Tag Archives: microbiome

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 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

May 28, 2022

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Highlights!

Recently, Science released a special issue about microbiomes, with the following articles:

Human and General Microbiome  

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes – Adair L Borges – Nature Microbiology

Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study – Takashi Takeda – PloS ONE

Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life – Ping Li – Journal of Microbiology

Metabolomics analysis reveals molecular linkages for the impact of vitamin D on childhood allergic airway diseases – Yu-Ho Chang – Pediatric Allergy and Immunology

Lysophosphatidylserines derived from microbiota in Crohn’s disease elicit pathological Th1 response – Yuriko Otake-Kasamoto – Journal of Experimental Medicine 

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis – Rizwana Hasan – Archives of Microbiology

Lung Microbiota of Critically Ill COVID-19 Patients are Associated with Non-Resolving Acute Respiratory Distress Syndrome – Robert F J Kullberg – American Journal of Respiratory and Critical care Medicine

Altered Gut Microbiome in Patients With Dermatomyositis – Sangmee Sharon Bae – ACR Open Rheumatology

Review: Importance of crosstalk between the microbiota and the neuroimmune system for tissue homeostasis – Kunyu Li – Clinical & Translational Immunology

Review: Dietary influences on symptomatic and non-symptomatic toxicities during cancer treatment: A narrative review – Alan J Kim – Cancer Treatment Reviews

Review: How can patients with Clostridioides difficile infection on concomitant antibiotic treatment be best managed? – Fidelma Fitzpatrick – The Lancet. Infectious Diseases

Model Animal Microbiome

Protocol: Mouse Model to Study Salmonella-Induced Colitis – Katrin Ehrhardt – Methods in Molecular Biology

Amino acid-balanced diets improved DSS-induced colitis by alleviating inflammation and regulating gut microbiota – Sen Li – European Journal of Nutrition

Excess growth hormone alters the male mouse gut microbiome in an age-dependent manner – Elizabeth A Jensen – Endocrinology

Non-Model Animal Microbiome

Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site – Wojciech Wilczynski – Toxics

Bacterial Symbionts in Ceratitis capitata – Alessia Cappelli – Insects

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle – Ana Sofia Carranco – Molecular Ecology

Unveiling the egg microbiota of the loggerhead sea turtle Caretta caretta in nesting beaches of the Mediterranean Sea – Luca Vecchioni – PloS ONE

Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis – Nyok-Sean Lau – Microbial Ecology

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates – Guangping Huang – The Science of the Total Environment

Beneficial Microbes and Compounds

Review: Functional fermented probiotics, prebiotics and synbiotics from non-dairy products: A perspective from nutraceutical – Dharmendra Kumar – Molecular Nutrition & Food Research

Bifidobacterium longum CCFM752 prevented hypertension and aortic lesion, improved antioxidative ability, and regulated the gut microbiome in spontaneously hypertensive rats – Wenwei Lu – Food & Function

Intestinal Flora Mediates Antiobesity Effect of Rutin in High-Fat-Diet Mice – Xu Yan – Molecular Nutrition & Food Research

Multi-Probiotics ameliorate Major depressive disorder and accompanying gastrointestinal syndromes via serotonergic system regulation – Peijun Tian – Journal of Advanced Research

Butyrate, a postbiotic of intestinal bacteria, affects pancreatic cancer and gemcitabine response in in vitro and in vivo models – Concetta Panebianco – Biomedicine & Pharmacotherapy

Plant and Fungi Microbiome

Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease – Kuleshwar Prasad Sahu – Environmental Microbiome

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts – Sunde Xu – Nature Microbiology

Other studies

Indoor microbiome, microbial and plant metabolites, chemical compounds and asthma symptoms in junior high school students: a multicentre association study in Malaysia – Yu Sun – The European Respiratory Journal

Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes – Marcos Pérez-Losada – Frontiers in Microbiology

May 21, 2022

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Human and General Microbiome

Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors – Jesse R Willis – NPJ Biofilms and Microbiomes

Gut Microbiome Was Highly Related to the Regulation of Metabolism in Lung Adenocarcinoma Patients – Sheng Wang – Frontiers in Oncology

Host-Population Microbial Diversity Scaling of Chinese Gut Microbiomes in Gout Patients – Jieshang Zhou – Evolutionary Bioinformatics Online

Combined Microbiome and Metabolome Analysis Reveals a Novel Interplay Between Intestinal Flora and Serum Metabolites in Lung Cancer – Sai Chen – Frontiers in Cellular and Infection Microbiology

Decreased Diversity of Gut Microbiota Is Associated with Decreased Muscle Mass and Function in Older Adults Residing in a Nursing Home – Y Ishida – The Journal of Nutrition, Health & Aging

The role of the mucin-glycan foraging Ruminococcus gnavus in the communication between the gut and the brain – Erika Coletto – Gut Microbes

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients – Jinyuan Yan – Scientific Data

The gut microbiota: stable bioreactor of variable composition? – Gilles Mithieux – Trends in Endocrinology and Metabolism

Characterizing the mucin-degrading capacity of the human gut microbiota – Janiece S Glover – Scientific Reports

Mapping microbiome-redox spectrum and evaluating Microbial-Redox Index in chronic gastritis – Manas Kumar Panigrahi – Scientific Reports

Endometrial microbiome: sampling, assessment, and possible impact on embryo implantation – Marco Reschini – Scientific Reports

Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort – Kui Deng – BMC Medicine

The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Masamitsu Shimizu – Thoracic Cancer

Cervicovaginal loads of Gardnerella spp. are increased in immunocompetent women with persistent high-risk human papillomavirus infection – Rafael Belleti – Journal of Medical Microbiology

Review: Dysbiotic relationship between arthritis and the oral-gut microbiome. A critical review – Rubelisa Candido Gomes de Oliveira – Journal of Periodontal Research

Microbiome and COVID19

Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C) – Cansu Suskun – European Journal of Pediatrics

Super Dominant Pathobiontic Bacteria in the Nasopharyngeal Microbiota Cause Secondary Bacterial Infection in COVID-19 Patients – Tian Qin – Microbiology Spectrum

Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome – Priti Devi – Microbiology Spectrum

Beneficial Microbes and Compounds

In vitro anti-tuberculosis effect of probiotic Lacticaseibacillus rhamnosus PMC203 isolated from vaginal microbiota – Md Abdur Rahim – Scientific Reports

Commensal bacteria-derived extracellular vesicles suppress ulcerative colitis through regulating the macrophages polarization and remodeling the gut microbiota – Liping Liang – Microbial Cell Factories

More Microbes

Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids – F Repoila – Scientific Reports

The OmpA of commensal Escherichia coli of CRC patients affects apoptosis of the HCT116 colon cancer cell line – Mahsa Mirzarazi – BMC Microbiology

Non-Model Animal Microbiome

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey – Anastasios Galanis – Molecular Ecology Resources

Time for a change! A spotlight on the many neglected facets of sponge microbial biotechnology – Bruno Francesco Rodrigues de Oliveira – Current Pharmaceutical Biotechnology

Dietary wheat and reduced methane yield are linked to rumen microbiome changes in dairy cows – Keith W Savin – PloS ONE

Review: Role of Insect Gut Microbiota in Pesticide Degradation: A Review – Junaid Ali Siddiqui – Frontiers in Microbiology

Plant Microbiome

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines – Birgit Wassermann – Microbial Biotechnology

Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides – Chunbo Dong – Frontiers in Microbiology

Acquisition of a complex root microbiome reshapes the transcriptomes of rice plants – Christian Santos-Medellín – The New Phytologist

Water deficit affects inter-kingdom microbial connections in plant rhizosphere – Kathryn E Bazany – Environmental Microbiology

Review: Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere – Posy E Busby – Annual Review of Phytopathology

Bioinformatics and Microbiome Analysis

The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling – Natalia Szóstak – Scientific Reports

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype – Wontack Han – Journal of Computational Biology

May 14, 2022

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Human and General Microbiome

Gut Microbiome

Noninvasive assessment of gut function using transcriptional recording sentinel cells – Florian Schmidt – Science

Perspective about this paper: Recording bacterial responses to changes in the gut environment – Liron Zahavi – Science

Contribution of the Microbiome to Western Diet-Induced Gene Expression Changes in the Intestine and Vasculature – Alyssa N Cavalier – FASEB Journal

The Gut Microbiota Metabolite Succinate promotes Adipose Tissue Browning in Crohn’s Disease – D Monfort-Ferré – Journal of Crohn’s & Colitis

Changes in Gut Microbiome Composition with Healthy Aging in Humans: Links to Vascular Endothelial Function – Nathan Greenberg – FASEB Journal

The Gut Microbiota Modulates Gene Expression in the Kidney – Brittni Moore – FASEB Journal

Rapid evolution and strain turnover in the infant gut microbiome – Daisy W Chen – Genome Research

Review: The role of short-chain fatty acids in Clostridioides difficile infection: A review – Zi-Rou Ouyang – Anaerobe

Respiratory Microbiome

Lung microbiome composition and bronchial epithelial gene expression in patients with COPD versus healthy individuals: a bacterial 16S rRNA gene sequencing and host transcriptomic analysis – Mohammadali Yavari Ramsheh – The Lancet. Microbe

Therapeutic Targeting of the Respiratory Microbiome – Sanjay H Chotirmall – American Journal of Respiratory and Critical Care Medicine

Temporal Dynamics of the Nasopharyngeal Microbiome and its Relationship with Childhood Asthma Exacerbation – Jinpao Hou – Microbiology Spectrum

Oral Microbiome

Role of Oral Microbiota Biofilms in Recurrent Tonsillitis and Sleep-Disordered Breathing in Children – Thibault Allain – FASEB Journal

Oral Microbiota of Amazonian Kichwa Infants From Equador During the First Six Months of Life – Diana Maldonado Lino – FASEB Journal

Child saliva microbiota and caries: a randomized controlled maternal education trial in rural Uganda – Grace K M Muhoozi – Scientific Reports

Microbiome and Cancer

Review: Gut microbiota: Role and Association with Tumorigenesis in Different Malignancies – Altamas Ali – Molecular Biology Reports

Fusobacterium nucleatum as a Marker for Epithelial to Mesenchymal Transition in Colorectal Cancer – Angela Huang – FASEB Journal

L-norvaline affects the proliferation of breast cancer cells based on the microbiome and metabolome analysis – Qin Zhu – Journal of Applied Microbiology

Microbiome across Age

Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans – Liwei Chen – Gut Microbes

Association of antibiotics exposure within the first 2 years after birth with subsequent childhood type 1 diabetes – Dahye Lee – Endocrine

Review: The resistance within: Antibiotic disruption of the gut microbiome and resistome dynamics in infancy – Robert Thänert – Cell Host & Microbe

Review: The developing infant gut microbiome: A strain-level view – Hagay Enav – Cell Host & Microbe

Multi-site Microbiome

The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle – Maria Christine Krog – Human Reproduction

Multi-scale study of the oral and gut environments in children with high and low threshold peanut allergy – Lingdi Zhang – The Journal of Allergy and Clinical Immunology

Beneficial Microbes and Compounds

Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants – Jumana Samara – Cell host & Microbe

Review: Effective Regulation of Gut Microbiota With Probiotics and Prebiotics May Prevent or Alleviate COVID-19 Through the Gut-Lung Axis – Lei Xu – Frontiers in Pharmacology

Review: A Reciprocal Link Between Gut Microbiota, Inflammation and Depression: A Place for Probiotics? – Ahmed Eltokhi – Frontiers in Neuroscience

Animal Model Microbiome

Reduced housing density improves statistical power of murine gut microbiota studies – Amber Russell – Cell Reports

Investigation of Effects of Hyperglycaemia on the Lung Microbiome in Diabetic Mice – Stanislavs Vasiljevs – FASEB Journal

Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome During Progression and Treatment of Cancer – Holly Paden – FASEB Journal

Impact of Gut R. torques on Type 2 Diabetes in Selenium-deficient Mice – Ying-Chen Huang – FASEB Journal

Interaction between gut microbiota dysbiosis and lung infection as gut-lung axis caused by Streptococcus suis in mouse model – Wenjie Yang – Microbiological Research

The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat – Kyoko Hasebe – Animal Microbiome

Lactoferrin modulates gut microbiota and Toll-like receptors (TLRs) in mice with dysbiosis induced by antibiotics – Andrea Bellés – Food & Function

Non-Model Animal Microbiome

Serotonin modulates insect gut bacterial community homeostasis – Tian Zeng – BMC Biology

Plant and Soil Microbiome

Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes – Peng Wang – Journal of Experimental Botany

Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils – Jianwei Zhang – Environmental Microbiome

Environmental Microbiome

The role of microbiome in carbon sequestration and environment security during wastewater treatment – Xuefeng Zhu – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Variational Approximation-Based Model Selection for Microbial Network Inference – Shibu Yooseph – Journal of Computational Biology

Review: Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Sijia Liu – Microbiome

May 7, 2022

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Human and General Microbiome

Signature of Alzheimer’s Disease in Intestinal Microbiome: Results From the AlzBiom Study – Christoph Laske – Frontiers in Neuroscience

The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients – Johanna Reinold – Frontiers in Cellular and Infection Microbiology

The associations between low abundance of Mycoplasma hominis and female fecundability: a pregnancy-planning cohort study – Xiang Hong – BMC Microbiology

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas – Yin Zhang – Environmental Science & Technology

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Shijia Hu – Journal of Crohn’s & Colitis

Systematic Review: SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review – Zohreh Tamanai-Shacoori – Journal of Medical Microbiology

Review: The Game for Three: Salmonella-Host-Microbiota Interaction Models – Krzysztof Grzymajlo – Frontiers in Microbiology

Review: Host gene effects on gut microbiota in type 1 diabetes – Keyu Guo – Biochemical Society Transactions

Minireview: Host-microbial interactions in metabolic diseases: from diet to immunity – Ju-Hyung Lee – Journal of Microbiology

Preprint: Bacterial association with metals enables in vivo tracking of microbiota using magnetic resonance imaging – Sarah C Donnelly – bioRxiv

Beneficial Microbes and Compounds

Natural Garlic Organosulfur Compounds Prevent Metabolic Disorder of Lipid and Glucose by Increasing Gut Commensal Bacteroides acidifaciens – Keyu Chen – Journal of Agricultural and food Chemistry

Animal Model Microbiome

Circulating gut microbiota-related metabolites influence endothelium plaque lesion formation in ApoE knockout rats – Hsiao-Li Chuang – PloS ONE

Depletion of the gut microbiota enhances the blood pressure-lowering effect of captopril: implication of the gut microbiota in resistant hypertension – Jun Kyoung – Hypertension Research

Non-Model Animal Microbiome

Fecal microbiota and diets of muskox female adults and calves – Ji-Yeon Cheon – Ecology and Evolution

Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee – Karen Luisa Haag – Microbial Ecology

Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat – Ramona Fleischer – Molecular Ecology

Review: Symbiont transmission in marine sponges: reproduction, development, and metamorphosis – Tyler J Carrier – BMC Biology

Preprint: A new microbiological weapon against lepidopteran pests – Vyacheslav Martemyanov – bioRxiv

Environmental Microbiome

Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile – Patricia Aguila-Torres – Environmental Pollution

Plant and Soil Microbiome

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons – Mingsheng Qi – The ISME Journal

A metagenomic study of the bacteria in snow algae microbiomes – Kurt Michael Yakimovich – Canadian Journal of Microbiology

Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data – Marianela Cobos – Data in Brief

Bioinformatics and Data Analysis

Accessible analysis of longitudinal data with linear mixed effects models – Jessica I Murphy – Disease Models & Mechanisms

Scalable in-memory processing of omics workflows – Vadim Elisseev – Computational and Structural Biotechnology Journal

DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation – Rui Gan – Frontiers in Genetics

A New Approach to Testing Mediation of the Microbiome at Both the Community and Individual Taxon Levels – Ye Yue – Bioinformatics

May 3, 2022

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General microbiome

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Worby et al. Nature Microbiology. 2022

Human gut microbiome

Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins – Yang et al. Gut

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Button et al. Cell Host & Microbe

Gut microbial similarity in twins is driven by shared environment and aging – Vilchez-Vargas et al. eBioMedicine

Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. Kwan et al. mSystems

Human respiratory & oral microbiome

Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation – Widder et al. Microbiome

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective – Zhang et al. mBio

Animal experiments

Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats – Hu et al. mSystems

Water/Extremophile microbiome

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans – Duncan et al. Microbiome

Bioinformatics

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Martino et al. mSystems

BiomeHorizon: Visualizing Microbiome Time Series Data in R – Fink et al. mSystems

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. Yarmosh et al. mSphere

Non microbiome picks

Ancestry-inclusive dog genomics challenges popular breed stereotypes – Morrill et al. Science. 

Dietary fibre in hypertension and cardiovascular disease management: systematic review and meta-analyses – Reynolds et al. BMC Medicine

March 25, 2022

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Human gut microbiome

In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort – Wosinska et al. Microorganisms

Cancer pharmacomicrobiomics: targeting microbiota to optimise cancer therapy outcomes – Ting et al. Gut

Human respiratory microbiome

Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza et al. Nature Communications

Probiotics

Gut microbiota and fermentation-derived branched chain hydroxy acids mediate health benefits of yogurt consumption in obese mice – Daniel et al. Nature Communications

Animal experiments

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue – Agranyoni et al. npj biofilms and microbiomes

The microbiota restrains neurodegenerative microglia in a model of amyotrophic lateral sclerosis – Cox et al. Microbiome

Water & Extremophile microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. Microbiome

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Murakami et al. Microbiome.

Virome

Phages and their satellites encode hotspots of antiviral systems – Rousset et al. Cell Host & Microbe

Fungi

Fungal sensing enhances neutrophil metabolic fitness by regulating antifungal Glut1 activity – Li et al. Cell Host & Microbe

The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors – Sharma et al. npj Biofilms and microbiomes

Bioinformatics

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases – Armstrong et al. mSystems