Category Archives: General Microbiome

December 16, 2022

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Highlights!

A microbiome-dependent gut-brain pathway regulates motivation for exercise – Lenka Dohnalová – Nature 

Here, we report on the discovery of a gut–brain connection in mice that enhances exercise performance by augmenting dopamine signalling during physical activity. We find that microbiome-dependent production of endocannabinoid metabolites in the gut stimulates the activity of TRPV1-expressing sensory neurons and thereby elevates dopamine levels in the ventral striatum during exercise.

Gut microbiota in the early stage of Crohn’s disease has unique characteristics – Xianzong Ma – Gut Pathogens

The present study aimed to identify dysbacteriosis in patients with early Crohn’s Disease (CD) and explore specific gut bacteria related to the progression of CD.

Human and General Microbiome

Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis – Rabab O Ali – Nature Microbiology

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome – Pablo Villoslada-Blanco – Scientific Reports

Consequences of collagen induced inflammatory arthritis on circadian regulation of the gut microbiome – Devin Amanda Simpkins – FASEB Journal

Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut – Jyoti Kashyap – Current Research in Microbial Sciences

HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome – Jingjing Meng – Microbiology Spectrum

Gut dysbiosis and bacterial translocation in the aneurysmal wall and blood in patients with abdominal aortic aneurysm – Ken Nakayama – PloS One

Review: Female reproductive tract microbiome and early miscarriages – Olga Lebedeva – APMIS

Review: Emerging roles of intratumor microbiota in cancer metastasis – Aikun Fu – Trends in Cell Biology

In Brief: Urine microbiota differ in bladder cancer – Louise Stone – Nature Reviews. Urology

Animal Microbiome

Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru – Jesús Rojas-Jaimes – BMC Microbiology

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets – Guang Pu – mSystems

Review: Involvement of Microbiota in Insect Physiology: Focus on B Vitamins – Javier Serrato-Salas – mBio

Plant Microbiome

The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria – Yiting Li – Microbiology Spectrum

Microbiome Analysis and Methods

Interpreting tree ensemble machine learning models with endoR – Albane Ruaud – PLoS Computational Biology

Analysis of Ancient Microbial DNA – Olivier Gorgé – Methods in Molecular Biology (Book)

Confocal Laser Scanning Microscopy Approach to Investigate Plant-Fungal Interactions – F Fracchia – Methods in Molecular Biology (Book)

December 12, 2022

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Today’s digest has the kind of articles I like best–they are all focused on the unique relationship between microbial communities and their niche environments. These environments span everything from rice seeds to the Mariana Trench to the gut microbiome and even Appalachian coalbeds. Happy reading!


Human gut microbiome

Gut microbiome of helminth-infected indigenous Malaysians is context dependent – Tee et al. – Microbiome

Animal experiments

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival – Wang et al. – Microbiome


Plant, root, and soil microbiome

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome – Mataigne et al. – Microbiome

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes – Zhang et al. – Microbiome


Water and extremophile microbiome

Comparison of prokaryotes between Mount Everest and the Mariana Trench – Liu et al. – Microbiome


Built environment

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms – Ross et al. – Environmental Microbiology

Evaluation of the Microbial Community and Geochemistry in Produced Waters Collected from CO2 EOR in the Niagaran Pinnacle Reef – Stemple et al. – ACS Earth Space Chem

December 9, 2022

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Today’s digest features global antimicrobial resistance, comammox and anammox bacteria in wastewater treatment, mOTUs3, and more. Check out Elisa Granato & Christoph Ziegenhain’s story about postdoc life. Happy Friday and see you next week at #MVIF!

