Monthly Archives: April 2023

May 1, 2023

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Human and General Microbiome

Th17 cells sense microbiome to promote depressive-like behaviors – Eva M Medina-Rodriguez – Microbiome

Obese-associated gut microbes and derived phenolic metabolite as mediators of excessive motivation for food reward – Alice de Wouters d’Oplinter – Microbiome

Alteration of taste perception, food neophobia and oral microbiota composition in children with food allergy – Enza D’Auria – Scientific Reports

Translocating Lactobacillus torments tumors via tryptophan catabolism – Márcia S Pereira – Cell

Global trends in research related to the links between microbiota and antibiotics: a visualization study – Sa’ed H Zyoud – Scientific Reports

Modulation of antibiotic effects on microbial communities by resource competition – Daniel P Newton – Nature Communications

Review: Less is more: Antibiotics at the beginning of life – Martin Stocker – Nature Communications

Review: The interaction between autophagy, Helicobacter pylori, and gut microbiota in gastric carcinogenesis – Ali Nabavi-Rad – Trends in Microbiology

Review: The orchestra of human bacteriome by hormones – Arif Luqman – Microbial Pathogenesis

Review: Targeting the human gut microbiome with small-molecule inhibitors – Amelia Y M Woo – Nature Reviews. Chemistry

Review: A precision environmental health approach to prevention of human disease – Andrea Baccarelli – Nature Communications

Review: Emerging role of bacterial outer membrane vesicle in gastrointestinal tract – Cheng-Mei Tian – Gut Pathogens

Review: The Gut Microbiota – Brain Axis: Potential Mechanism of Drug Addiction – Xiao Luo – Current Topics in Medicinal Chemistry

Beneficial Microbes and Compounds

The effects of live and pasteurized Akkermansia muciniphila on DSS-induced ulcerative colitis, gut microbiota, and metabolomics in mice – Liangyu Xue – Food & Function

Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium – Renan Oliveira Corrêa – Microbiome

Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice – Haibo Tang – Life Sciences

Animal Microbiome

Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition – Søren B Hansen – Genomics

Review: Environmental Effects on Bee Microbiota – Phuong N Nguyen – Microbial Ecology

Review: Illuminating the Oral Microbiome and its Host Interactions: Animal models of disease – George Hajishengallis – FEMS Microbiology Reviews

Plant Microbiome

Review: How does plant sex alter microbiota assembly in dioecious plants? – Qingxue Guo – Trends in Microbiology

Environmental Microbiome

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems – Ignacio Ramos-Tapia – Microbiology Spectrum

Built Environment

Dynamics of microbial community composition during degradation of silks in burial environment – Bowen Wang – The Science of the Total Environment

Bioinformatics

DeepMicroGen: a generative adversarial network based method for longitudinal microbiome data imputation – Joung Min Choi – Bioinformatics

April 26, 2023

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General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere

Bioinformatics

[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv

April 24, 2023

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Human and General Microbiome

Review: Effects of ultra-processed foods on the microbiota-gut-brain axis: The bread-and-butter issue – Zheyi Song – Food Research International 

Review: The emerging role of the small intestinal microbiota in human health and disease – Renate Ruigrok – Gut Microbes

Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma – Takuma Sasaki – Esophagus

Multi-omics signatures in new-onset diabetes predict metabolic response to dietary inulin: findings from an observational study followed by an interventional trial – N Ďásková – Nutrition & Diabetes

Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes – Kang Xiao – Journal of Microbiology

Sentinel or accomplice – gut microbiota and microglia cross-talk in disorders of gut-brain interaction – Haonan Zheng – Protein & Cell

Beneficial Microbes and Compounds

Effects of dietary fibers or probiotics on functional constipation symptoms and roles of gut microbiota: a double-blinded randomized placebo trial – Hao Lai – Gut Microbes

Review: Use of probiotic lactobacilli in the treatment of vaginal infections: In vitro and in vivo investigations – Peng Liu – Frontiers in Cellular and Infection Microbiology

Animal Microbiome

The hindgut microbiome contributes to host oxidative stress in postpartum dairy cows by affecting glutathione synthesis process – Fengfei Gu – Microbiome

Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons – Qi Li – NPJ Biofilms and Microbiomes

Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community – Manar El Samak – Marine Genomics

Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain – Dianshu Zhao – Microbiology Spectrum

Antibiotic Conditioning Shapes Pseudosterile Mouse Models by Deleting Colonic Microbes Rather than Small Intestinal Microbes – Qingxue Chen – Microbiology Spectrum

Plant Microbiome

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage – Zhiqiang Pang – Microbiome

Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions – Simrandeep Singh – Environmental Microbiome

Effects of vermicompost leachate on nitrogen, phosphorus, and microbiome in a food waste bioponic system – Sumeth Wongkiew – Journal of Environmental Management

The effect of wheat genotype on the microbiome is more evident in roots and varies through time – Liliana Quiza – ISME Communications

Environmental Microbiome

Disentangling temporal associations in marine microbial networks – Ina Maria Deutschmann – Microbiome

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota – Jie Kong – Microbiology Spectrum

Built Environment

BioMateriOME: to understand microbe-material interactions within sustainable, living architectures – Beatriz Delgado Corrales – Advances in Applied Microbiology

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Deciphering associations between gut microbiota and clinical factors using microbial modules – Ran Wang – Bioinformatics

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis – Jackie Zorz – ISME Communications

Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways – Krishna Kumar – Methods in Molecular Biology

Other

Interactions between the lipidome and genetic and environmental factors in autism – Chloe X Yap – Nature Medicine

April 19, 2023

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Pregnancy and early life

[REVIEW]The maternal gut microbiome during pregnancy and its role in maternal and infant health – Sinha et al. – Current Opinion in Microbiology

Human oral microbiome

Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses – Beall et al. – mBio

[REVIEW]Oral microbial changes and oral disease management before and after the treatment of hematological malignancies: a narrative review – Lin et al. – Clinical Oral Investigations

Human vaginal microbiome

[REVIEW]Gardnerella Revisited: Species Heterogeneity, Virulence Factors, Mucosal Immune Responses, and Contributions to Bacterial Vaginosis – Shvartsman et al. – Infection and Immunity

Human gut microbiome/virome

[REVIEW]Intrahost evolution of the gut microbiota – Barreta & Gordo – Nature Reviews Microbiology

The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice – Fan et al. – Nature Microbiology

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori – Wang et al. – Nature Communications

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Spatz et al. – Microbiome

Metabolic independence drives gut microbial colonization and resilience in health and disease – Watson et al. – Microbiome

Development of the gut microbiota in the first 14 years of life and its relations to internalizing and externalizing difficulties and social anxiety during puberty – Ou et al. – European Child & Adolescent Psychiatry

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals – Segota et al. – NAR

Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease – Poudel et al. – PLOS One

Seasonal variations in gut microbiota and disease course in patients with inflammatory bowel disease – Tani et al. – PLOS One

The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study – Oh et al. – Journal of Translational Medicine volume

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

Effects of Extended Cage Component Sanitation Interval on the Microenvironment, Health, and Gastrointestinal Microbiome of Rats (Rattus norvegicus) – Taylor et al. – Journal of the American Association for Laboratory Animal Science

Music-based interventions in the feeding environment on the gut microbiota of mice – Niu et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality – Maidment et al. – Microbiome

[PREPRINT]Microbiome variability of mosquito lines is consistent over time and across environments – Accoti et al. – bioRxiv

Differences in the luminal and mucosal gut microbiomes and metabolomes of oriental rat snake (Ptyas mucosus) – Wei et al. – Applied Microbiology and Biotechnology

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Bazant et al. – Microbiome

Techniques

Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle – Liu et al. – Microbiome

April 17, 2023

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Human and General Microbiome

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Felix M Key – Cell Host & Microbe

Staphylococcal diversity in atopic dermatitis from an individual to a global scale – Sara Saheb Kashaf – Cell Host & Microbe

A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis – Hongdi Ma – Cell Research

Coliphages of the human urinary microbiota – Elias Crum – PloS ONE

Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study – Aina Qu – BMC Pediatrics

Aerobic exercise training-induced alteration of gut microbiota composition affects endurance capacity – Masataka Uchida – The Journal of Physiology

Fusobacterium nucleatum aggravates rheumatoid arthritis through FadA-containing outer membrane vesicles – Mukeng Hong – Cell Host & Microbe

Review: Dental caries and their microbiomes in children: what do we do now? – Apoena Aguiar Ribeiro – Journal of Oral Microbiology

Review: Role of the Microbiome in Gut-Heart-Kidney Cross Talk – Griet Glorieux – Circulation Research

Review: Influence of Microbiota on Vaccine Effectiveness: Is the Microbiota the Key to Vaccine-induced Responses? – So-Hee Hong – Journal of Microbiology 

Review: Deciphering the quorum-sensing lexicon of the gut microbiota – Rita A Oliveira – Cell Host & Microbe

Review: The intratumoral microbiota: friend or foe? – Valentina Ferrari – Trends in Cancer

