August 22, 2022

Highlights!!

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance – Jotham Suez – Cell a randomized-controlled trial (120 healthy adults) observed the effects of saccharin, sucralose, aspartame, and stevia on the human microbiome showed person-specific, microbiome-dependent glycemic alterations. Saccharin and sucralose significantly impaired glycemic responses.

A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions – Lu Yang – Microbiome → assessment of several differential abundance analysis (DAA) tools, using real data-based simulations, suggests that “none of the evaluated methods is simultaneously robust, powerful, and flexible, which makes the selection of the best DAA tool difficult”. These findings suggest that the application of a DAA method depends of data context.  

Systematic Review: Probiotics and Synbiotics Supplementation Improve Glycemic Control Parameters in Subjects with Prediabetes and Type 2 Diabetes Mellitus: A GRADE-assessed systematic review, meta-analysis, and meta-regression of randomized clinical trials – Kaveh Naseri – Pharmacological Research → “Our findings suggest that probiotic and synbiotic intake has favorable effects on glycemic profile in patients with prediabetes and T2DM.”

Human and General Microbiome

The diversity and abundance of gut microbiota are associated with the pain sensation threshold in the Japanese population – Yuki Takeuchi – Neurobiology of Disease

Oral microbiota associated with gingiva of healthy, gingivitis and periodontitis cases – Nemmat A Hussein – Microbial Pathogenesis

Effects of extracellular vesicles derived from oral bacteria on osteoclast differentiation and activation – Hyun Young Kim – Scientific Reports

Porphyromonas gingivalis is a risk factor for the development of nonalcoholic fatty liver disease via ferroptosis – Chao Yao – Microbes and Infection

Review: The Role of a Gut Microbial-Derived Metabolite, Trimethylamine N-Oxide (TMAO), in Neurological Disorders – Sankar Simla Praveenraj – Molecular Neurobiology

Review: The association between early-life gut microbiota and childhood respiratory diseases: a systematic review – Cristina Garcia-Maurino Alcazar – The Lancet. Microbe

Beneficial Microbes and Compounds

Effect of Bifidobacterium animalis subsp. lactis SF on enhancing the tumor suppression of irinotecan by regulating the intestinal flora – Zhongyue Ren – Pharmacological Research

Effect of probiotic supplementation on plasma metabolite profile after Roux-Y gastric bypass: a prospective, randomized, double-blind, placebo-controlled clinical trial – Marília Rizzon Zaparolli Ramos – International Journal of Obesity 

Faecalibaculum rodentium remodels retinoic acid signaling to govern eosinophil-dependent intestinal epithelial homeostasis – Y Grace Cao – Cell Host & Microbe

Human milk nutrient fortifiers alter the developing gastrointestinal microbiota of very-low-birth-weight infants – Michelle R Asbury – Cell Host & Microbe

More Microbes

Diversity of ethanolamine utilization by human commensal Escherichia coli – Maria Ines Moreira de Gouveia – Research in Microbiology

Review: Archaea from the gut microbiota of humans: Could be linked to chronic diseases? – Denise Mafra – Anaerobe

Animal Microbiome

Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates – Zongjun Li – The ISME Journal

Environmental Microbiome

Microbiota and mobile genetic elements influence antibiotic resistance genes in dust from dense urban public places – Tianshu Feng – Environmental Pollution 

Review: Synergy between microalgae and microbiome in polluted waters – Noreen Ashraf – Trends in Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Review: Molecular tools for probing the microbiome – Marcelo Der Torossian Torres – Current Opinion in Structural Biology

August 6, 2022

Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology

August 03, 2022

Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

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

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology

Bioinformatics

Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

July 23, 2022

Greetings from Chile! Today, in this Digest, a variety of papers covering different subjects, such as the relationships between microbiome and C. difficile infection, new skin microbiome sampling techniques, FMT donor-recipient microbiome interplay, microbiome and biodiversity conservation, microbiome and vitamin metabolism, etc.; also, take a look at the papers from the “Bioinformatics and Microbiome Analysis Techniques” section.  

Human and General Microbiome

A 3D-printed transepidermal microprojection array for human skin microbiome sampling – Kun Liang – PNAS

Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort – Yangchun Cao – Microbiology Spectrum

Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders – J E Vazquez Bucheli – Beneficial Microbes

The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity – Nicholas A Lesniak – mBio

The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation – Ruiqiao He – Gut Microbes

Gut commensals expand vitamin A metabolic capacity of the mammalian host – Maryam Bonakdar – Cell Host & Microbe

A reappraisal of microbiome dysbiosis during experimental periodontitis – Marion Arce – Molecular Oral Microbiology

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber – Bryan J Killinger – NPJ Biofilms and Microbiomes

Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function – Sawako Tomioka – Cell Reports

Model Animal Microbiome

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice – Shauni Doms – eLife

Non-Model Animal Microbiome

Metagenomic insights into the microbe-mediated B and K(2) vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Qian Jiang – Microbiome

Exploring the Transient Microbe Population on Citrus Butterfly Wings – P D Kamala Jayanthi – Microbiology Spectrum

Review: Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter – Júnia Schultz – mSystems

Plant Microbiome

Plant genetic effects on microbial hubs impact host fitness in repeated field trials – Benjamin Brachi – PNAS

Review: Beneficial and pathogenic plant-microbe interactions during flooding stress – Clara Martínez-Arias – Plant, Cell & Environment

Environmental Microbiome

Review: Harnessing the microbiome to prevent global biodiversity loss – Raquel S Peixoto – Nature Microbiology

More Microbes

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach – Md Tahsin Khan – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control – Yingtian Hu – PNAS

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination – Omary Mzava – Nature Communications

Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans-Proteomic Pipeline – Steven He – Current Protocols

June 29, 2022

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 15, 2022

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 3, 2022

Happy Friday!

Today’s digest has articles on COVID-19 vaccine hesitancy, a new R package to extract network backbones, and a class of novel antibiotics that targets a Mycobacterium tuberculosis PE-PGRS protein. There also preprints on biofilm winkling in Bacillus subtilis, the dental calculus microbiome, and the relationship between eukaryotic genomes and ocean plankton in a global metagenomic dataset.

Events

Next week is ASM Microbe! I’ll be there, wearing a KN-95 and clutching a box of rapid tests. Feel free to comment or reach out if you’re also attending.

COVID-19

Oro-facial mucocutaneous manifestations of Coronavirus Disease-2019 (COVID-19): A systematic review – Fakhruddin et al. – PLOS ONE

Preprint: The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity – Kim et al. – bioRxiv

Determinants of the COVID-19 vaccine hesitancy spectrum – Piltch-Loeb et al. – PLOS ONE

General microbiome

Preprint: Fatty acid synthesis knockdown promotes biofilm wrinkling and inhibits sporulation in Bacillus subtilis – Arjes et al. – bioRxiv

Association of Strongyloides stercoralis infection and type 2 diabetes mellitus in northeastern Thailand: Impact on diabetic complication-related renal biochemical parameters – Yingklang et al. – PLOS ONE

Analysis of secondary metabolite gene clusters and chitin biosynthesis pathways of Monascus purpureus with high production of pigment and citrinin based on whole-genome sequencing – Zhang et al. – PLOS ONE

Human respiratory microbiome

A novel class of antimicrobial drugs selectively targets a Mycobacterium tuberculosis PE-PGRS protein – Seo et al. – PLOS Biology

Human oral microbiome

Preprint: Assessing the influence of the Mediterranean diet on dental calculus microbiome composition: a pilot study – Innocenti et al. – bioRxiv

Human gut microbiome

Lactobacillus plantarum improves LPS-induced Caco2 cell line intestinal barrier damage via cyclic AMP-PKA signaling – Wei et al. – PLOS ONE

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

Preprint: Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton – Alexander et al. – bioRxiv

Bioinformatics

backbone: An R package to extract network backbones – Neal – PLOS ONE


May 21, 2022

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

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 11, 2022

General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

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

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv

Bioinformatics

Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment