Category Archives: Techniques

March 13, 2024

Posted on by

Human gut microbiome

Gut microbiota–tryptophan metabolism–GLP-1 axis participates in β-cell regeneration induced by dapagliflozin – Yafei Jiang et al – Diabetes

Inhibition of inosine metabolism of the gut microbiota decreases testosterone secretion in the testis – Lei Tang et al – mSystems

[REVIEW] Exploring the gut microbiota and its potential as a biomarker in gliomas – Dana Aljarrah et al – Biomedicine & Pharmacotherapy

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin and acacia gum in Kenyan infant gut microbiota during iron supplementation – Paula Momo Cabera et al – ISME Communications

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Ekaterina Buzun et al – Cell Host and Microbe

Animal Microbiome

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves – Thomas Hartinger et al – BMC Animal Microbiome

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves – Jiancheng Qi et al – BMC Microbiome

Efficacy of a novel multi-enzyme feed additive on growth performance, nutrient digestibility and gut microbiome of weanling pigs fed corn-wheat or wheat-barley based diet – Ayodeji S Aderibigbe et al – Journal of Animal Science

Plant and soil microbiome

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition – Jia Wang et al – mSystems

Plasma Treatment Modifies Element Distribution in Seed Coating and Affects Further Germination and Plant Growth through Interaction with Soil Microbiome – Tetiana Kalachova et al – Journal of Agricultural and Food Chemistry

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils – Prinpida Sonthiphand et al – Bulletin of Environmental Contamination and Toxicology

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria – Katarina Hrovat et al – ISME Communications

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process – Liqun Jiang et al – Microbiology Spectrum

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes – Ziguo Zhang et al – mSystems

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis – Eliza P.-I. Loo et al – Cell Host and Microbe

Built environment microbiome

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station – Tomoro Warashina et al – Applied and Environmental Microbiology

Bioinformatics and Techniques

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas et al – BMC Microbiome

Proportion-based normalizations outperform compositional data transformations in machine learning applications – Aaron Yerke et al – BMC Microbiome

A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria – Geraldine J. Sullivan et al – mSystems

[PREPRINT] Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach – Federica Palma et al – bioRXiv

February 13, 2024

Posted on by

General microbiome

Model-free prediction of microbiome compositions – Asher & Bashan – Microbiome

Pregnancy and early life

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition – Mercer et al. – Microbiome

Human airway microbiome

Genomic attributes of airway commensal bacteria and mucosa – Cuthbertson et al. – Communications Biology

Human skin microbiome

[REVIEW]Triggers for the onset and recurrence of psoriasis: a review and update – Liu et al. – Cell Communication and Signaling

Human vaginal microbiome

Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound – Robbins – PLOS One

Human gut microbiome

Microbial-derived imidazole propionate links the heart failure-associated microbiome alterations to disease severity – Raju et al. – Genome Medicine

Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome

Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe – Colorado et al. – Microbiome

Gut microbiome signature of metabolically healthy obese individuals according to anthropometric, metabolic and inflammatory parameters – Lee et al. – Scientific Reports

Animal microbiome

Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties – Shen et al. – Microbiome

Falcon gut microbiota is shaped by diet and enriched in Salmonella – Ahmad et al. – PLOS One

Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer – Chang et al. – Scientific Reports

Cadaver decomposition microbiome

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables – Burcham et al. – Nature Microbiology

Bioinformatics

YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample – Koslicki et al. – Bioinformatics

Gut microbiome-metabolome interactions predict host condition – Shtossel et al. – Microbiome

Techniques

Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions – Barko et al. – PLOS One

January 31, 2024

Posted on by

General microbiome

Finding Candida auris in public metagenomic repositories – Mario-Vasquez et al. – PLOS One

Pregnancy and early life

A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome – Letourneau et al. – PLOS One

[PREPRINT]Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk – Allert et al. – bioRxiv

Human nasal microbiome

A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome – Liu et al. – Communications Biology

Human gut microbiome

Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans – Link et al. – Nature Medicine

Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago – Nishimura et al. – PLOS One

[PREPRINT]Unravelling the ancient fungal DNA from the Iceman’s gut – Oskolkov et al. – bioRxiv

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

Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice – Fu et al. – Cell

Gut complement induced by the microbiota combats pathogens and spares commensals – Wu et al. – Cell

Complement in breast milk modifies offspring gut microbiota to promote infant health – Xu et al. – Cell

Antidiabetic effects and mechanism of γ-polyglutamic acid on type II diabetes mice – Li et al. – International Journal of Biological Macromolecules

Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources – Srinivasan et al. – PLOS One

Animal microbiome (for animals in the wild)

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids – Chai et al. – Microbiome

[PREPRINT]Thermal fluctuations independently modulate physiological plasticity and the dynamics of the gut microbiome in a tropical rocky shore oyster – Arromrak et al. – bioRxiv

[PREPRINT]Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean – Williams et al. – bioRxiv

Plant, root, and soil microbiome

[PREPRINT]Temporal and spatial dynamics within the fungal microbiome of grape fermentation – Onetto et al. – bioRxiv

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

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism – Valentin-Alvarado et al. – Microbiome

Phages and viruses

[PREPRINT]Viroid-like colonists of human microbiomes – Zheludev et al. – bioRxiv

Bioinformatics

[PREPRINT]DeepGOMeta: Predicting functions for microbes – Hoehndorf et al. – bioRxiv

[PREPRINT]Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences – Øyås et al. – bioRxiv

Techniques

[REVIEW]Unraveling metagenomics through long-read sequencing: a comprehensive review – Kim et al. – Journal of Translational Medicine

Microbes in the news

Non-prescription therapeutics for IBS: where are we? – Costantino – Gut Microbiota for Health by ESNM

January 17, 2024

Posted on by

Pregnancy and early life

Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study – Adeniyi-Ipadeola et al. – Pediatric Research

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Buzun et al. – Cell Host & Microbe

Multi-site human microbiome

[DATA]Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults – Rashidi et al. – Scientific Data

Human respiratory microbiome

[REVIEW]Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies – Cauwenberghs et al. – Cell Reports Medicine

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

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling – Lai et al. – npj Biofilms and Microbiomes volume

Nonylphenol induces depressive behavior in rats and affects gut microbiota: A dose–dependent effect – Pan et al. – Environmental Pollution

Animal microbiome (for animals in the wild)

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity – Kong et al. – Microbiome

Plant, root, and soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Alahmad et al. – Microbiome

Biogeographic survey of soil bacterial communities across Antarctica – Varliero et al. – Microbiome

Microbes in space

[PREPRINT]Testing microbial biomining from asteroidal material onboard the International Space Station – Santomartino et al. – bioRxiv

Bioinformatics

[PREPRINT]AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods – Wei et al. – bioRxiv

Techniques

Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly – Hu et al. – Scientific Reports

January 8, 2024

Posted on by

The microbiome digest team, Juan Pablo Cardenas Astudillo, Axel Künstner and Svetlana Ugarcina Perovic (it’s me), wishes you happy and healthy 2024! Also, we wish to have more members in our team in order to cover all daily microbiome science news: if you are interested in reviewing microbiome papers at your convenience (with our support!) and digest them for the community, feel free to contact us. We are happy to welcome you!

And, yes, see you at MVIF #25!

Vaginal microbiome

Vaginal Lactobacillus fatty acid response mechanisms reveal a novel strategy for bacterial vaginosis treatment – Meilin Zhu – bioRxiv

Gut microbiome

BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen – Brantley Hall – Nature Microbiology

Influence of feeding practices in the composition and functionality of infant gut microbiota and its relationship with health – Misael Martínez-Martínez – PlosOne

Mucin-degrading gut bacteria promote anti-parasitic immunity – Mathis Wolter – bioRxiv

Host genetic regulation of human gut microbial structural variation – Daria V. Zhernakova – Nature

Animal microbiome

Deciphering the gut microbiome of grass carp through multi-omics approach – Ming Li – Microbiome

Spotting disease disrupts the microbiome of infected purple sea urchins, Strongylocentrotus purpuratus – Chloe G. Shaw – BMC Microbiology

Animal experiments

Desulfovibrio vulgaris interacts with novel gut epithelial immune receptor LRRC19 and exacerbates colitis – Runxiang Xie – Microbiome

Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity – Erica Bonazzi – Microbiome

A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice – Rachel M. Bleich – Microbiome

Environmental microbiome

A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes – Victor Borin Centurion – Environmental Microbiome

Plant, root, soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Abdelrahman Alahmad – Microbiome

Methods

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome – Lei Cao – Nature Methods

Bioinformatics

A catalogue of small proteins from the global microbiome – Yiqian Duan – bioRxiv

December 15, 2023

Posted on by

Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii – Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv

November 28, 2023

Posted on by

Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

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

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

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

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi

October 13, 2023

Posted on by

Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

October 11, 2023

Posted on by

General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

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

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 4, 2023

Posted on by

General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

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

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols