Category Archives: Human skin

December 20, 2021

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Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

November 12, 2021

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Today’s digest features the study on the Amazon River microbiome, Spanish gut microbiome, review on nanopore sequencing, 16S rRNA metabarcoding study to characterize the responses of the active gut microbiome of fathead minnows to exposure with a model contaminant (benzo[a]pyrene), and more. Happy Friday!

Lung microbiome

Review: The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

Skin microbiome

Charting host-microbe co-metabolism in skin aging and application to metagenomics data – Wynand Alkema – PlosOne

Gut microbiome

*The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet – Adriel Latorre-Pérez – Scientific Reports

Autism-related dietary preferences mediate autism-gut microbiome associations – Chloe X. Yap – Cell

Animal microbiome

*16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene – Abigail DeBofsky – Science of The Total Environment

Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs – Morag Clinton – BMC Microbiology

Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing – Xiaofen Hu – BMC Microbiology

Animal experiment

The composition of human vaginal microbiota transferred at birth affects offspring health in a mouse model – Eldin Jašarević – Nature Communications

Polyamine metabolism links gut microbiota and testicular dysfunction – Qi Zhao – Microbiome

A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites – Hongli Shi – Microbiome

Water microbiome

*Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters – Célio Dias Santos-Júnior – Molecular Ecology

Bioinformatics

*Review: Nanopore sequencing technology, bioinformatics and applications – Yunhao Wang – Nature Biotechnology

mBodyMap: a curated database for microbes across human body and their associations with health and diseases – Hanbo Jin – Nucleic Acids Research

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper – Alexander G McFarland – Bioinformatics

OptiFit: an improved method for fitting amplicon sequences to existing OTUs – Kelly L Sovacool – bioRxiv

October 22, 2021

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Happy Friday!

Today’s digest includes an article on the role of age in the human intestinal microbiome, research on the role of a novel Acidobacteriota in seafloor sulfur cycling, work demonstrating the use of machine learning to predict camplyobacter source data, and much more! I also included the link to a page on “The Secret World Inside You”, a science exhibit focused on the human microbiome that is at the Witte Museum in San Antonio, Texas from now until April 10, 2022. If anyone ends up checking it out, I’d love to hear about it!

Events

A microbiome science exhibit, “The Secret World Inside You,” is at The Witte Museum in San Antonio, Texas from October 16, 2021 to April 10, 2022 .

Human gut microbiome

Bile acid-independent protection against Clostridioides difficile infection – Aguirre et al. – PLOS PATHOGENS

The importance of age in compositional and functional profiling of the human intestinal microbiome – Herzog et al. – PLOS ONE

Plant, root, and soil microbiome

The chosen few—variations in common and rare soil bacteria across biomes – Bickel & Or – The ISME Journal

The fungus Kalmusia longispora is able to cause vascular necrosis on Vitis vinifera – Karácsony et al. – PLOS ONE

Water and extremophile microbiome

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling – Flieder et al. – The ISME Journal

Beach sand oil spills select for generalist microbial populations – Heritier-Robbins et al. – The ISME Journal

Preprint: Influence of DNA extraction kits on the fungal DNA metabarcoding for freshwater environmental DNA – Matsuoka et al. – bioRxiv

Marine signature taxa and core microbial community stability along latitudinal and vertical gradients in sediments of the deepest freshwater lake – Reboul et al. – The ISME Journal

Phages and viruses

Review: Community context matters for bacteria-phage ecology and evolution – Blazanin & Turner – The ISME Journal

Bioinformatics

Machine learning to predict the source of campylobacteriosis using whole genome data – Arning et al. – PLOS GENETICS

October 06, 2021

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General microbiome

The intestinal 3M (microbiota, metabolism, metabolome) Zeitgeist – from fundamentals to future challenges – Dey et al. – Free Radical Biology and Medicine

Pregnancy and early life

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women – Huang et al. – BMC Microbiology

Human respiratory microbiome

Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing – Ikegami et al. – Scientific Reports

Human skin microbiome

Experimental Dermatology Special Issue with Focus on ‘Skin microbiome and antimicrobial peptides’

Human gut microbiome

[REVIEW]Gut microbiome in pediatric acute leukemia: from predisposition to cure – Masetti et al. – Blood Advances

Animal microbiome

Effects of moderate exercise on hepatic amino acid and fatty acid composition, liver transcriptome, and intestinal microbiota in channel catfish (Ictalurus punctatus) – Zhang et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep – Xie, Wang & Mao – mSystems

Plant, root, and soil microbiome

Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil – Sun et al. – Journal of Hazardous Materials

Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic – Melekhina et al. – Scientific Reports

Fast and persistent responses of alpine permafrost microbial communities to in situ warming – Perez-Mon et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

Environmental dynamics of hospital microbiome upon transfer from a major hospital to a new facility – Ashokan et al. – Journal of Infection

Bioinformatics

[Commentary]Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles – Schmidt, Ghadermazi & Chan – mSystems

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data – Armstrong et al. – mSystems

October 1, 2021

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Multi-site human microbiome

Diagnostic and prognostic potential of the oral and gut microbiome for lung adenocarcinoma – Lim et al. – Clinical and Translational Medicine

Human oral microbiome

Individuals with substance use disorders have a distinct oral microbiome pattern – Kosciolek et al. – Brain, Behavior, & Immunity – Health

Human skin microbiome

[REVIEW]The Dynamics of Skin Microbiota in Shoulder Surgery Infections – Fatima, Bjarnsholt & Bay – Journal of Pathology, Microbiology and Immunology

Human gut microbiome

[REVIEW]Mucins, gut microbiota, and postbiotics role in colorectal cancer – Pothuraju et al. – Gut Microbes

Age and the aging process significantly alter the small bowel microbiome – Leite et al. – Cell Reports

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

Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols – Secombe et al. – Gut Microbes

Alpha-synuclein alters the faecal viromes of rats in a gut-initiated model of Parkinson’s disease – Stockdale et al. – Communications Biology

[PREPRINT]First trimester gut microbiome induces Inflammation-dependent gestational diabetes phenotype in mice – Pinto et al. – medRxiv

[PREPRINT]High-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice provides novel insight on the impact of host genetics – Doms et al. – bioRxiv

Plant, root, and soil microbiome

Effects of microplastics on soil microbiome: The impacts of polymer type, shape, and concentration – Sun et al. – Science of the total Environment

Bioinformatics

Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA preprocessing chimeric reads – Kiguchi et al. – DNA Research

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes – Andreu et al. – mSystems

Increasing the power of interpretation for soil metaproteomics data – Jouffret – Microbiome

September 14, 2021

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General microbiome

[REVIEW]Host specificity of the gut microbiome – Mallott & Amato – Nature Reviews Microbiology

[COMMENT]Harnessing the power of host–microbe symbioses to address grand challenges – Hentschel – Nature Reviews Microbiology

The intratumoral microbiome: Characterization methods and functional impact – Heymann et al. – Cancer Letters

Human oral microbiome

Oral hygiene and oral microbiota in children and young people with neurological impairment and oropharyngeal dysphagia – Fregatto et al. – Scientific Reports

Human skin microbiome/virome

[PREPRINT]The Application of The Skin Virome for Human Identification – Graham et al. – bioRxiv

Human vaginal microbiome

Vaginal microbiome topic modeling of laboring Ugandan women with and without fever – Movassagh et al. – NPJ Biofilms and Microbes

Human nearly-sterile sites (blood, organs, brain)

Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis – Kisat et al. – The Journal of Trauma and Acute Care Surgery

Human gut microbiome

The gut microbiome in konzo – Bramble et al. – Nature Communications

High-salt diet mediates interplay between NK cells and gut microbiota to induce potent tumor immunity – Rizvi et al. – Science Advances

The Firmicutes/Bacteroidetes ratio of the human gut microbiota is associated with prostate enlargement – Takezawa et al. – The Prostate

