Category Archives: Metagenomics & Bioinformatics

July 13, 2022

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Today’s digest features studies on the leaf-microbiome of πŸ… and πŸ“ plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko PeuranpÀÀ – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv

July 12, 2022

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Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution

Bacteriophages

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association

July 9, 2022

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Have a nice weekend! 

Human and General Microbiome

Review: Bladder cancer, inflammageing and microbiomes – Austin Martin – Nature Reviews. Urology

Review: Gut associated metabolites and their roles in Clostridioides difficile pathogenesis – Andrea Martinez Aguirre – Gut Microbes

Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease – Sungyang Jo – NPJ Parkinson’s Disease

Transcriptional programming in a Bacteroides consortium – Brian D Huang – Nature Communications

Gut microbiota composition in colorectal cancer patients is genetically regulated – Francesca Colombo – Scientific Reports

Relative contributions of the host genome, microbiome, and environment to the metabolic profile – Kangjin Kim – Genes & Genomics

Beneficial Microbes and Compounds

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals – Maria Magdalena Coman – Journal of Applied Microbiology

Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation – Mohamed Mokrani – Gut Pathogens

Lactobacillus acidophilus LA85 ameliorates cyclophosphamide-induced immunosuppression by modulating Notch and TLR4/NF-ΞΊB signal pathways and remodeling the gut microbiota – Liangyu Xue – Food & Function

Animal Model Microbiome

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis – Anshul Sinha – Microbiome

Non-Model Animal Microbiome

Rickettsia helvetica infection is associated with microbiome modulation in Ixodes ricinus collected from humans in Serbia – Apolline Maitre – Scientific Reports

Environmental Microbiome

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms – Javier Edo Varg – Environmental Microbiome

Estuarine plastisphere as an overlooked source of N(2)O production – Xiaoxuan Su – Nature Communications

Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics – Joon-Yong Lee – Journal of Proteome Research

Other

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic – Andrea Shin – Ethics & Human Research

Bioinformatics and Experimental Microbiome Analysis

Review: Metagenomics Approaches to Investigate the Neonatal Gut Microbiome – Zakia Boudar – Frontiers in Pediatrics

Editorial: Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes – Arwyn Edwards – Microbiology

A Bayesian method for identifying associations between response variables and bacterial community composition – Adrian Verster – PLoS Computational Biology

GenBank as a Source to Monitor and Analyze Host-Microbiome Data – Vivek Ramanan – Bioinformatics

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies – Hayley B Hassler – Microbiome

July 2, 2022

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Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journal β†’ this paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature Microbiology β†’By using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORΞ³t+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – Microbiome β†’ This article demonstrates the existence of β€œa novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”.Β 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

June 29, 2022

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General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – MΓΌnzker et al. – Microbiome

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

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

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

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

June 24, 2022

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Today we have a report in Science on bacterium which is 1cm long, a great review of the gut virome in human health, and a meta-analysis of mycobiota signatures in colorectcal cancer among some other great papers.

General microbiology

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles – Volland et al. – Science

Virome

Filamentous bacteriophage delays healing of Pseudomonas-infected wounds – Bach et al. – Cell Reports Medicine

[REVIEW] The gut virome: A new microbiome component in health and disease – Cao et al. – eBioMedicine

Gut Microbiome

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function – Mayneris-Perxachs et al. – ISME

Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multi-cohort fecal metagenomic analyses – Lin et al. – Gastroenterology

[REVIEW] Small molecules in the big picture of gut microbiome-host cross-talk – Ma et al. – eBioMedicine

Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity – Sanidad et al. – Science Immunology

Non-Microbiome picks

Time for better time-restricted eating trials to lessen the burden of metabolic diseases – Taub and Panda – Cell Reports Medicine

What SARS-CoV-2 does to our brains – Aschman et al. – Immunity

June 20, 2022

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Highlights!

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A Shetty – The ISME Journal β†’ This study shows the experimental setting of a minimal microbiome composed of 16 bacterial species, characterizing their metabolic relationships, dynamics, and stability.Β Β 

Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain – Xingzhi Guo – Frontiers in Microbiology β†’ Members of Blautia, a relatively common genus in the human gut, was β€œconsistently depleted across feces, blood, and brain samples of PD patients”. This study suggests a link between Blautia and PD.

Human and General Microbiome

A Microbiota-Dependent Response to Anticancer Treatment in an In Vitro Human Microbiota Model: A Pilot Study With Hydroxycarbamide and Daunorubicin – Claire Amaris Hobson – Frontiers in Cellular and Infection Microbiology

Examination of host genetic effects on nasal microbiome composition – Haritz Irizar – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Kimchi improves irritable bowel syndrome: results of a randomized, double-blind placebo-controlled study – Hee-Young Kim – Food & Nutrition Research

Non-Model Animal Microbiome

Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized – Baptiste Sadoughi – Microbiome

Model Animal Microbiome

Sodium alginate and galactooligosaccharides ameliorate metabolic disorders and alter the composition of the gut microbiota in mice with high-fat diet-induced obesity – Yao Li – International Journal of Biological Macromolecules

Plant Microbiome

From the bacterial citrus microbiome to the selection of potentially host-beneficial microbes – RamΓ³n Penyalver – New Biotechnology

Review: Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes – Sang-Woo Han – Current Opinion in Microbiology

Environmental Microbiome

Microbiome assembly in thawing permafrost and its feedbacks to climate – Jessica G Ernakovich – Global Change Biology

Other

Rapid sourdough yeast identification using panfungal PCR combined with high resolution melting analysis – Olga BazalovΓ‘ – Journal of Microbiological Methods

June 18, 2022

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Have a nice weekend! Today, in this Digest: The effect of the gut dysbiosis on prostate cancer, microbial inheritance, bee microbiome, rhizosphere microbiota, a comparison of DNA isolation techniques for deep amplicon sequencing, and more…

