Author Archives: Nkiruka Efenji

November 28, 2025

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Human Microbiome

Awareness of human microbiome may promote healthier lifestyle and more positive environmental attitudes – Olga Rook – Nature

Viruses and Phages

Long-read metagenomics reveals phage dynamics in the human gut microbiome – Jakob Wirbel- Nature

Gut microbiome

Association Between Gut Microbiota Diversity and Body Mass Index (BMI) in Healthy Young Adults in the United States: Insights Into the Gut-Brain-Metabolic Axis Using the Curated Metagenomic Data – Nenrot S. Gopep – Cureus

Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro – Indra Roux – Nature

Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease – Rémy Villette – Microbiome

Respiratory Microbiome

Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes – Kristel S. Knudsen – Respiratory Research

Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection– Xiaohui Zou –  Signal Transduction and Targeted Therapy

Animal microbiome

Non-pasteurized milk enhances early colonization and persistence of Lactobacillus species in dairy calves promoting a stable hindgut microbiome – Shengnan Qiu – Animal Advances

The interaction of microplastics with the ruminal ecosystem in vitro – J. Eichinger – Journal of Hazardous Materials

Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Water Microbiome

Spontaneous fermentation of raisin water to form wine – Mamoru Hio – Scientific Reports

Nasal Microbiome

Comparative meta-transcriptomic analysis of nasal and anal microbiota in respiratory syncytial virus mono and co-infected children – Iman Dandachi – Microbiology

Bioinformatics

SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease – Youngro Lee – Scientific Reports

November 7, 2025

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General Microbiome

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes – Ricardo Leon-Sampedro – Nature

Gut microbiome

Pushing the frontier of gut microbiome health cross-kingdom and cross-organ – Tao Zuo  (左涛) – Nature

The early-life gut microbiome in common pediatric diseases: roles and therapeutic implications – Taiwo Bankole – Frontiers in Nutrition

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals – Christophe Boetto – Communications Biology

Respiratory Microbiome

Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort – Baolin Jia – Frontiers in Public Health

Distinguishing tuberculosis from non-tuberculous mycobacteria and other respiratory conditions by microbiome patterns – Jee Youn Oh –  Scientific Reports

Animal microbiome

Effects of avian Plasmodium exposure on the microbiota of Culex pipiens – Marta Garrigos – Nature

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P. Schmartz – Nature Communications

Animal Experiments

Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition – Leigh A. Frame – mSystems

Water Microbiome

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals – Ganiyu Oladunjoye Oyetibo – Scientific Reports

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems – Congmin Zhu – Nature Communications

Bringing the uncultivated microbial majority of freshwater ecosystems into culture – Michaela M. Salcher – Nature Communications

Bioinformatics

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand– Watchaporn Chuchaona – Scientific Reports

Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing – Shirin Ashraf – Nature Communications

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well – Eli K. Moore – Communications Earth & Environment 

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

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

September 10, 2025

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General Microbiome

The multi-kingdom cancer microbiome – Anders B. Dohlman – Nature Microbiology

Gut microbiome

Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection – Shrushti Shah – BMC Microbiology

Gut microbial production of imidazole propionate drives Parkinson’s pathologies – Hyunji Park – nature communications

Vaginal microbiome

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis – Smrutiti Jena – bioRxiv

Animal microbiome

Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics – Md Asaduzzaman – bioRxiv

Water microbiome

Net rate of lateral gene transfer in marine prokaryoplankton – Ramunas Stepanauskas – The ISME Journal

Virome

Spatio-temporal factors shape mosquito virome diversity and composition in a host and virus phylogeny-dependent manner – Cassandra Koh – bioRxiv

Bioinformatics

Dietary Protein Source Shapes Gut Microbial Structure and Predicted Function: A Meta-Analysis with Machine Learning – SAMSON A. ADEJUMO – bioRxiv

Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity – Magdalena J Mayr – The ISME Journal

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease – Stefano Romano – nature communications

Microbes on the market

Microbiome Manufacturing Market Size to Hit USD 130.37 Billion by 2034 – Deepa Pandey – Precedence Research