Tag Archives: bioinformatics

November 14, 2025

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Gut Microbiome & Host Health

Sleep deprivation disrupts diurnal rhythmicity of gut microbiota and blood inflammatory cytokines in mice — Weiran Shan et al. (PLOS ONE)

Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts — Guo Hu et al. (PLOS Biology)

The role of hypothyroidism in cirrhosis pathogenesis: A retrospective cohort study and multi-omics integration analysis — Ziyang Yang et al. (PLOS Genetics)

Multi-omics analysis reveals metabolic regulation of phosphatidylcholine, triglycerides, phosphatidylethanolamine, and cardiolipin metabolism in mouse liver with MASLD — Hong Liang & Kang Song (PLOS ONE)

Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study — Ulrika Andersson-Hall et al. (PLOS ONE)

Microbial Pathogens, Immunity & Infection

Exploring the gut microbiota of Pacific white shrimp suffering pale shrimp disease — Lalitphan Kitsanayanyong et al. (PLOS ONE)

Dominance of Zygosaccharomyces and shifts in bacterial pathways under antimicrobial pressure — Maria Cecilia Rasuk et al. (PLOS ONE)

How transcriptional networks control Verticillium plant infection — Ying-Yu Chen et al. (PLOS Pathogens)

Integrative machine learning and multi-omics framework identifies shared biomarkers for rheumatoid arthritis and ulcerative colitis — Meili Liu et al. (PLOS ONE)

The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the ectocervical epithelium — Vilde Kaldhusdal et al. (PLOS Pathogens)

Characterization of ORF19.7608 (PPP1), a biofilm-induced gene of Candida albicans — Nmerichukwu C. Iwuchukwu et al. (PLOS ONE)

Differential regulation of the eicosanoid biosynthesis pathway during Enterocytozoon hepatopenaei infection in shrimp — Wananit Wimuttisuk et al. (PLOS ONE)

Animal, Environmental & Soil Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and fiber fractions in Asiatic lions — Mengmeng Sun et al. (PLOS ONE)

From pre-oral secretions to gut digestion: How Lucilia sericata larvae handle Leishmania major — Azam Malekian et al. (PLOS ONE)

Targeted pathogen profiling of ancient feces reveals common enteric infections (725–920 CE) — Drew Capone et al. (PLOS ONE)

Starve or share? Phosphate availability shapes plant–microbe interactions — Maja Schmidt et al. (PLOS Pathogens)

Pathogenicity and transmission of Morganella morganii in honey bees — Yijun Chen & Qiang Huang (PLOS Pathogens)

Mitogenomics of the tropical bont tick reveals vertical and horizontal transmission of Rickettsia africae — Elisha Chatanga et al. (PLOS NTDs)

Differentiation of bacterial communities in the coral Orbicella faveolata across life-cycle stages — Amanda Pérez-Trejo et al. (PLOS ONE)

Insect-derived polymer hydrogel based on fibroin matrix from whole silkworm larvae — Maki Yamazaki et al. (PLOS ONE)

Thermophilic microbiome acclimation improves anaerobic digestion of food waste — Hengxuan Shao et al. (PLOS ONE)

Epidemiology, Public Health & Clinical Microbiology

Assessing piperacillin/tazobactam vs. ceftriaxone + metronidazole for children with perforated appendicitis — Daniel Briatico et al. (PLOS ONE)

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis in raw milk — Inamullah et al. (PLOS ONE)

Hematological ratios, immune-related adverse events, and mortality in patients receiving immune checkpoint inhibitors — Sophie Lekkerkerker et al. (PLOS ONE)

Geographical and climatic risk factors for COVID-19 in southwest Iran — Koorosh Nikaein et al. (PLOS ONE)

Anthropometric and neurocognitive consequences of Campylobacter, ETEC, and norovirus infections: A systematic review — Patricia B. Pavlinac et al. (PLOS NTDs)