Human and General Microbiome

Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-ΞΊB-IL6-STAT3 axis – Weibo Zhong – Microbiome

On the effect of inheritance of microbes in commensal microbiomes – RomΓ‘n ZapiΓ©n-Campos – BMC Ecology and Evolution

Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth – Sunwha Park – Scientific Reports

Deep Grouping Analysis of the Altered Cervical Canal Microbiota in Intrauterine Adhesion Patients – Xiangdong Hua – Reproductive Sciences

Intestinal microbiota transplantation: do not forget the metabolites – Benjamin H Mullish – The Lancet. Gastroenterology & Hepatology

Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up – Guang-Ying Cui – Military Medical Research

Congenitally underdeveloped intestine drives autism-related gut microbiota and behavior – Jie Li – Brain, Behavior, and Immunity

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus HA-114 improves eating behaviors and mood-related factors in adults with overweight during weight loss: a randomized controlled trial – BΓ©atrice S-Y Choi – Nutritional Neuroscience

Model Animal Microbiome

New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy – Hye Rim Byeon – Journal of Medicinal food

Non-Model Animal Microbiome

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes – Wyatt A Shell – Communications Biology

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review – Sonam Dixit – Animal Biotechnology

Plant Microbiome

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees – Maximilian Fernando Becker – Environmental Microbiome

Identifying plant genes shaping microbiota composition in the barley rhizosphere – Carmen Escudero-Martinez – Nature Communications

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Ben O Oyserman – Nature Communications

Environmental Microbiome

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables – Jessica L Gronniger – Environmental Microbiology

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments – Cheng Chen – Water Research

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China – Lei Zhou – Scientific Data

Food Microbiome

Microbiome and -omics application in food industry – Ilario Ferrocino – International Journal of Food Microbiology

Bioinformatic and Experimental Microbiome Analysis

A comparison of six DNA extraction protocols for 16S, ITSΒ and shotgun metagenomic sequencing of microbial communities – Justin P Shaffer – BioTechniques

Review: Machine Learning Advances in Microbiology: A Review of Methods and Applications – Yiru Jiang – Frontiers in Microbiology

June 15, 2022

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General microbiome

[PREPRINT]Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica – Escudero-Leyva et al. – bioRxiv

Pregnancy and early life

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life – Wells et al. – Annual Review of Nutrition

Multi-site human microbiome

A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao – Han et al. – Clinical and Translational Medicine

Human oral microbiome

The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine – Herremans et al. – Microbiome

Human skin microbiome

Altered skin fungal and bacterial community compositions in tinea capitis – Rong et al. – Mycoses

Effects of short chain fructo-oligosaccharides on selected skin bacteria – Le Bourgot et al. – Scientific Reports

Human vaginal microbiome

Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome – Ruotsalainen et al. – Medical Microbiology and Immunology

Human gut microbiome

Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients – Hoang et al. – BMC Cancer

Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study – Miao et al. – BMC Medicine

[REVIEW]The role of virome in the gastrointestinal tract and beyond – Tiamani et al. – FEMS Microbiology Reviews

[REVIEW]Time-limited diets and the gut microbiota in cardiometabolic disease – Ratiner et al. – Journal of Diabetes

Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial – Huang et al. – Journal of Autoimmunity

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

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer – Fu et al. – Cell

Pharmacokinetic and gut microbiota analyses revealed the effect of Lactobacillus acidophilus on the metabolism of Olsalazine in ulcerative colitis rats – Li et al.

Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis – Forster et al. – Nature Microbiology

Plant, root, and soil microbiome

The plant host environment influences competitive interactions between bacterial pathogens – Ehau-Taumaunu & Hockett – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data – Darcy et al. – bioRxiv

June 13, 2022

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Today’s digest features metagenomics for clinical UTI diagnostics, microbial diversity in kombucha tea, microbial source tracking using single nucleotide variants, and more. Happy reading!

Neonatal microbiome

Editorial: More data needed on neonatal microbiome seeding – W. Florian Fricke & Jacques Ravel – Microbiome

Urinary microbiome

The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis – Cara Joyce – Frontiers in Cellular and Infection Microbiology

*Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study – Victoria A Janes – The Lancet Microbe

Gut microbiome

Perspective: Tiny Gatekeepers: Microbial Control of Host Drug Transporters – Than S. Kyaw and Peter J. Turnbaugh – Clinical Pharmacology & Therapeutics

Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids – Henry H. Le – Cell Host & Microbe

Linking gastrointestinal microbiota and metabolome dynamics to clinical outcomes in paediatric haematopoietic stem cell transplantation – Gintare Vaitkute – Microbiome

Animal microbiome

Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis – Vittorio Boscaro – Nature Microbiology

Water microbiome

Cyanopeptides restriction and degradation co-mediate microbiota assembly during a freshwater cyanobacterial harmful algal bloom (CyanoHAB) – Han Gao – Water Research

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster – Irmarie Cotto – bioRxiv

Soil microbiome

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies – Ying Wang – Frontiers in Microbiology

In-depth characterization of denitrifier communities across different soil ecosystems in the tundra – Igor S. Pessi – bioRxiv

Food

*Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations – Elizabeth A. Landis – mSystems

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods – Irina Spacova, Sarah Ahannach – Frontiers in Nutrition

Bioinformatics

coda4microbiome: compositional data analysis for microbiome studies – M.Luz Calle & Antoni Susin – bioRxiv

GeneToList: A web application to assist with gene identifiers for the non-bioinformatics-savvy scientist – Joshua D. Breidenbach – bioRxiv

*Microbiome source tracking using single nucleotide variants – Leah Briscoe – bioRxiv