Category Archives: General Microbiome

June 29, 2022

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General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

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

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

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

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv

June 25, 2022

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Highlights!

Microbiome-associated human genetic variants impact phenome-wide disease risk – Robert H George Markowitz – PNAS → In this paper, the use of an integrative framework of case-control studies and extensive health records, authors could find associations between microbiome-associated variants (MAVs) and different phenotypes associated with human diseases.

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Julia Münzker – Microbiome → This study presents evidence for the role of the gut microbiome in the weight loss and metabolic success of gastric bypass surgery. The increment of taurine-conjugated bile acid species can activate systemic TGR5 signaling to stimulate adaptive thermogenesis, with consequences on the host metabolism.

Human and General Microbiome

Human gut microbiota composition and its predicted functional properties in people with western and healthy dietary patterns – Anna M Malinowska – European Journal of Nutrition

Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut – Kyung Hyun Kim – mSystems

Characteristics and interplay of esophageal microbiota in esophageal squamous cell carcinoma – Zheng Lin – BMC Cancer

Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV – María José Gosalbes – Gut Microbes

Disentangling the relationship of gut microbiota, functional gastrointestinal disorders and autism: a case-control study on prepubertal Chinese boys – Oscar W H Wong – Scientific Reports

Beneficial Microbes and Compounds

Dietary supplementation with biogenic selenium nanoparticles alleviate oxidative stress-induced intestinal barrier dysfunction – Lei Qiao – NPJ Science of Food

Non-Model Animal Microbiome

Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem – Laure Bellec – FEMS Microbiology Ecology

Social microbiota and social gland gene expression of worker honey bees by age and climate – Kirk E Anderson – Scientific Reports

Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research – T G Sumithra – Applied Microbiology and Biotechnology

Concept: Inter-individual variation in parasite manipulation of host phenotype: a role for parasite microbiomes? – Robert Poulin – The Journal of Animal Ecology

Environmental Microbiome

Review: A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses – Jean Legeay – Microbial Ecology

The influence of bioclimate on soil microbial communities of cork oak – Daniela Costa – BMC Microbiology

Techniques

Liposome Delivery of Nucleic Acids in Bacteria: Toward In Vivo Labeling of Human Microbiota – Luís Moreira – ACS Infectious Diseases

Other

Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics – Mayank Baranwal – eLife

June 24, 2022

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Today we have a report in Science on bacterium which is 1cm long, a great review of the gut virome in human health, and a meta-analysis of mycobiota signatures in colorectcal cancer among some other great papers.

General microbiology

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles – Volland et al. – Science

Virome

Filamentous bacteriophage delays healing of Pseudomonas-infected wounds – Bach et al. – Cell Reports Medicine

[REVIEW] The gut virome: A new microbiome component in health and disease – Cao et al. – eBioMedicine

Gut Microbiome

Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function – Mayneris-Perxachs et al. – ISME

Altered mycobiota signatures and enriched pathogenic Aspergillus rambellii are associated with colorectal cancer based on multi-cohort fecal metagenomic analyses – Lin et al. – Gastroenterology

[REVIEW] Small molecules in the big picture of gut microbiome-host cross-talk – Ma et al. – eBioMedicine

Maternal gut microbiome–induced IgG regulates neonatal gut microbiome and immunity – Sanidad et al. – Science Immunology

Non-Microbiome picks

Time for better time-restricted eating trials to lessen the burden of metabolic diseases – Taub and Panda – Cell Reports Medicine

What SARS-CoV-2 does to our brains – Aschman et al. – Immunity

June 22, 2022

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General microbiome

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection – Long et al. – Communications Biology

Pregnancy and early life

[PREPRINT]Strong pathogen competition in neonatal gut colonisation – Mäklin et al. – bioRxiv

Human skin microbiome

Dysbiosis of Skin Microbiota with Increased Fungal Diversity is Associated with Severity of Disease in Atopic Dermatitis – Schmid et al. – JEADV

Human gut microbiome

Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China – Sun et al. – mSystems

A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer – Yuan et al. – Investigational New Drugs

[REVIEW]Vegetarianism, Microbiota and Cardiovascular health: Looking back, and forward – Kumar et al. – European Journal of Preventive Cardiology

[REVIEW]Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis – So, Loughman & Staudacher – The American Journal of Clinical Nutrition

Profiling gut microbiota and bile acid metabolism in critically ill children – Kean et al. – Scientific Reports

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. – BMC Bioinformatics

The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease – Xu et al. – Gut Pathogenes

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

Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota – Hu et al. – PNAS

Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems – Weinert-Nelson, Biddle & Williams – Animal Microbiome

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

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States – LaMartina, Schmoldt & Newton – Microbiology Resource Announcements

Techniques

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level – Ge et al. – PNAS

June 20, 2022

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Highlights!

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A Shetty – The ISME Journal → This study shows the experimental setting of a minimal microbiome composed of 16 bacterial species, characterizing their metabolic relationships, dynamics, and stability.  

Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain – Xingzhi Guo – Frontiers in Microbiology → Members of Blautia, a relatively common genus in the human gut, was “consistently depleted across feces, blood, and brain samples of PD patients”. This study suggests a link between Blautia and PD.

Human and General Microbiome

A Microbiota-Dependent Response to Anticancer Treatment in an In Vitro Human Microbiota Model: A Pilot Study With Hydroxycarbamide and Daunorubicin – Claire Amaris Hobson – Frontiers in Cellular and Infection Microbiology

Examination of host genetic effects on nasal microbiome composition – Haritz Irizar – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Kimchi improves irritable bowel syndrome: results of a randomized, double-blind placebo-controlled study – Hee-Young Kim – Food & Nutrition Research

Non-Model Animal Microbiome

Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized – Baptiste Sadoughi – Microbiome

Model Animal Microbiome

Sodium alginate and galactooligosaccharides ameliorate metabolic disorders and alter the composition of the gut microbiota in mice with high-fat diet-induced obesity – Yao Li – International Journal of Biological Macromolecules

Plant Microbiome

From the bacterial citrus microbiome to the selection of potentially host-beneficial microbes – Ramón Penyalver – New Biotechnology

Review: Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes – Sang-Woo Han – Current Opinion in Microbiology

Environmental Microbiome

Microbiome assembly in thawing permafrost and its feedbacks to climate – Jessica G Ernakovich – Global Change Biology

Other

Rapid sourdough yeast identification using panfungal PCR combined with high resolution melting analysis – Olga Bazalová – Journal of Microbiological Methods

June 8, 2022

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Happy Friday! Today’s digest includes articles about Gardnerella vaginalis clades in pregnancy, how a Japanese herbal medicine may alleviate a leaky gut, and a feasibility study of the impact of oral activated charcoal on healthy volunteers.

General microbiome

Clinical Burkholderia pseudomallei isolates from north Queensland carry diverse bimABm genes that are associated with central nervous system disease and are phylogenomically distinct from other Australian strains – Burnard et al. – PLOS Neglected Tropical Diseases

Preprint: The energy requirements of ion homeostasis determine the lifespan of starving bacteria – Schink et al. – bioRxiv

Preprint: A novel bacterial speciation process observed in a symbiotic marine population – Wang et al. – bioRxiv

Human vaginal microbiome

Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome – Severgnini et al. – PLOS One

Human gut microbiome

Saireito, a Japanese herbal medicine, alleviates leaky gut associated with antibiotic-induced dysbiosis in mice – Ozaka et al. – PLOS One

A dose-finding safety and feasibility study of oral activated charcoal and its effects on the gut microbiota in healthy volunteers not receiving antibiotics – Rashidi et al. – PLOS One

Water and extremophile microbiome

The microbial community and functional potential in the Midland Basin reveal a community dominated by both thiosulfate and sulfate-reducing microorganisms – Tinker et al. – Microbiology Spectrum

Techniques

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations – Ganz et al.- PLOS One

June 15, 2022

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General microbiome

[PREPRINT]Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica – Escudero-Leyva et al. – bioRxiv

Pregnancy and early life

Babies, Bugs, and Barriers: Dietary Modulation of Intestinal Barrier Function in Early Life – Wells et al. – Annual Review of Nutrition

Multi-site human microbiome

A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao – Han et al. – Clinical and Translational Medicine

Human oral microbiome

The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine – Herremans et al. – Microbiome

Human skin microbiome

Altered skin fungal and bacterial community compositions in tinea capitis – Rong et al. – Mycoses

Effects of short chain fructo-oligosaccharides on selected skin bacteria – Le Bourgot et al. – Scientific Reports

Human vaginal microbiome

Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome – Ruotsalainen et al. – Medical Microbiology and Immunology

Human gut microbiome

Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients – Hoang et al. – BMC Cancer

Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study – Miao et al. – BMC Medicine

[REVIEW]The role of virome in the gastrointestinal tract and beyond – Tiamani et al. – FEMS Microbiology Reviews

[REVIEW]Time-limited diets and the gut microbiota in cardiometabolic disease – Ratiner et al. – Journal of Diabetes

Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial – Huang et al. – Journal of Autoimmunity

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

Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer – Fu et al. – Cell

Pharmacokinetic and gut microbiota analyses revealed the effect of Lactobacillus acidophilus on the metabolism of Olsalazine in ulcerative colitis rats – Li et al.

Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis – Forster et al. – Nature Microbiology

Plant, root, and soil microbiome

The plant host environment influences competitive interactions between bacterial pathogens – Ehau-Taumaunu & Hockett – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data – Darcy et al. – bioRxiv

June 11, 2022

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Have a nice weekend! In this digest: An interesting study about the effect of various dietary fibers (e.g., arabinoxylan, inulin) on the human microbiome (Lancaster, Cell Host & Microbe). Additionally, this digest includes more papers about maternal IgG interplay with neonatal microbiome. 

Human and General Microbiome

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans – Samuel M. Lancaster – Cell Host & Microbe

–> A preview for the paper: Stitching together a healthy gut microbiome with fiber – Thomas M Schmidt – Cell Host & Microbe

Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity – Katherine Z Sanidad – Science Immunology

Altered Metabolomics in Bipolar Depression With Gastrointestinal Symptoms – Xiang-Jie Guo – Frontiers in Psychiatry

Meta-analysis of mucosal microbiota reveals universal microbial signatures and dysbiosis in gastric carcinogenesis – Changan Liu – Oncogene

Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D Gerson – Journal of Reproductive Immunology

Beneficial Microbes and Compounds

Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity – Raquel Alonso-Roman – Nature Communications

Honeys with anti-inflammatory capacity can alter the elderly gut microbiota in an ex vivo gut model – Daoyan Wu – Food Chemistry

Model Animal Microbiome

Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice – Julia L Drewes – Cancer Discovery

Non-Model Animal Microbiome

Variation in gut microbiome structure across the annual hibernation cycle in a wild primate – Lydia K Greene – FEMS Microbiology Ecology

A high-throughput DNA sequencing study of fecal bacteria of seven Mexican horse breeds – Fernando Hernández-Quiroz – Archives of Microbiology

Species- and site-specific circulating bacterial DNA in Subantarctic sentinel mussels Aulacomya atra and Mytilus platensis – Sophia Ferchiou – Scientific Reports

Plant Microbiome

Review: The unsung roles of microbial secondary metabolite effectors in the plant disease cacophony – Lorena I Rangel – Current Opinion in Plant Biology

Plant-microbe interactions in the rhizosphere via a circular metabolic economy – Elisa Korenblum – The Plant Cell

Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest – Mengjiao Li – Environmental Microbiome

Nitrogen availability determines plant growth promotion and the induction of root branching by the probiotic fungus Trichoderma atroviride in Arabidopsis seedlings – José López-Bucio – Archives of Microbiology

Environmental Microbiome

Review: Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies – Shengnan Li – The Science of the Total Environment

More Microbes

Perspective: Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation – Mariana O Barcoto – Frontiers in Microbiology

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials – Jiarui Sun – Microbial Genomics

Bioinformatics and Experimental Microbiome Analysis

DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization – Anna M Forsman – Integrative and Comparative Biology

Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies – Jacqueline Rehner – Genomics, Proteomics & Bioinformatics

June 10, 2022

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Several great microbiome papers out today including a review on rethinking healthy eating in Cell Host & Microbe, a large population study on the development of the infant gut microbiome (n=1900) in Science, and two studies showcasing metabolomics predictive value for recurrent CDI and NAFLD.  

Gut Microbiome

[REVIEW] Rethinking healthy eating in light of the gut microbiome – Armet et al. Cell Host & Microbe.

Gut metabolites predict Clostridioides difficile recurrence – Dawkins et al. Microbiome

Robust variation in infant gut microbiome assembly across a spectrum of lifestyles – Olm et al. Science

Risk assessment with gut microbiome and metabolite markers in NAFLD development. Leung et al. Science Translational Medicine.

Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer – Bi et al. Nature Communications

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. Cell Host & Microbe

Animal experiments

Nisin probiotic prevents inflammatory bone loss while promoting reparative proliferation and a healthy microbiome – Gao et al. npj Biofilms & Microbiomes

Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs – Hui et al. npj Biofilms & Microbiomes

Virome

A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome – Li et al. iScience

Bioinformatics

Phylogeny-guided microbiome OTU-specific association test (POST) – Huang et al. Microbiome

June 08, 2022

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General microbiome

Tet2 deficiency drives liver microbiome dysbiosis triggering Tc1 cell autoimmune hepatitis – Pandey et al. – Cell Host & Microbe

Human gut microbiome

[PREPRINT]Mucosal host–microbe interactions associate with clinical phenotypes in inflammatory bowel disease – Hu et al. – bioRxiv

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

Gut microbiome mediates the protective effects of exercise after myocardial infarction – Zhou et al. – Microbiome

Animal microbiome (for animals in the wild)

Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny – Bechade et al. – FEMS Microbiology Ecology

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

[PREPRINT]Summer dynamics of microbial diversity on a mountain glacier – Hotaling, Price & Hamilton – bioRxiv

Bioinformatics

MIAOME: Human microbiome affect the host epigenome – Wang et al. – Computational and Structural Biotechnology Journal

Beta-diversity distance matrices for microbiome sample size and power calculations — How to obtain good estimates – By IMPACTT investigators – Computational and Structural Biotechnology Journal

phyloMDA: an R package for phylogeny-aware microbiome data analysis – Liu et al. – BMC Bioinformatics

MeShClust v3.0: high-quality clustering of DNA sequences using the mean shift algorithm and alignment-free identity scores – Girgis – BMC Genomics