Category Archives: Plant Root Soil microbiome

July 2, 2022

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Have a nice weekend!

Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journal → this paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature Microbiology →By using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – Microbiome → This article demonstrates the existence of “a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”. 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

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 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 18, 2022

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Have a nice weekend! Today, in this Digest: The effect of the gut dysbiosis on prostate cancer, microbial inheritance, bee microbiome, rhizosphere microbiota, a comparison of DNA isolation techniques for deep amplicon sequencing, and more…

Human and General Microbiome

Gut dysbiosis promotes prostate cancer progression and docetaxel resistance via activating NF-κB-IL6-STAT3 axis – Weibo Zhong – Microbiome

On the effect of inheritance of microbes in commensal microbiomes – Román Zapién-Campos – BMC Ecology and Evolution

Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth – Sunwha Park – Scientific Reports

Deep Grouping Analysis of the Altered Cervical Canal Microbiota in Intrauterine Adhesion Patients – Xiangdong Hua – Reproductive Sciences

Intestinal microbiota transplantation: do not forget the metabolites – Benjamin H Mullish – The Lancet. Gastroenterology & Hepatology

Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up – Guang-Ying Cui – Military Medical Research

Congenitally underdeveloped intestine drives autism-related gut microbiota and behavior – Jie Li – Brain, Behavior, and Immunity

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus HA-114 improves eating behaviors and mood-related factors in adults with overweight during weight loss: a randomized controlled trial – Béatrice S-Y Choi – Nutritional Neuroscience

Model Animal Microbiome

New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy – Hye Rim Byeon – Journal of Medicinal food

Non-Model Animal Microbiome

Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes – Wyatt A Shell – Communications Biology

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review – Sonam Dixit – Animal Biotechnology

Plant Microbiome

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees – Maximilian Fernando Becker – Environmental Microbiome

Identifying plant genes shaping microbiota composition in the barley rhizosphere – Carmen Escudero-Martinez – Nature Communications

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Ben O Oyserman – Nature Communications

Environmental Microbiome

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables – Jessica L Gronniger – Environmental Microbiology

Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments – Cheng Chen – Water Research

500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China – Lei Zhou – Scientific Data

Food Microbiome

Microbiome and -omics application in food industry – Ilario Ferrocino – International Journal of Food Microbiology

Bioinformatic and Experimental Microbiome Analysis

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities – Justin P Shaffer – BioTechniques

Review: Machine Learning Advances in Microbiology: A Review of Methods and Applications – Yiru Jiang – Frontiers in Microbiology

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 6, 2022

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Have a nice Monday! Today, in this Digest we have some pendant papers from last week.

Human and General Microbiome

The role of immune cells in the liver tumor microenvironment: an involvement of gut microbiota-derived factors – Tomonori Kamiya – International Immunology

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention – Stephanie B Orchanian – Advanced Biology

Short chain fatty acids-producing and mucin-degrading intestinal bacteria predict the progression of early Parkinson’s disease – Hiroshi Nishiwaki – NPJ Parkinson’s Disease

Intestinal inflammation alters the antigen-specific immune response to a skin commensal – Geil R Merana – Cell Reports

Characterization of resistome in Lactobacillus genomic sequences from the human gut – Jale Moradi – Journal of Global Antimicrobial Resistance

Clustering Analysis of the Multi-Microbial Consortium by Lactobacillus Species Against Vaginal Dysbiosis Among Ecuadorian Women – David Pacha-Herrera – Frontiers in Cellular and Infection Microbiology

Nutritional Intake and Gut Microbiome Composition Predict Parkinson’s Disease – Michal Lubomski – Frontiers in Aging Neuroscience

Beneficial Microbes and Compounds

Review: Bacteriocin-Producing Probiotic Lactic Acid Bacteria in Controlling Dysbiosis of the Gut Microbiota –  Anjana – Frontiers in Cellular and Infection Microbiology

Review: Relationship between gut microbiota and colorectal cancer: Probiotics as a potential strategy for prevention – Seung Yun Lee – Food Research International 

Review: Health benefits of microalgae and their microbiomes – Ines Krohn – Microbial Biotechnology

Lactobacillus reuteri J1 prevents obesity by altering the gut microbiota and regulating bile acid metabolism in obese mice – Chenxi Zhang – Food & Function

Non-Model Animal Microbiome 

16S rRNA Gene Sequencing Reveals Specific Gut Microbes Common to Medicinal Insects – Jin Geng – Frontiers in Microbiology

Antioxidant potential of Pediococcus pentosaceus strains from the sow milk bacterial collection in weaned piglets – Leli Wang – Microbiome

Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa – Meiqi Ma – Microbial Ecology

Gut microbiota-derived ursodeoxycholic acid from neonatal dairy calves improves intestinal homeostasis and colitis to attenuate extended-spectrum β-lactamase-producing enteroaggregative Escherichia coli infection – Zhiyuan He – Microbiome

Plant Microbiome

Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes – Pin Su – Scientific Data

Environmental Microbiome

Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies – Qiang Pu – Journal of Hazardous Materials

The sanitary indoor environment-a potential source for intact human-associated anaerobes – Manuela-Raluca Pausan – NPJ Biofilms and Microbiomes

More Microbes

Review: Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications – Pranami Goswami – NPJ Biofilms and Microbiomes

Bioinformatic and Experimental Microbiome Analysis

Review: Emerging technologies in the study of the virome – Sophie E Smith – Current Opinion in Virology

EasyMap – An Interactive Web Tool for Evaluating and Comparing Associations of Clinical Variables and Microbiome Composition – Ehud Dahan – Frontiers in Cellular and Infection Microbiology

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples – Anaïs Biclot – Microbiome

BiGAMi: Bi-Objective Genetic Algorithm Fitness Function for Feature Selection on Microbiome Datasets – Mike Leske – Methods and Protocols

June 4, 2022

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Highlights!

Review: Translating Microbiome Research From and To the Clinic – Zhenrun J Zhang – Annual Review of Microbiology → An exploration of different experimental studies associating the gut microbiota with certain human diseases, highlighting translational advances 

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome – Wenshan Zheng – Science → A powerful technique to obtain single amplified genomes (SAG) from human microbiome samples 

Human and General Microbiome

Review: Gut microbiota and atopic dermatitis in children: a scoping review – Yue Liu – BMC Pediatrics

Review: Gut microbiome and autoimmune disorders – Walaa Abdelaty Shaheen – Clinical and Experimental Immunology

Altered Vaginal Microbiota Composition Correlates With Human Papillomavirus and Mucosal Immune Responses in Women With Symptomatic Cervical Ectopy – Mariana López-Filloy – Frontiers in Cellular and Infection Microbiology

Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients – Ornella la Fortune Tchoupou Saha – Frontiers in Microbiology

Machine learning aided construction of the quorum sensing communication network for human gut microbiota – Shengbo Wu – Nature Communications

Metagenomic assembled plasmids of the human microbiome vary across disease cohorts – S R Stockdale – Scientific Reports

Gut microbial metabolites in Parkinson’s disease: Association with lifestyle, disease characteristics, and treatment status – Robin M Voigt – Neurobiology of Disease

Mechanistic insights into accelerated α-synuclein aggregation mediated by human microbiome-associated functional amyloids – Sujeet S Bhoite – The Journal of Biological Chemistry

Gut bacterial isoamylamine promotes age-related cognitive dysfunction by promoting microglial cell death – Yun Teng – Cell Host & Microbe

Beneficial Microbes and Compounds

Review: A Review: Cereals on Modulating the Microbiota/Metabolome for Metabolic Health – Jayani Kulathunga – Current Nutrition Reports

Anti-Diabetic Potential of Chlorella pyrenoidosa-Based Mixture and its Regulation of Gut Microbiota – Wenyu Xiong – Plant Foods for Human Nutrition

Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment – Chiara Argentini – Applied and Environmental Microbiology

Animal Microbiome

Synchrony and idiosyncrasy in the gut microbiome of wild baboons – Johannes R Björk – Nature Ecology & Evolution

Environmental Microbiome

A synergistic bacterial pool decomposes tebuthiuron in soil – Edivaldo Wilson de Lima – Scientific Reports

The microbiome of cryospheric ecosystems – Massimo Bourquin – Nature Communications

Extremophiles

Bacterial diversity and community structure in the rhizosphere of the halophyte Halocnemum strobilaceum in an Algerian arid saline soil – Sabrina Behairi – Extremophiles

Bioinformatics and Microbiome Analysis

Multiscale analysis of count data through topic alignment – Julia Fukuyama – Biostatistics

SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling – Yongqiang Luo – Small Methods

June 01, 2022

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General microbiome

[REVIEW]Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms – Cani et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Role of Microbiota in Viral Infections and Pathological Progression – Mizutani et al. – Viruses

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Newbury et al. – PNAS

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales – Martinez-Gutierrez & Aylward – PLOS Genetics

Interspecies commensal interactions have nonlinear impacts on host immunity – Rice et al. – Cell Host & Microbe

Human skin myco-/microbiome

Distinct skin microbiome community structures in congenital ichthyosis – Tham et al. – British Journal of Dermatology

Biodiversity of mycobial communities in health and onychomycosis – Olbrich et al. – Scientific Reports

Human gut microbiome

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study – Jiang et al. – Genome Medicine

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

Discovery of bioactive microbial gene products in inflammatory bowel disease – Zhang et al. – Nature

Animal microbiome (for animals in the wild)

The functional evolution of termite gut microbiota – Arora et al. – Microbiome

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods – Oba et al. – Journal of Animal Science

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth – Zhang et al. – Front. Microbiol.

Plant, root, and soil microbiome

Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships – Schäfer et al. – Nature Microbiology

Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis – Mehlferber et al. – Current Biology