Neuroscience, Immunology & Molecular Networks

Skin melanin is associated with body temperature regulation in humans and mice — Kale S. Bongers et al. (PLOS ONE)

Oxytocin neurons drive melanocortin circuit maturation via vesicle release — Pierre-Yves Barelle et al. (PLOS Biology)

Elucidation and application of the neuroimmune axis between depression and autoimmune diseases — Fu Sun et al. (PLOS ONE)

Quantifying microbial interactions using an iterative generalized Lotka–Volterra approach — Yue Huang et al. (PLOS Computational Biology)

October 13, 2025

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General Microbiome

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome

Gut microbiome

Gut microbiota alterations are linked to COVID-19 severity in North African and European populations – Marius Bredon – Nature

Expanding the human gut microbiome atlas of Africa -Dylan G. Maghini – Nature

Vaginal microbiome

Changes in the vaginal microbiome in female patients with condyloma acuminatum and its impact on persistent HPV infection – Zhiyu Liu – Nature

Associations among HPV persistence, the vaginal microbiome, and cervical cancer recurrence – Despina Tsementzi – Journal of Translational Medicine

Respiratory Microbiome

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing – Alice Michel – BMC Genomics

Animal microbiome

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog – Shuang Liu – Nature

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails – Yiyue Zhang – Microbiome

Water Microbiome

Decoding the genetic drivers of marine bacterial blooms through comparative genomics – Xavier Rey-Velasco – Microbiome

Bioinformatics

Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics – Kang Mao – BMC Microbiology

Computational microbiome pharmacology analysis elucidates the anti-cancer potential of vaginal microbes and metabolites – Damilola C Lawore  – Frontiers

October 10, 2025

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Gut Microbiome & Health

Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand – Tanapon Seetaraso – PLOS ONE

Relationship between Gut microbiome and brain volumes among Japanese Men – Sabrina Ahmed – PLOS ONE

Association of serum intestinal fatty-acid binding protein, inflammatory and oxidative stress markers with colorectal cancer among Ghanaian patients – Genevieve Kwao-Zigah – PLOS ONE

Trends in incidence, mortality and disability-adjusted life years of colorectal cancer in East Asia (1990–2021): An analysis of the Global Burden of Disease study 2021 – Yuanyi Cao – PLOS ONE

Pathogens, Immunity & Host Interactions

Host- and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression – Sabrina J. Arif – PLOS Pathogens

Blockade of mTOR ameliorates IgA nephropathy by correcting CD89 and CD71 dysfunctions in humanized mice – Alexandra Cambier – PLOS ONE

Single-cell analysis reveals an important role of CD137L+ macrophages in the host response to uropathogenic Escherichia coli infection in the bladder – Yaxiao Liu – PLOS Pathogens

Intestinal inflammation induced by heat-labile toxin-producing enterotoxigenic E. coli infection and impact on immune responses in an experimental human challenge model – Xueyan Zhang – PLOS Neglected Tropical Diseases

Vector-Borne & Parasitic Infections

The effects of mating and blood feeding on the immune defense of female Aedes aegypti mosquitoes – Brendan J. Kelly – PLOS Neglected Tropical Diseases

Temporal and spatial profiling of Aedes albopictus immune responses to chikungunya virus infection – Maria Greta Dipaola – PLOS Neglected Tropical Diseases

Distribution of schistosomes and soil-transmitted helminth infections and their association with growth and nutritional status of school-aged children in Cameroon – Estelle Mezajou Mewamba – PLOS Neglected Tropical Diseases

Risk factors influencing Coxiella burnetii seropositivity in water buffalo populations of Egypt’s Nile Delta – Abdelfattah Selim – PLOS ONE

Global genomic and antimicrobial resistance profiling of Neisseria gonorrhoeae: Insights from whole genome sequencing and minimum inhibitory concentration analysis – Elaheh Ebrahimi – PLOS Neglected Tropical Diseases

Oral & Other Microbiomes

Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients – Duangnapa Roongpiboonsopit – PLOS ONE

Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission – Victoria A. Sadowski – PLOS ONE

Captivity-driven microbiota reshaping: A cross-species analysis of divergent patterns in the gut microbiota of giant pandas, red pandas, and Asiatic black bears – Lin Xu – PLOS ONE

Environmental & Soil Microbiomes

Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities – Santiago Rosas-Plaza – PLOS ONE

The spatial distribution of salt tolerant bacteria and other soil parameters under different agricultural systems of the Indian Sundarbans – Sreemoyee Mitra – PLOS ONE

Pilot-scale depuration demonstrates the suitability of non-pathogenic Vibrio parahaemolyticus as a surrogate for commercial-scale validation studies – Spencer L. Lunda – PLOS ONE

Public Health & Perception

Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance – Christopher L. Cummings – PLOS ONE

Nutritional status and bacteremia patterns in children with diarrheal diseases: A comparative analysis of bacteremia from Salmonella Typhi versus other pathogens – Md Rezaul Hossain – PLOS ONE

Exploration of common biomarkers and pathogenesis of primary Sjögren’s syndrome and interstitial lung disease by machine learning and weighted gene co-expression networks – Jingqi Dong – PLOS ONE

September 23, 2025

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General Microbiome

Specialty grand challenge: how can we use integrative approaches to understand microbial community dynamics? – Umer Zeeshan Ijaz- Frontiers in Systems Biology

Gut microbiome

Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis – Sunhee Jung – nature metabolism

Repopulation of the gut microbiota after a screening colonoscopy – Yezaz A Ghouri – PLOS One

Leveraging the Role of Microbiome in Endometriosis: Novel Non-Invasive Diagnostic and Therapeutic Approaches – Eleni Andria Kalopedis – Frontiers in Immunology

Vaginal microbiome

Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort – Noriaki Oguri – Nature Communications

Animal microbiome

Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds – Wouter F. D. van Dongen – PLOS One

Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria – Chika Ejikeugwu – bioRxiv

Virome

Duck Slurry as a Matrix for Avian Influenza Virus Surveillance and Genetic Characterization in Domestic Flocks – Clément Castille – bioRxiv

Bioinformatics

Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics – Banaz Star-Shirko – BMC research notes

Bioinformatics-based stereochemical elucidation of MM 46115: an unusual antiviral spirotetronate that inhibits clathrin-mediated endocytosis – Afifah Tasnim – bioRxiv

April 22, 2025

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General microbiome

[Editorial] A blueprint for contemporary studies of microbiomes – Bindels et al. Microbiome

[Perspective] Moving from genome-scale to community-scale metabolic models for the human gut microbiome – Quinn-Bohmann et al. Nature Microbiology

[Review] Clinical translation of microbiome research – Gilbert et al. Nature Medicine

Gut microbiome

Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine – Feng et al. Cell Host & Microbe

Animal models

Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice – Zhang et al. Microbiome

Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model  – Cuisiniere et al. Microbiome

Virome

The T-series bacteriophages are reductionist models that continue to shape the field  – Barr. Nature Microbiology

Phollow reveals in situ phage transmission dynamics in the zebrafish gut microbiome at single-virion resolution  – Ortiz de ora et al. Nature Microbiology

Bioinformatics 

FGeneBERT: function-driven pre-trained gene language model for metagenomics – Duan et al. Briefings in Bioinformatics. 

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases – Cong et al. Briefings in Bioinformatics. 

April 3, 2025

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General microbiome

[REVIEW] The regulatory framework for microbiome-based therapies: insights into European regulatory developments – Rodriguez et al. npj Biofilms and microbiomes

Early life microbiome

Bifidobacteria support optimal infant vaccine responses – Ryan et al. Nature

Gut microbiome evolution from infancy to 8 years of age – Sawhney et al. Nature Medicine

Animal experiments

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice – Litichevskyiy et al. Nature Microbiology

Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice – Sommer et al. Microbiome

Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection – Xing et al. Microbiome

Bioinformatics

Elementary methods provide more replicable results in microbial differential abundance analysis – Pelto et al. Briefings in Bioinformatics

DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts – Weng et al. BMC Bioinformatics

March 2, 2025

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Hello, have a nice Sunday! In this Digest, we have some highlights from the literature during this week. 

Human/General Microbiome

Gastrointestinal Tract

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals – Dayi Deng – Scientific Reports

Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer – Ping Cai – mSystems

Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients – Yuling Qin – mSystems

Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages – Nejc Stopnisek – BMC Microbiology

Review: Helicobacter pylori, microbiota and gastric cancer – principles of microorganism-driven carcinogenesis – Jonas Wizenty – Nature Reviews. Gastroenterology & Hepatology

Skin

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes – Diana M Proctor – Nature

Oral – Respiratory Tract

A gut Eggerthella lenta-derived metabolite impairs neutrophil function to aggravate bacterial lung infection – Le-Le Wang – Science Translational Medicine

Involvement of propionate, citrulline, homoserine, and succinate in oral microbiome metabolite-driven periodontal disease progression – Chikako Ishihara – Scientific Reports

Regulation of tryptophan-indole metabolic pathway in Porphyromonas gingivalis virulence and microbiota dysbiosis in periodontitis – Jing Ding – NPJ Biofilms and Microbiomes

Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis – Ying Liao – Cell Reports. Medicine

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types – Zizheng Wang – Microbiology Spectrum

Other Sites

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – Microbiology Spectrum

Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer’s disease? – Arnav Bhattacharya – Current Opinion in Psychiatry

Beneficial Microbes and Compounds

Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device – João Gabriel S Souza – NPJ Biofilms and Microbiomes

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function – Benjamin S Beresford-Jones – Microbiome

Antibacterial activity and impact on keratinocyte cell growth of Cutibacterium acnes bacteriophages in a Cutibacterium acnes IA(1)- colonized keratinocyte model – Juan C Farfán-Esquivel – Current Research in Microbial Sciences

Microbiota-derived urolithin A in monoclonal gammopathies and multiple myeloma therapy – Alba Rodríguez-García – Microbiome

Environmental Microbiome / Ecology

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns – Rodolfo A Salido – Cell

Residence Time Structures Microbial Communities Through Niche Partitioning – Emmi A Mueller – Ecology Letters

Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission – Reena Debray – Microbiome

Microbiome Analysis: Resources, Tools and Techniques

Tandem metabolic reaction-based sensors unlock in vivo metabolomics – Xuanbing Cheng – PNAS

Review: Antarctic bacterial natural products: from genomic insights to drug discovery – William Medeiros – Natural Product Reports

December 6, 2024

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Gut Microbiome

Protection against Clostridioides difficile disease by a naturally avirulent strain – Dong et al. Cell Host & Microbe

Animal experiments 

The host genotype actively shapes its microbiome across generations in laboratory mice – Benga et al. Microbiome

Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis – Pietrasanta et al. Cell Host & Microbe

Oral and respiratory microbiomes

Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner – Jaber et al. npj biofilms and microbiomes

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies – Kim et al. Communications biology

The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children – Kristensen et al. Cell Reports Medicine

Plant and environmental microbiomes

Plant microbiota feedbacks through dose-responsive expression of general non-self response genes – Keppler et al. Nature Plants

Dynamics of rice seed-borne bacteria from acquisition to seedling colonization – Chen et al. Microbiome

Bioinformatics

Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets – Bradford et al. BMC Bioinformatics

[PREPRINT] TaxSEA: an R package for rapid interpretation of differential abundance analysis output – Ryan. bioRxiv 

November 17, 2024

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Human and General Microbiome

F. prausnitzii potentially modulates the association between citrus intake and depression – Chatpol Samuthpongtorn – Microbiome

Perturbations in the airway microbiome are associated with type 2 asthma phenotype and severity – Wei Zhang – Annals of Allergy, Asthma & Immunology

Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis – Hua Zhang – Tuberculosis

Mendelian randomization analyses support causal relationships between gut microbiome and longevity – Shu Chen – Journal of Translational Medicine

Natal factors influencing newborn’s oral microbiome diversity – Yoon-Hee Kim – Scientific Reports

Age-related loss of intestinal barrier integrity plays an integral role in thymic involution and T cell ageing – Jessica Conway – Aging Cell

Early-life Upper Airway Microbiota are Associated with Decreased Lower Respiratory Tract Infections – Susan Zelasko – The Journal of Allergy and Clinical Immunology

Human Milk Microbiome Is Associated With Allergic Diseases in Early Childhood – Jie Ma – Allergy

Faecal microbiota composition and impulsivity in a cohort of older adults with metabolic syndrome – Prokopis Konstanti – Scientific Reports

Microbiota-induced alteration of kynurenine metabolism in macrophages drives formation of creeping fat in Crohn’s disease – Jinjie Wu – Cell Host & Microbe

Review: Estimates of microbiome heritability across hosts – Andrew H Morris – Nature Microbiology

Beneficial Microbes and Compounds

High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study – Satoko Maruyama – Frontiers in Nutrition

Review: Prebiotics in food and dietary supplements: a roadmap to EU health claims – Kieran Tuohy – Gut Microbes

Animal Models

The Microbiome Modifies Manifestations of Hemophagocytic Lymphohistiocytosis in Perforin-Deficient Mice – Jasmin Mann – European Journal of Immunology

Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut – Guillaume Urtecho – Cell Systems

Non-Model Animal Microbiome

Multi-omics investigation into long-distance road transportation effects on respiratory health and immunometabolic responses in calves – Jiancheng Qi – Microbiome

Plant and Soil Microbiome

Wild again: recovery of a beneficial Cannabis seed endophyte from low domestication genotypes – Carolina Lobato – Microbiome

Trade-offs and adaptation to metalliferous soils: The role of soil microbiome in metal tolerance and uptake in Arabidopsis halleri ecotypes from a reciprocal transplant experiment – Priyanka Kushwaha – The Science of the Total Environment

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better – Tingting Wang – Microbiome

Environmental Microbiome

Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing – Anxo Méndez – Journal of Photochemistry and Photobiology (B, Biology)

Synthetic communities derived from the core endophytic microbiome of hyperaccumulators and their role in cadmium phytoremediation – Lukuan Huang – Microbiome

Other Microbes

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays – Victoria de la Sovera – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Procedures and Resources

Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls – Ida Marie Bruun Grønbæk – BMC Research Notes

HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors – Jiaying Li – Molecular Ecology Resources

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data – Theresa Rzehak – BMC Genomics

MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies – Aidan Foo – PLoS Biology

November 14, 2024

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General human microbiome

Mapping the gut microbial structural variations in healthy aging within the Chinese population – Shen et al. Cell Reports

Association between butyrate-producing gut bacteria and the risk of infectious disease hospitalisation: results from two observational, population-based microbiome studies – Killberg et al. The Lancet Microbe

[Correspondence related to the above article] Reassessing the role of butyrate-producing bacteria in infection risk – Parsanathan. The Lancet Microbe

Microbiome science of human excrement composting – Meilander & Caporaso. ISME

Microbiota-derived lysophosphatidylcholine alleviates Alzheimer’s disease pathology via suppressing ferroptosis – Zha et al. Cell Metabolism

Probiotics

Probiotics and their metabolite spermidine enhance IFN-γ+CD4+ T cell immunity to inhibit hepatitis B virus – Wang et al. Cell Reports Medicine

Virome

The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission – Majzoub et al. Nature Communications

Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions – Du et al. ISME

Bioinformatics & metagenomics

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data – Tan et al. Briefings in Bioinformatics. 

AMRColab – a user-friendly antimicrobial resistance detection and visualization tool – Lam et al. Microbial Genomics

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections – Benoit et al. Nature Medicine