Global microbiome & resistome

Experimental temperatures shape host microbiome diversity and composition – Jingdi Li – Global Change Biology

Global biogeography and projection of soil antibiotic resistance genes – Zheng et al. – Science Advances

*Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications

Blood microbiome

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan – bioRxiv

Gut microbiome

Effects of dog ownership on the gut microbiota of elderly owners – Chaona Jiang – Plos One

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases – Yoshihiko Tomofuji – Cell Genomics

Gut microbiome-wide association study of depressive symptoms – Djawad Radjabzadeh – Nature Communications

Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis – Jacqueline Wyss – bioRxiv

The microbiome’s fiber degradation profile and its relationship with the host diet – Yotam Cohen & Elhanan Borenstein – BMC Biology

Animal microbiome

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission – Gang Wang – Microbiome

Live biotherapeutics

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections – Irina Spacova – Microbial Biotechnology

Soil/root/plant microbiome

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient – Yangquanwei Zhong – iMeta

Water microbiome

*Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process – Katherine J Vilardi – bioRxiv

Full-scale activated sludge transplantation reveals a highly resilient community structure – Giulia Dottorini – Water Research

Bioinformatics

Towards complete representation of bacterial contents in metagenomic samples – Xiaowen Feng, Heng Li – arXiv

*Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments – Hans-Joachim Ruscheweyh – Microbiome

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023 – CNCB-NGDC Members and Partners – Nucleic Acids Research

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes – Lei Liu – Microbiome

December 2, 2022

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Human and General Microbiome

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum

The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population – Wen Zhang – Microbiology Spectrum

The Gut Microbiota is Important for the Maintenance of Blood-Cerebrospinal Fluid Barrier Integrity – Emily G Knox – The European Journal of Neuroscience

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections – James B Thissen – PloS One

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – mBio

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species – Shushan Sargsian – Cell Reports

Genome Watch: Zooming into the structure of the microbiome – Gemma G R Murray – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Saussurea involucrata oral liquid regulates gut microbiota and serum metabolism during alleviation of collagen-induced arthritis in rats – Shan Cong – Phytotherapy Research

Prebiotic oligofructose protects against high-fat diet-induced obesity by changing the gut microbiota, intestinal mucus production, glycosylation and secretion – Paola Paone – Gut Microbes

Review: Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health – Car Reen Kok – Annual Review of Food Science and Technology

Animal Microbiome

Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia – Caijun Zhao – Microbiome

Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines – Holly Kristin Arnold – PloS One

Plant and Soil Microbiome

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions – Zhonghua Wang – Microbiology Spectrum

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites – Keke Li – Environmental Microbiology

Environmental Microbiome

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt – Ricardo Amils – Environmental Microbiology

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes – N V Patin – mSystems

Bioinformatics and Microbiome Analysis

The Application of Spearman Partial Correlation for Screening Predictors of Weight Loss in a Multiomics Dataset – Joel Correa da Rosa – Omics

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals – Benjamin Torres Salazar – Methods in Molecular Biology

November 28, 2022

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Human and General Microbiome

Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Gautam Mahajan – Microbiome

Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis – Savannah J Taylor – Microbiome

Review: The immunomodulatory roles of the gut microbiome in autoimmune diseases of the central nervous system: Multiple sclerosis as a model – Kristina Hoffman – Journal of Autoimmunity

Review: The role of NOD2 in intestinal immune response and microbiota modulation: A therapeutic target in inflammatory bowel disease – Ziyue Liu – International Immunopharmacology

Review: Strategizing the human microbiome for small molecules: approaches and perspectives – Aehtesham Hussain – Drug Discovery Today

Animal Microbiome

Timing matters: age-dependent impacts of the social environment and host selection on the avian gut microbiota – Öncü Maraci – Microbiome

Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems – Elsi Hietaranta – Oecologia

A longitudinal census of the bacterial community in raw milk correlated with Staphylococcus aureus clinical mastitis infections in dairy cattle – Soyoun Park – Animal Microbiome

Hypomagnetic Field Exposure Affecting Gut Microbiota, Reactive Oxygen Species Levels, and Colonic Cell Proliferation in Mice – Aisheng Zhan – Bioelectromagnetics

Environmental Microbiome

Metagenomic insights into feasibility of agricultural wastes on optimizing water quality and natural bait by regulating microbial loop – Lingling Wan – Environmental Research