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

Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis – Wu et a. – Microbiome

Differential perturbations of gut microbial profiles and co-occurrence networks among phases of methamphetamine-induced conditioned place preference – Wang et al. – Journal of Neuroscience Research

Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis – Foley et al. – Microbiome

Vitamin A supplementation ameliorates ulcerative colitis in gut microbiota–dependent manner – Pang et al. – Food Research International

Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period – Suriyaphol et al. – Scientific Reports

Bioinformatics

A statistical model for describing and simulating microbial community profiles – Ma et al. – PLOS Computational Biology

September 10, 2021

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In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv

Bioinformatics

SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

For more, check out a collection of microbiome events HERE!

August 18, 2021

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Call for Papers

Cells is calling for papers for a special issue on “Interplay of Gene Expression Regulation and Microbiome”. Deadline for paper submission: 30th of November 2021

General microbiome

[REVIEW]The Cancer Microbiome: Recent Highlights and Knowledge Gaps – Knippel, Drewes & Sears – Cancer Discoveries

[REVIEW]Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren’s Syndrome in a Systematic Review – Doare et al. – Frontiers in Immunology

[REVIEW]The varying effects of antibiotics on gut microbiota – Yang et al. – AMB Express

[REVIEW]Prevotella diversity, niches and interactions with the human host – Tett et al. – Nature Reviews Microbiology

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study – Klassert et al. – Microbiome

Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children – Roslund et al. – Environment International

Multi-site human microbiome

Different responses of the oral, nasal and lung microbiomes to cigarette smoke – Pfeiffer et al. – Thorax

Human skin microbiome

[REVIEW]The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases – Alenius et al. – Experimental Dermatology

[PREPRINT]Bacterial DNA on the skin surface overrepresents the viable skin microbiome – Acosta et al. – bioRxiv

Human oral microbiome

[REVIEW]The role of oral bacteria in inflammatory bowel disease – Read, Curtis & Neves

Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID – Haran et al. – JCI insight

Human gut microbiome

[REVIEW]Phage Diversity in the Human Gut Microbiome: a Taxonomist’s Perspective – Adriaenssens – mSystems

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

IL-10 Deficiency Accelerates Type 1 Diabetes Development via Modulation of Innate and Adaptive Immune Cells and Gut Microbiota in BDC2.5 NOD Mice – Huang et al. – Frontiers in Immunology

Genetically determined hypertensive phenotype affects gut microbiota composition, but not vice versa – Konopelski et al. – Journal of Hypertension

Plant, root, and soil microbiome

Plant developmental stage drives the differentiation in ecological role of the maize microbiome – Xiong et al. – Microbiome

Bioinformatics

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach – Dovrolis et al. – PLOS Computational Biology

[PREPRINT]SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) – Pan et al. – bioRxiv

[PREPRINT]Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification – Passarelli-Araujo, Franco & Venancio – bioRxiv

Techniques

[PREPRINT]The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS – Lao et al. – bioRxiv

July 14, 2021

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General microbiome

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals – Kirsch et al. – Annual Review of Virology

Helicobacter pylori infection has a detrimental impact on the efficacy of cancer immunotherapies – Oster et al. – Gut

Pregnancy and early life

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort – Flaviani et al. – JCI Insight

[REVIEW][Early-life gut microbiota and its connection to metabolic health in children: Perspective on ecological drivers and need for quantitative approach – Jian et al. – EBBioMedicine

Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study – Gisler et al. – Environmental Research

Human respiratory microbiome

Multi-omics profiling predicts allograft function after lung transplantation – Watzenböck et al. – European Respiratory Journal

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis – Liu et al. – Genomics, Proteomics & Bioinformatics

Human skin microbiome

[REVIEW]Novel mechanisms of microbial crosstalk with skin innate immunity – Chinnappan & Harris-Tyron – Experimental Dermatology

Shifts in the skin bacterial and fungal communities of healthy children transitioning through puberty – Park et al. – Journal of Investigative Dermatology

Human gut microbiome

Gut-microbiota-targeted diets modulate human immune status – Wastyk et al. – Cell

