Category Archives: Human oral

March 15, 2023

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Pregnancy and early life

The impact of prenatal dog keeping on infant gut microbiota development – Panzer et al. – Clinical & Experimental Allergy

Human oral microbiome

Host microbiome interactions in apical periodontitis: the endodontic microbiome in relation to circulatory immunologic markers – Georgiou et al. – International Endodontic Journal

Human gut microbiome

[REVIEW]Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome? – Kapoor et al. – Autoimmunity Reviews

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury – Bai et al. – Rapid Communications in Mass Spectrometry

A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy – Stein-Thoeringer et al. – Nature Medicine

The gut microbiome modulates the transformation of microglial subtypes – Huang et al. – Molecular Psychiatry

Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age – Wang et al. – Molecular Omics

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

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain – Webb et al. – Microbiology Spectrum

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

Abiotic selection of microbial genome size in the global ocean – Ngugi et al. – Nature Communications

Bioinformatics

Benchmarking genome assembly methods on metagenomic sequencing data – Zhang et al. – Briefings in Bioinformatics

March 8, 2023

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Pregnancy and early life

[PREPRINT]The influence of early life exposures on the infant gut virome – Zhang et al. – bioRxiv

[PREPRINT]Maternal diet and gut microbiome composition modulate early life immune responses – Grant et al. – bioRxiv

Human oral microbiome

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease – Tamashiro et al. – Scientific Reports

Human gut microbiome

Gut microbiota and risk of five common cancers: A univariable and multivariable Mendelian randomization study – Wei et al. – Cancer Medicine

The role of the sex hormone-gut microbiome axis in tumor immunotherapy – Wang et al. – Gut Microbes

[REVIEW]The Influence of the Microbiome on Aggressive Behavior: an Insight into Age Related Aggression – Gulledge, Oyebode & Donaldson – FEMS Microbiology Letters

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

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity – Daoust et al. – Gut

Animal microbiome (for animals in the wild)

[REVIEW]The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions – Mohamed et al. – FEMS Microbiology Reviews

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet – Feng et al. – Front. Vet. Sci.

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

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function – Shi et al. – BMC Microbiology

Species invasions shift microbial phenology in a two-decade freshwater time series – Rohwer et al. – PNAS

Bioinformatics

Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – BMC Microbiology

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies – Luz Calle, Pujolassos & Susin – BMC Bioinformatics

[PREPRINT]You can move, but you can’t hide: identification of mobile genetic elements with geNomad – Camargo et al. – bioRxiv

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing – Wick, Judd & Holt – PLOS Computational Biology

February 24, 2023

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Human and General Microbiome

Review: Gut microbiome lipid metabolism and its impact on host physiology – Brown et al. Cell Host & Microbe

Review: Modelling human immune responses using microbial exposures in rodents – Li and Baldridge. Nature Microbiology

Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis – Sun et al. Gut

An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants – Hall et al. Nature Communications

Antibiotic use and inflammatory bowel disease: number needed to harm? – Ludvigsson. Gut

Oral & Respiratory Microbiome

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis – Brewer et al. Science Translational Medicine

Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease – Abotsi et al. Microbiome

Animal experiments

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut – Zhang et al. Nature Microbiology

Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice – Schwarzer et al. Science

Gamma-delta T cells modulate the microbiota and fecal micro-RNAs to maintain mucosal tolerance – Rezende et al. Microbiome

Phages and viruses

Review: Bacteriophage discovery to advance biotechnology and biotherapeutics – Mu and Lawley Nature Reviews Microbiology

Bioinformatics

Impact of microbial genome completeness on metagenomic functional inference – Eisenhofer et al. ISME

Pharokka: a fast scalable bacteriophage annotation tool – Bouras et al. Bioinformatics

Non Microbiome Picks

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines – Ryan et al. Cell Reports Medicine

Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs – Wang et al. Nature Immunology

January 25, 2023

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Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

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

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research

Bioinformatics

[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

November 30, 2022

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Human respiratory microbiome

Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients – Cai et al. – BMC Microbiology

Human oral microbiome

Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis – Heng et al. – Microbiology Spectrum

Human gut microbiome

[REVIEW]Double-edged sword: impact of fecal microbiome transplants on the gut resistome – Hallowell, Gao & Suez – Current Opinion in Gastroenterology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Gut microbiome alterations in preclinical Alzheimer’s disease – Jung et al. – PLOS One

[REVIEW]Sex, puberty, and the gut microbiome – Sisk-Hackworth, Kelley & Thackray

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

Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity – Montgomery et al. – Microbiome

Animal microbiome (for animals in the wild)

Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont – Sylvain et al. – Microbiology Spectrum

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids – Haji et al. – Scientific Reports

Plant, root, and soil microbiome

Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions – Jaiswal et al. – Microbiology Spectrum

Changes of the microbial community in kiwifruit during storage after postharvest application of Wickerhamomyces anomalus – Zhao et al. – Food Chemistry

Food microbiology

[PREPRINT]A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter – Ito et al. – bioRxiv

November 23, 2022

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General microbiome

[PREPRINT]Patterns and determinants of the global herbivorous mycobiome – Meili et al. – bioRxiv

[EDITORIAL]Helicobacter pylori: Have potential benefits been overlooked? – Schubert et al. – JGH Open

Pregnancy and early life

Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin – Young et al. – Arch Dis Child Fetal Neonatal Ed

Human oral microbiome

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture – Quagliariello et al. – Nature Communications

Human vaginal microbiome

[PREPRINT]Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle – Costello et al. – bioRxiv

Human gut microbiome

[REVIEW]Maternal obesity and resistance to breast cancer treatments among offspring: Link to gut dysbiosis – Andrade, Verma & Hilakivi-Clark

Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis – Baumgartner et al. – Gut Microbes

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

Impact of antibiotic perturbation on fecal viral communities in mice – Anderson et al. – G3

Animal microbiome (for animals in the wild)

Assessing Fungal Diversity and Abundance in the Black Soldier Fly and its Environment – Vitenberg & Opatovsky – Journal of Insect Science

Plant, root, and soil microbiome

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front – Scherer, Mason & Rast – FEMS Microbiology Ecology

Bioinformatics

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes – Fullam et al. – NAR

[PREPRINT]Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life – Gorman & Lladser

Techniques

[PREPRINT]Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing – Poursalavati et al. – bioRxix

November 16, 2022

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General microbiome

Enhancing nutritional niche and host defenses by modifying the gut microbiome – Sun et al. – Molecular Systems Biology

Evolution of immune genes is associated with the Black Death – Klunk et al. – Nature

Pregnancy and early life

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report – Wei et al. – Microbiome

Multi-site human microbiome

Age-Related Changes, Influencing Factors, and Crosstalk Between Vaginal and Gut Microbiota: A Cross-Sectional Comparative Study of Pre- and Postmenopausal Women – Yoshikata et al. – Journal of Women’s Health

Human oral microbiome

Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes – Chan et al. – Oral Oncology

Human gut microbiome

[REVIEW]Making gut microbiomes from scratch – Tiang & Bisanz – Cell Host &Microbe

Impairments of intestinal arginine and NO metabolisms trigger aging-associated intestinal barrier dysfunction and ‘inflammaging’ – Brandt et al. – Redox Biology

Dietary fiber ameliorates sleep disturbance connected to the gut–brain axis – Tang et al. – Food & Function

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases – Cheng et al. – BMC Microbiology

Relationships between dietary diversity and gut microbial diversity in the elderly – Amamoto et al. – Beneficial Microbes

Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project – Xu et al. – Beneficial Microbes

Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis – Liang et al. – Translational Neurodegeneration

Microbiome insights into pediatric familial adenomatous polyposis – Attard et al. – Orphanet Journal of Rare Diseases

[REVIEW]The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression – Wen et al. – Clinical and Translational Oncology

[REVIEW]Epigenetic regulation by metabolites from the gut microbiome – Marin-Tello et al. – Benefical Microbes

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

A tetrapeptide from maize combined with probiotics exerted strong anti-inflammatory effects and modulated gut microbiota in DSS-induced colitis mice – Li et al. – Food & Function

IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet – Perez-Matute et al. – Front. Endocrinol.

