changes in soil microbiome abundance and diversity due to different cover crop techniques, Wang and Wu et al., PLOS ONE

Preprint: Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field, Selma Cadot et al., bioRxiv

Water and extremophile microbiome

The role of changing temperature in microbial metabolic processes during permafrost thaw, Komi S. Messan et al., PLOS ONE

Built environment

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths, De Natale and Mele et al., PLOS ONE

Probiotics/prebiotics

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers, Denise R. Rodrigues et al., PLOS ONE

Phages and viruses

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants, Cristian Alejandro Suarez et al., PLOS ONE

Bioinformatics

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease, Tataru and David, PLOS Computational Biology

Sequence count data are poorly fit by the negative binomial distribution, Stijn Hawinkel et al., PLOS ONE

Preprint: sPepFinder expedites genome-wide identification of small proteins in bacteria, Li and Chao, bioRxiv

Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data, Fukunaga and Iwasaki, PLOS ONE