[REVIEW]Silent hypoxia in COVID-19: a gut microbiota connection – Gopal et al. – Current Opinion in Physiology

[REVIEW]The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training – Bongiovanni, Yin & Heaney

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Verma et al. – PLOS One

Kefir Ameliorates Specific Microbiota-Gut-Brain Axis Impairments in a Mouse Model Relevant to Autism Spectrum Disorder – van de Wouw et al. – Brain, Behavior, and Immunity

Animal microbiome

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand – Sawaswong et al. – Scientific Reports

Impact of the dietary inclusion of dried food residues on the apparent nutrient digestibility and the intestinal microbiota of dogs – Paßlack et al. – Archives of Animal Nutrition

Triphenyltin exposure causes changes in health-associated gut microbiome and metabolites in marine medaka – He et al. – Environmental Pollution

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota – Bermudez-Martin et al. – Microbiome

Microbes in space

Seven years of Progress in Determining Fungal Diversity and Characterization of Fungi Isolated from the Japanese Experiment Module KIBO, International Space Station – Satoh et al. – Microbiology and Immunology

Food microbiology

[REVIEW]Virome studies of food production systems: time for ‘farm to fork’ analyses – Mahony & van Sinderen – Current Opinion in Biotechnology

Bioinformatics

D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies – Chen & Zhang – Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model – Hosoda, Fukunaga & Hamada – Bioinformatics

[PREPRINT]Stool Studies Don’t Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning – Quinn – arXiv

Techniques

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost – Harrison, Randolph & Buerkle – mSystems

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing – Cho et al. – mSystems

Statistical approaches for differential expression analysis in metatranscriptomics – Zhang et al. – Bioinformatics

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets – Kameoka et al. – BMC Genomics

In vitro models of gut digestion across childhood: current developments, challenges and future trends – Fournier et al. – Biotechnology Advances

June 23, 2021

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Happy Wednesday!

Today’s digest includes a review on the microbial transformations of human bile acids as well as research articles focused on extremophiles including Arthrobacter, Acidithiobacillus, and Atribacteria. Also included are a wide variety of preprints on topics such as CRISPR-Cas, the vaginal microbiome, immunocompetence in pigs, the evaluation of RNAlater for preserving field samples for metaproteomics, and more!

Happy reading!

General microbiome

Preprint: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids – Pinilla-Redondo et al. – bioRxiv

Human respiratory microbiome

Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students – Fu et al. – Microbiome

Human vaginal microbiome

Preprint: Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data – France et al. – bioRxiv

Human gut microbiome

Review: Microbial transformations of human bile acids – Guzior & Quinn – Microbiome

Preprint: Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes – Tso et al. – bioRxiv

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants – Xie et al. – Microbiome

Animal experiments

Preprint: Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs – Ramayo-Caldas et al. – bioRxiv

Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens – Wen et al. – Microbiome

Animal microbiome

Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish – Röthig et al. – Microbiome

Plant, root, and soil microbiome

Preprint: Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments – Glass et al. – bioRxiv

Preprint: Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – bioRxiv

Preprint: The activity and functions of subarctic soil microbial communities vary across vegetation types – Viitamäki et al. – bioRxiv

Water and extremophile microbiome

Preprint: Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep – Chen et al. – bioRxiv

Preprint: Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures – Li et al. – bioRxiv

Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir – Mo et al. – Microbiome

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution – Shen et al. – Microbiome

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs – Sriaporn et al. – Microbiome

Built environment

Preprint: Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking – Suttner et al. – bioRxiv

Phages and viruses

Preprint: Expanding clinical phage microbiology: Simulating phage inhalation for respiratory tract infections – Porat et al. – bioRxiv

Techniques

Ultra-accurate microbial amplicon sequencing with synthetic long reads – Callahan et al. – Microbiome

Preprint: Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses – Jensen et al. – bioRxiv

Preprint: Predicting microbiome compositions through deep learning – Michel-Mata et al. – bioRxiv