Animal microbiome (for animals in the wild)

Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species – McIlroy et al. – Microbiome

Plant, root, and soil microbiome

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea – Wicaksono et al. – mSystems

Bioinformatics

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments – Hempel et al. – NAR

Metagenome-assembled genome extraction and analysis from microbiomes using KBase – Chivian et al. – Nature Protocols

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies – Aytan-Aktug et al. – Microbiology Spectrum

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes – Gupta et al. – mSystems

Techniques

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution – Clokie et al. – Microbiology Spectrum

November 14, 2022

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Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications

November 7, 2022

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Human and General Microbiome

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure – Matthew R Stutz – Nature Communications

Taxonomic Abundance in Primary and Secondary Root Canal Infections – Ronald Ordinola-Zapata – International Endodontic Journal

Review: The intestinal barrier in disorders of the central nervous system – Carolina Pellegrini – The Lancet. Gastroenterology & Hepatology

Review: Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution – Emma Slack – Mucosal Immunology

Correspondence: A critical analysis of eating disorders and the gut microbiome – Sydney M Terry – Journal of Eating Disorders

Beneficial Microbes and Compounds

Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity – Gihyeon Kim – Microbiome

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota – Yu Gu – Food & Function

Animal Model Microbiome

Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome – Baraa Altaha – Molecular Metabolism

Strains producing different short-chain fatty acids alleviate DSS-induced ulcerative colitis by regulating intestinal microecology – Shuo Yang – Food & Function

Non-Model Animal Microbiome

Microbiome assembly and maintenance across the lifespan of bumble bee workers – Tobin J Hammer – Molecular Ecology

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone – Danny P Nielsen – Ecology Letters

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition – Ziyue Zhang – Archives of Microbiology

Forensic Microbiome

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes – Thomas Clarke – Scientific Reports

Plant Microbiome

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation – Hetty KleinJan – Molecular Ecology

Built Environment Microbiome

Review: Microplastics in urban waters and its effects on microbial communities: a critical review – Saber Entezari – Environmental Science and Pollution Research International

Microbiome Analysis and Techniques

Assessing the Dark Field of Metaproteome – Haonan Duan – Analytical Chemistry

October 05, 2022

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Pregnancy and early life

Multi-omic factors associated with future wheezing in infants – Beheshti et al. – Pediatric Research

Multi-site human microbiome

Race is a key determinant of the human intratumor microbiome – Lua et al. – Cancer Cell

Human respiratory microbiome

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance – Merenstein, Bushman & Collman – Microbiome

Human milk microbiome

Maternal weight status and the composition of the human milk microbiome: A scoping review – Daiy et al. – PLOS One

Human oral microbiome

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study – Carda-Dieguez, Mazzez & Mira – Microbiome

Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection – Austin et al. – Communications Biology

Human gut microbiome

[REVIEW]SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis – Mozaffari et al. – Pathology – Research and Practice

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin – Ma et al. – Genome Biology

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Kawano et al. – Cell

Rural environment reduces allergic inflammation by modulating the gut microbiota – Yang et al. – Gut Microbes

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

Six types of tea extracts attenuated high-fat diet-induced metabolic syndrome via modulating gut microbiota in rats – Zhou et al. – Food Research International

Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity – Connor et al. – The Journal of Nutritional Biochemistry

Animal microbiome (for animals in the wild)

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle – Teseo et al. – Microbiome

Comparative multiomics study of the effects of Ellagic acid on the gut environment in young and adult mice – Duan et al. – Food Research International

[REVIEW]Crosstalk between the microbiota and insect postembryonic development – Girard et al. – Trends in Microbiology

Culturomic, metagenomic, and transcriptomic-based characterization of commensal lactic acid bacteria isolated from domestic dogs using Caenorhabditis elegans as a model for aging – Kang et al. – Journal of Animal Science

Plant, root, sponge and soil microbiome

Recruitment of specific microbes through exudates affects cadmium activation and accumulation in Brassica napus – Wu et al. – Journal of Hazardous Materials

Novel trends of genome evolution in highly complex tropical sponge microbiomes – Kelly et al. – Microbiome

[Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities](Ecotoxicology and Environmental Safety) – Li et al. –

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

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics – Seong et al. – Microbiome

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China – Chen et al. – Water Research

Bioinformatics/Software

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics – Weissman et al. – mSystems

[SOFTWARE]PhyloDM is a high-performance library that converts a phylogenetic tree into a pairwise distance matrix. – Aaron Mussig – github