November 26, 2022

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Human and General Microbiome

Essay: Autobiography of a gut bacterium – Florian Schmidt – Science

Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions – Jacob J Haffner – mSystems

Diet standardization reduces intra-individual microbiome variation – Clara Delaroque – Gut Microbes

Investigation of the gut microbiome, bile acid composition and host immunoinflammatory response in a model of azoxymethane-induced colon cancer at discrete timepoints – J M Keane – British Journal of Cancer

A comparative study to determine the association of gut microbiome with schizophrenia in Zhejiang, China – Fuyang Yan – BMC Psychiatry

Review: Gut Microbiome Analysis for Personalized Nutrition: The State of Science – Marie-Christine Simon – Molecular Nutrition & Food Research

Review: The nonindustrialised microbiome in a modern world – Fergus Shanahan – Clinical Science

Beneficial Microbes and Compounds

A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis – Lucas J Osborn – PNAS

Akkermansia muciniphila ameliorates depressive disorders in a murine alcohol-LPS (mALPS) model – Dingming Guo – Food & Function

Animal Microbiome

The Kitty Microbiome Project: Defining the Healthy Fecal Core Microbiome in Pet Domestic Cats – Holly H Ganz – Veterinary Sciences

Bioinformatics and Microbiome Analysis

Bioinformatic Approaches for Describing the Oral Microbiota – Kristi Biswas – Methods in Molecular Biology

Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data – Berenike Kircher – Gut Microbes

Review: Machine learning for data integration in human gut microbiome – Peishun Li – Microbial Cell Factories

More Microbes 

Impact of innovative nanoadditives on biodigesters microbiome – Fatma Y Hassaneen – Microbial Biotechnology

Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola – Lise Alonso – Environmental Microbiology Reports

November 23, 2022

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General microbiome

[PREPRINT]Patterns and determinants of the global herbivorous mycobiome – Meili et al. – bioRxiv

[EDITORIAL]Helicobacter pylori: Have potential benefits been overlooked? – Schubert et al. – JGH Open

Pregnancy and early life

Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin – Young et al. – Arch Dis Child Fetal Neonatal Ed

Human oral microbiome

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture – Quagliariello et al. – Nature Communications

Human vaginal microbiome

[PREPRINT]Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle – Costello et al. – bioRxiv

Human gut microbiome

[REVIEW]Maternal obesity and resistance to breast cancer treatments among offspring: Link to gut dysbiosis – Andrade, Verma & Hilakivi-Clark

Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis – Baumgartner et al. – Gut Microbes

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

Impact of antibiotic perturbation on fecal viral communities in mice – Anderson et al. – G3

Animal microbiome (for animals in the wild)

Assessing Fungal Diversity and Abundance in the Black Soldier Fly and its Environment – Vitenberg & Opatovsky – Journal of Insect Science

Plant, root, and soil microbiome

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front – Scherer, Mason & Rast – FEMS Microbiology Ecology

Bioinformatics

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes – Fullam et al. – NAR

[PREPRINT]Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life – Gorman & Lladser

Techniques

[PREPRINT]Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing – Poursalavati et al. – bioRxix

November 21, 2022

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Highlights!

The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota – Kaitlyn D LaCourse – Cell Reports

Enterococci enhance Clostridioides difficile pathogenesis – Alexander B Smith – Nature

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species – Jeremiah J Minich – Nature Communications

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave – Gabriele Scorrano – Communications Biology

Human and General Microbiome

Gut microbiota analysis for prediction of clinical relapse in Crohn’s disease – Sylvie Buffet-Bataillon – Scientific Reports

Implications of oral streptococcal bacteriophages in autism spectrum disorder – Zhan Tong – NPJ Biofilms and Microbiomes

Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls – Farnaz Fouladi – Gut Microbes

Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers – Valérie O Baede – Scientific Reports

BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection – Surya D Aggarwal – Cell host & Microbe

Treasures from trash in cancer research – Fabiano Cordeiro Moreira – Oncotarget

Human Gut Metagenomes Encode Diverse GH156 Sialidases – Evan Mann – Applied and Environmental Microbiology

Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits – Sudarshan A Shetty – mSphere

Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer – Jorge Luis Galeano Niño – Nature

Broad-spectrum antibiotics associated gut microbiome disturbance impairs T cell immunity and promotes lung cancer metastasis: a retrospective study – Ke Xu – BMC Cancer

Diet-induced modifications to human microbiome reshape colonic homeostasis in irritable bowel syndrome – Hadar Bootz-Maoz – Cell Reports

Review: The dynamic lung microbiome in health and disease – Jake G Natalini – Nature Reviews. Microbiology

Non-model Animal Microbiome 

Modulation of gut microbiota, blood metabolites, and disease resistance by dietary β-glucan in rainbow trout (Oncorhynchus mykiss) – Simon Menanteau-Ledouble – Animal Microbiome

Living in honey: bacterial and fungal communities in honey of sympatric populations of Apis mellifera and the stingless bee Melipona beecheii, in Yucatan, Mexico – Diana Fátima Jacinto-Castillo – Archives of Microbiology

Plant Microbiome

Review: The involvement of organic acids in soil fertility, plant health and environment sustainability – Satyavir S Sindhu – Archives of Microbiology

Bioinformatics and Microbiome Analysis

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H Smith – Animal Microbiome

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes – Jinfang Zheng – Nucleic Acids Research

Gene co-expression network analysis of the human gut commensal bacterium Faecalibacterium prausnitzii in R-Shiny – Sandrine Auger – PloS One

November 16, 2022

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General microbiome

Enhancing nutritional niche and host defenses by modifying the gut microbiome – Sun et al. – Molecular Systems Biology

Evolution of immune genes is associated with the Black Death – Klunk et al. – Nature

Pregnancy and early life

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report – Wei et al. – Microbiome

Multi-site human microbiome

Age-Related Changes, Influencing Factors, and Crosstalk Between Vaginal and Gut Microbiota: A Cross-Sectional Comparative Study of Pre- and Postmenopausal Women – Yoshikata et al. – Journal of Women’s Health

Human oral microbiome

Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes – Chan et al. – Oral Oncology

Human gut microbiome

[REVIEW]Making gut microbiomes from scratch – Tiang & Bisanz – Cell Host &Microbe

Impairments of intestinal arginine and NO metabolisms trigger aging-associated intestinal barrier dysfunction and ‘inflammaging’ – Brandt et al. – Redox Biology

Dietary fiber ameliorates sleep disturbance connected to the gut–brain axis – Tang et al. – Food & Function

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases – Cheng et al. – BMC Microbiology

Relationships between dietary diversity and gut microbial diversity in the elderly – Amamoto et al. – Beneficial Microbes

Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project – Xu et al. – Beneficial Microbes

Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis – Liang et al. – Translational Neurodegeneration

Microbiome insights into pediatric familial adenomatous polyposis – Attard et al. – Orphanet Journal of Rare Diseases

[REVIEW]The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression – Wen et al. – Clinical and Translational Oncology

[REVIEW]Epigenetic regulation by metabolites from the gut microbiome – Marin-Tello et al. – Benefical Microbes

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

A tetrapeptide from maize combined with probiotics exerted strong anti-inflammatory effects and modulated gut microbiota in DSS-induced colitis mice – Li et al. – Food & Function

IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet – Perez-Matute et al. – Front. Endocrinol.

Animal microbiome (for animals in the wild)

Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species – McIlroy et al. – Microbiome

Plant, root, and soil microbiome

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea – Wicaksono et al. – mSystems

Bioinformatics

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments – Hempel et al. – NAR

Metagenome-assembled genome extraction and analysis from microbiomes using KBase – Chivian et al. – Nature Protocols

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies – Aytan-Aktug et al. – Microbiology Spectrum

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes – Gupta et al. – mSystems

Techniques

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution – Clokie et al. – Microbiology Spectrum

November 14, 2022

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Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications