Author Archives: JP Cardenas

September 24, 2022

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Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 18, 2022

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Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe

September 12, 2022

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Human and General Microbiome

CAR-T cell therapy-related cytokine release syndrome and therapeutic response is modulated by the gut microbiome in hematologic malignancies – Yongxian Hu – Nature Communications

Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection – Leonardo Mancabelli – Environmental Microbiology

Trimethylamine-N-oxide (TMAO) promotes balloon injury-induced neointimal hyperplasia via upregulating Beclin1 and impairing autophagic flux – Qingqing Hong – Biomedicine & Pharmacotherapy 

Weizmannia faecalis sp. nov., isolated from a human stool sample – Hoang Thong Kieu – Archives of Microbiology

Fusobacterium nucleatum aggravates ulcerative colitis through promoting gut microbiota dysbiosis and dysmetabolism – Shulan Lin – Journal of Periodontology

The evaluation of fecal microbiota transplantation vs vancomycin in a Clostridioides difficile infection model – Qiaomai Xu – Applied Microbiology and Biotechnology

Review: The early-life gut microbiome and vaccine efficacy – Anne Jordan – The Lancet. Microbe

Review: Crucial nuances in understanding (mis)associations between the neonatal microbiome and Cesarean delivery – Alexa M Sassin – Trends in Molecular Medicine

Beneficial Microbes and Compounds

L-Theanine regulates lipid metabolism by modulating gut microbiota and bile acid metabolism – Wei Xu – Journal of the Science of food and Agriculture

Structural and prebiotic activity analysis of the polysaccharide produced by Lactobacillus helveticus SNA12 – Xiaomeng Wang – Carbohydrate Polymers

Review: Unlocking a novel determinant of athletic performance: The role of the gut microbiota, short-chain fatty acids, and biotics in exercise – Kate M Sales – Journal of Sport and Health Science

Animal Microbiome

Comparative analysis of gut microbiota and immune genes linked with the immune system of wild and captive Spodoptera frugiperda (Lepidoptera: Noctuidae) – Renwen Zheng – Developmental and Comparative Immunology

A global dataset of microbial community in ticks from metagenome study – Mei-Chen Liu – Scientific Data

Exposure to dechlorane 602 induces perturbation of gut immunity and microbiota in female mice – Yunping Li – Environmental Pollution 

Plant Microbiome

Dynamics of bacterial and fungal communities of mango: From the tree to ready-to-Eat products – Ahmed Taïbi – Food Microbiology

Forensic Microbiome

The microbiome of fly organs and fly-human microbial transfer during decomposition – Heather L Deel – Forensic Science International

September 10, 2022

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Human and General Microbiome

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life – Conner L Jackson – mBio

Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer – Woraseth Saifon – BMC Cancer

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome – Anuradha Ravi – Communications Biology

Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence – Yi-Wei Chen – mBio

Preprint: Genomic and ecologic characteristics of the airway microbial-mucosal complex – Leah Cuthbertson – BioXriv 

Beneficial Microbes and Compounds

Lactiplantibacillus plantarum Regulated Intestinal Microbial Community and Cytokines to Inhibit Salmonella typhimurium Infection – Rui-Han Liu – Probiotics and Antimicrobial Proteins

Animal Microbiome

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach – Munni Khatoon – Gene

Plant Microbiome

The core bacterial microbiome of banana (Musa spp.) – Henry W G Birt – Environmental Microbiome

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome – Yaping Guo – Environmental Microbiology

Environmental Microbiology

Virome analysis in lakes of the South Shetland Islands, Antarctica – 2020 – Tatiana Prado – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Investigating differential abundance methods in microbiome data: A benchmark study – Marco Cappellato – PLoS Computational Biology

A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples – Ana Zúñiga – Frontiers in Bioengineering and Biotechnology

September 5, 2022

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Human and General Microbiome

Inflammatory bowel disease and cardiovascular diseases – Bing Chen – The American Journal of Medicine

Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity? – Fengping Liu – Journal of Translational Medicine

Polymorphic microbes: a new emerging hallmark of cancer – Mark P Lythgoe – Trends in Microbiology

Does exposure to different types of menstrual protections affect the vaginal environment? – Nicolas Tessandier – Molecular Ecology

Gut commensal E. coli outer membrane proteins activate the host food digestive system through neural-immune communication – Shengya Geng – Cell Host & Microbe

A shared mucosal gut microbiota signature in primary sclerosing cholangitis before and after liver transplantation – Mikal Jacob Hole – Hepatology

Beneficial Microbes and Compounds

The antidiabetic effects of Bifidobacterium longum subsp. longum BL21 through regulating gut microbiota structure in type 2 diabetic mice – Junyu Hao – Food & Function

Morchella esculenta polysaccharide attenuate obesity, inflammation and modulate gut microbiota – Ata Ur Rehman – AMB Express

Animal Microbiome

Review: Comparative biology of germ-free and conventional poultry – A J Cowieson – Poultry Science

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure – Stephanie P Gill – Journal of Applied Microbiology

September 3, 2022

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Highlights!!!

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome – Shuqin Zeng – Nature Communications → Authors presented and described the main features of the  Early-Life Gut Genomes (ELGG) catalog: a dataset of 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3-years old from different regions.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond – Brendon J Medley – The Journal of Biological Chemistry → AMUC_1438, a previously uncharacterized gene from A. muciniphila, encodes an O-glycopeptidase with mucin degrading capacity. This article shows relevant aspects of its enzymatic function. 

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression – David Jose Delgado-Diaz – Microbiome → metaproteomic analysis on vaginal swab samples and transcriptomics analysis of cervicovaginal epithelial cell cultures showed that lactic acid, a commonly produced metabolite by the vaginal lactobacilli, is capable of enhancing genital epithelial barrier integrity; this microbial feature may help prevent invasion by sexually transmitted pathogens.

Human and General Microbiome

Review: A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections – A Review – Rigoberto Pallares-Mendez – Current Urology Reports

Review: Methanogenic archaea in the human gastrointestinal tract – Christoph Hoegenauer – Nature Reviews. Gastroenterology & Hepatology

Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes – Mark C Butcher – APMIS

Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure – Tatiana V Karpinets – BMC Cancer

Horizontal gene transfer enables programmable gene stability in synthetic microbiota – Teng Wang – Nature Chemical Biology

A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota – David M Versluis – mSystems

Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation – J Casper Swarte – Science Translational Medicine

Beneficial Microbes and Compounds

Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice – Weiling Guo – Probiotics and Antimicrobial Proteins

An Alternative Oat-Containing Ready-To-Use Therapeutic Food Does Not Alter Intestinal Permeability or the 16S rRNA Fecal Microbiome Configuration Among Children With Severe Malnutrition in Sierra Leone: A Randomized Controlled Trial – D Taylor Hendrixson – The Journal of Nutrition

Study on the Effect of Molecular Weight on the Gut Microbiota Fermentation Properties of Blackberry Polysaccharides In Vitro – Qiao-Yun Li – Journal of Agricultural and Food Chemistry

Animal Model Microbiome

Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition – Iman Zarei – Scientific Reports

Gut microbiota mediates the inhibition of lymphopoiesis in dietary-restricted mice by suppressing glycolysis – Si Tao – Gut Microbes

Non-Model Animal Microbiome

Limited microbiome differences in captive and semi-wild primate populations consuming similar diets – Sahana Kuthyar – FEMS Microbiology Ecology

Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome – Kathrin Busch – Nature Communications

Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts – Yujie Meng – Microbiome

Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model – Bing Xia – Microbiome

Plant Microbiome

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa – Antoine Hénault – Environmental Microbiology Reports

Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure – Andrzej Tkacz – Environmental Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Gut bacterial nutrient preferences quantified in vivo – Xianfeng Zeng – Cell

Metric learning for comparing genomic data with triplet network – Zhi Ma – Briefings in Bioinformatics

STENSL: Microbial Source Tracking with ENvironment SeLection – Ulzee An – mSystems

Review: Emerging microfluidic technologies for microbiome research – Yue Yu – Frontiers in Microbiology

August 27, 2022

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Highlights!

Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation – Allison K Guitor – Microbiome → A survey of the microbiome from preterm infants showed that probiotics use during hospitalization of these infants reduced the diversity and prevented the persistence of antibiotic resistance genes in the gut microbiome. The authors used a targeted capture approach involving lower costs.

Human gut microbiota after bariatric surgery alters intestinal morphology and glucose absorption in mice independently of obesity – Fernando F Anhê – Gut → The exposition of mice to human gut microbiota after restrictive or malabsorptive bariatric surgery could improve glycaemic control, involving, for example, the inhibition of host sodium-glucose cotransporter (Sglt)-1.

Human and General Microbiome

Temporal dynamics of oropharyngeal microbiome among SARS-CoV-2 patients reveals continued dysbiosis even after Viral Clearance – Suman Kalyan Paine – NPJ Biofilms and Microbiomes

Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples – Todd N Wylie – mSphere

Oral Microbiota from Periodontitis Promote Oral Squamous Cell Carcinoma Development via γδ T Cell Activation – Wei Wei – mSystems

Gut Microbiota and Coronary Plaque Characteristics – Akihiro Nakajima – Journal of the American Heart Association

Toward FAIR Representations of Microbial Interactions – Alan R Pacheco – mSystems

Review: Gut microbiome-mediated mechanisms for reducing cholesterol levels: implications for ameliorating cardiovascular disease – Baolei Jia – Trends in Microbiology

Review: Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era – Yoscelina Estrella Martínez-López – Gut Microbes

Beneficial Microbes and Compounds

Human gut bifidobacteria inhibit the growth of the opportunistic fungal pathogen Candida albicans – Liviana Ricci – FEMS Microbiology Ecology

Animal Model Microbiome

Orally administered Odoribacter laneus improves glucose control and inflammatory profile in obese mice by depleting circulating succinate – Isabel Huber-Ruano – Microbiome

Experimental methods modestly impact interpretation of the effect of environmental exposures on the larval zebrafish gut microbiome – Keaton Stagaman – Scientific Reports

A Metabologenomic approach reveals alterations in the gut microbiota of a mouse model of Alzheimer’s disease – Francesco Favero – PloS ONE

Non-Model Animal Microbiome

Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine – Mika Uehara – mSystems

A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl – Caiquan Zhao – Frontiers in Microbiology

IHNV Infection Induces Strong Mucosal Immunity and Changes of Microbiota in Trout Intestine – Zhenyu Huang – Viruses

Fungi and Soil Microbiome

Wildfire-dependent changes in soil microbiome diversity and function – Amelia R Nelson – Nature Microbiology

Fungal succession on the decomposition of three plant species from a Brazilian mangrove – Marta A Moitinho – Scientific Reports

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi – Felix Richter – FEMS Microbiology Reviews

Environmental Microbiome

Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with Distinct Genetic Repertoires – Myriam Labbé – Applied and Environmental Microbiology

Food Microbiome

Profiling of the microbiota in the remaining sports drink and orange juice in plastic bottles after direct drinking – Miho Kawachi – Journal of Oral Biosciences

Bioinformatic Tools and Microbiome Analysis Techniques

K-Clique Multiomics Framework: A Novel Protocol to Decipher the Role of Gut Microbiota Communities in Nutritional Intervention Trials – Carlo Mengucci – Metabolites

Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data – Aslı Boyraz – Briefings in Bioinformatics

Analysis of Gut Microbiome Using Fecal Samples – Ahmed Gamal – Methods in Molecular Biology 

August 22, 2022

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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 20, 2022

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Have a nice weekend! Today, in this brief Digest: Lung microbiota and PM exposure, Akkermansia genomic variability, sulfonation, microbiome and cholesterol, and a new role for Blautia wexlerae.

Human and General Microbiome

The Lung Microbiota Affects Pulmonary Inflammation and Oxidative Stress Induced by PM(2.5) Exposure – Simin Wang – Environmental Science & Technology

A thousand metagenome-assembled genomes of Akkermansia reveal phylogroups and geographical and functional variations in the human gut – Qing-Bo Lv – Frontiers in Cellular and Infection Microbiology

Intestinal TLR4 deletion exacerbates acute pancreatitis through gut microbiota dysbiosis and Paneth cells deficiency – Mei Qi-Xiang – Gut Microbes

A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria – Lina Yao – Nature Microbiology

Review: Altered gut microbiota patterns in COVID-19: Markers for inflammation and disease severity – Chiranjib Chakraborty – World Journal of Gastroenterology

Animal Model Microbiome and Experiments

Characterization of interactions of dietary cholesterol with the murine and human gut microbiome – Henry H Le – Nature Microbiology

Gut-derived bacterial flagellin induces beta-cell inflammation and dysfunction – Torsten P M Scheithauer – Gut Microbes

Rapid evolution of a novel protective symbiont into keystone taxon in Caenorhabditis elegans microbiota – Alejandra Wu-Chuang – Scientific Reports

Beneficial Microbes and Compounds

Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota – Koji Hosomi – Nature Communications

Fecal microbiota transplantation can improve cognition in patients with cognitive decline and Clostridioides difficile infection – Soo-Hyun Park – Aging

August 16, 2022

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Human and General Microbiome

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome – Jonathan P Jacobs – Genome Medicine

Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease – Marina Burgos da Silva – Blood

Cobamide Sharing Is Predicted in the Human Skin Microbiome – Mary Hannah Swaney – mSystems

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age – Maximilian J Bailey – Gut Microbes

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites – Qingzhen Wei – Frontiers in Microbiology

Review: Recent insights into the role of microbiome in the pathogenesis of obesity – Eduard W J van der Vossen – Therapeutic Advances in Gastroenterology

Model Animal Microbiome

Impact of habitual chewing on gut motility via microbiota transition – Fukie Yaoita – Scientific Reports

Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function – Alexandra Proctor – mSystems

Non-model Animal Microbiome

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate – David M Needham – Nature Microbiology

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism – Sara Ricci – Scientific Reports

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts – Min Hui – PeerJ

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure – Angela Zou – Microbiome

Environmental Microbiome

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction – Alessandro Rossi – Microbiome

Food Microbiome

Microbiome and Metabiotic Properties of Kefir Grains and Kefirs Based on Them –  Ding Fan – Microbiology

Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco – Xinying Wu – BMC Microbiology