Review: Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions – Rita A Oliveira – Cell Host & Microbe

Review: One population, multiple lifestyles: Commensalism and pathogenesis in the human mycobiome – Diana M Proctor – Cell Host & Microbe

Review: Cross-feeding in the gut microbiome: Ecology and mechanisms – Elizabeth J Culp – Cell Host & Microbe

Minireview: Networking between helminths, microbes, and mammals – P’ng Loke – Cell Host & Microbe

Commentary: The intratumoral microbiota: From microniches to single cells – Susan Bullman – Cell

Perspective: Designer bugs as cancer drugs? – Sairaj M Sajjath – Science

Animal Microbiome

Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota – Sarah J Morgan – Microbiology Spectrum

Integration host factor regulates colonization factors in the bee gut symbiont Frischella perrara – Konstantin Schmidt – eLife

Research Highlight: Urban bees reveal a city’s microbiome – Ashley York – Nature Reviews. Microbiology

Environmental Microbiome

Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat – Jian Li – Environment International

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring – Shekhar Nagar – Applied Microbiology and Biotechnology

April 14, 2023

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Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Madeleine Spatz – Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

Methodology

Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

April 10, 2023

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Human and General Microbiome

Review: Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans – Julia Montenegro – Advances in Nutrition

Review: Ruminococcus gnavus: friend or foe for human health – Emmanuelle H Crost – FEMS Microbiology Reviews

Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing – Bin Ai – Scientific Reports

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism – Xiangwei Hu – NPJ Biofilms and Microbiomes

The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery – Panayiotis Louca – Cell Reports. Medicine

Forging the microbiome to help us live long and prosper – Rachel R Rock – PLoS Biology

Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression – Yan Li – Gut Microbes

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites – Guangqi Gao – EBioMedicine

Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems – Samuel Zimmerman – mSystems

New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota – Akil Akhtar – Communications Biology

Animal Microbiome

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community – Jacob Agerbo Rasmussen – Microbiological Research

Plant Microbiome

Cofunctioning of bacterial exometabolites drives root microbiota establishment – Felix Getzke – PNAS

Environmental Microbiome

Review: Unveiling the role of emerging metagenomics for the examination of hypersaline environments – Kiran Dindhoria – Biotechnology & Genetic Engineering Reviews

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data – Shulei Wang – Bioinformatics

The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection – Ruijie Xu – PloS ONE

An in vitro platform for study of the human gut microbiome under an oxygen gradient – James Comolli – Biomedical Microdevices

Machine learning model to predict obesity using gut metabolite and brain microstructure data – Vadim Osadchiy – Scientific Reports

April 3, 2023

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Human and General Microbiome

Review: Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome – Stephen R Stockdale – Current Opinion in Microbiology

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

Genetic correlations between Alzheimer’s disease and gut microbiome genera – Davis Cammann – Scientific Reports

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma – Christopher Delaney – APMIS

Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity – Xiaomin Liu – Scientific Reports

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections – Anna Both – Microbiology Spectrum

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition – Kayla A Carter – mSystems

Review: Interspecies Interactions within the Host: the Social Network of Group B Streptococcus – Marlyd E Mejia – Infection and Immunity

Beneficial Microbes and Compounds

Review: Kefir as a therapeutic agent in clinical research: a scoping review – Milena Klippel Bessa – Nutrition Research Reviews

Interaction between β-glucans and gut microbiota: a comprehensive review – Reza Karimi – Critical Reviews in Food Science and Nutrition

Combination of vitamin D and probiotics inhibits chemically induced colorectal carcinogenesis in Wistar rats – Carolina S de Oliveira – Life Sciences

Animal Microbiome

Review: Recent advancements in coral health, microbiome interactions and climate change – Nizam Ashraf – The Science of the Total Environment

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome – Line Jensen Ostenfeld – PloS One

Microbial Species-Area Relationships on the Skins of Amphibian Hosts – Fan Yang – Microbiology Spectrum

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species – Heather R Skeen – Molecular Ecology

Food Microbiome

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus – Kohei Ito – Journal of Bioscience and Bioengineering

Built Environment

Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes – Elizabeth Hénaff – Environmental Microbiome

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Contamination detection and microbiome exploration with GRIMER – Vitor C Piro – GigaScience

Annotation-free discovery of functional groups in microbial communities – Xiaoyu Shan – Nature Ecology & Evolution

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis – Jinlong Ru – Gut Microbes

Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition – Line Roager – Microbiology Spectrum

Preprint: Identifying keystone species in microbial communities using deep learning – Xu-Wen Wang – bioRxiv