Author Archives: Feargal

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

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 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

November 1, 2024

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General human microbiome

[Review] Examining the healthy human microbiome concept – Joos et a. Nature Reviews Microbiology

Bifidobacteria with indole-3-lactic acid-producing capacity exhibit psychobiotic potential via reducing neuroinflammation – Qian et al. Cell Reports Medicine

Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients – Macandog et al. Cell Host & Microbe

Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease – Hacker et al. Cell Host & Microbe

Identification of gut microbiome features associated with host metabolic health in a large population-based cohort – Keshet & Segal. Nature Communications

Probiotics

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome – Whelan et al. Nature Microbiology

Virome

Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information – Gaborieau et al. Nature Microbiology

Bioinformatics

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata – Fenske et al. Microbial Genomics

A long-context language model for deciphering and generating bacteriophage genomes – Shao and Yan. Nature Communications

Non Microbiome Piks

We continue to learn more about the mechanisms underpinning long COVID in recent weeks 

Blood transcriptomic analyses do not support SARS-CoV-2 persistence in patients with post-COVID-19 condition with chronic fatigue syndrome – Rahmati et al. The Lancet Microbe

Post-acute sequelae of SARS-CoV-2 cardiovascular symptoms are associated with trace-level cytokines that affect cardiomyocyte function – Sinclair et al. Nature Microbiology

October 18, 2024

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Human microbiome

Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery  – Boukadida et al  – Microbiome 

Vaginal lactobacilli produce anti-inflammatory β-carboline compounds – Glick et al – Cell Host & Microbe

An ancient ecospecies of Helicobacter pylori  – Tourrette et al – Nature

Review – Intestinal fungal-host interactions in promoting and maintaining health – Hill & Round – Cell Host & Microbe

Review – Gut microbiome and health: mechanistic insights – de Vos et al – Gut

Animal microbiome

Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health – de Leon et al – Nature Microbiology

Stress triggers irritable bowel syndrome with diarrhea through a spermidine-mediated decline in type I interferon – Zhang et al – Cell Metabolism

Built environment

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments  – Tong et al – Microbiome 

Plant microbiome

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations  – de Celis et al – Microbiome

Viruses

Using artificial intelligence to document the hidden RNA virosphere – Cell – Hou et al.

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae – Rotman et al – Cell Host & Microbe

Bioinformatics

SurvBal: Compositional microbiome balances for survival outcomes – Li et al – Bioinformatics

q2-metnet: QIIME2 package to analyze 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota – Balzerani et al – Bioinformatics 

Non-microbiome

News feature – Your diet can change your immune system — here’s how – Nature

August 6, 2024

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Human Gut Microbiota

Review – The role of the gut microbiota in regulating responses to vaccination: current knowledge and future directions – Rossouw et al. FEBS

Systemic antibody responses against gut microbiota flagellins implicate shared and divergent immune reactivity in Crohn’s disease and chronic fatigue syndrome – Bourgonje et al. – Microbiome

Pregnancy and early life

Diet at birth is critical for healthy growth, independent of effects on the gut microbiota – Lieke et al. – Microbiome

Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics – Leech et al. Microbial Genomics.

Association of breast milk-derived arachidonic acid-induced infant gut dysbiosis with the onset of atopic dermatitis – Jiang et al. – Gut

General Human Microbiota

The potential role of lung microbiota and lauroylcarnitine in T-cell activation associated with checkpoint inhibitor pneumonitis – Yu et al. eBioMedicine

Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota – Atkins et al. – Microbial Genomics

A human commensal-pathogenic fungus suppresses host immunity via targeting TBK1 – Lou et al. Cell Host & Microbe

Bacteriophage

Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses – Van den Berg et al. – Cell Host & Microbe

Genomic and induction evidence for bacteriophage contributions to sargassum-bacteria symbioses – Stiffler et al. – Microbiome

April 24, 2024

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General microbiome

A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes – Science 

Gut Microbiome

Gut microbial metabolism of 5-aminosalicylic acid in inflammatory bowel disease – Gut

Smoking-related Lactobacillus and immune cell infiltration in colorectal cancer: evidence from a population-based study – Gut. 

Gut microbiota dysbiosis contributes to depression-like behaviors via hippocampal NLRP3-mediated neuroinflammation in a postpartum depression mouse model – Brain, Behavior, and Immunity

Respiratory microbiome

Outlook/Review – Exploring the lung microbiome’s role in disease – Nature

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes – Nature Microbiology

Probiotics

Multi-strain probiotics ameliorate Alzheimer’s-like cognitive impairment and pathological changes through the AKT/GSK-3β pathway in senescence-accelerated mouse prone 8 mice – Brain, Behavior, and Immunity

Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase – Gut

Virome

Phage predation, disease severity, and pathogen genetic diversity in cholera patients – Science

Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment – Nature Microbiology 

Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia – mSphere 

Bioinformatics

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota – Cell Host & Microbe 

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes – Genome Biology

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes – Genome Biology

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies – Genome Biology

Non Microbiome Pick

Refining the impact of genetic evidence on clinical success – Nature

February 24, 2023

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Human and General Microbiome

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

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

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

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

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

Oral & Respiratory Microbiome

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

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

Animal experiments

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

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

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

Phages and viruses

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

Bioinformatics

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

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

Non Microbiome Picks

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

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

January 27, 2023

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General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics