September 5, 2022

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

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

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

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 13, 2022

Human and General Microbiome

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer – Cheng Kong – Gut

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients – Soon Kyu Lee – Gut Microbes

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor – Yoshiko Sakabe – Fujita Medical Journal

Oral microbiome and serological analyses on association of Alzheimer’s disease and periodontitis – Kuan-Lun Fu – Oral Diseases

Review: Ultra-processed foods and human health: from epidemiological evidence to mechanistic insights – Bernard Srour – The Lancet. Gastroenterology & Hepatology

Beneficial Microbes, Compounds and Interventions

Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer’s Mouse Model – Daniel Cuervo-Zanatta – Cellular and Molecular Neurobiology

Functional and safety characterization of beneficial vaginal lactic acid bacteria for the design of vaginal hygiene products – Jessica Alejandra Silva – Journal of Applied Microbiology

Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis – Haiyang Lu – Cell host & Microbe

Review: The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management – Ali Nabavi-Rad – Gut Microbes

Non-Model Animal Microbiome

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen – Matthew Grisnik – Microbial Ecology

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss) – N Hodkovicova – The Science of the Total Environment

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens – Yahya Al Naggar – The Science of the Total Environment

Plant Microbiome

Host genotype controls ecological change in the leaf fungal microbiome – Acer VanWallendael – PLoS Biology

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress – Yongdong Wang – Microbiology Spectrum

Review: Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions – Zhikun Duan – Molecular Plant Pathology

Food Microbiome

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome – Xiaoning Huang – eLife

Bioinformatic Tools and Microbiome Analysis Techniques

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa – Kevin S Kuchinski – BMC Genomics

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications – Maaly Nassar – GigaScience

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening – Caitlin M A Simopoulos – mSystems

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

July 30, 2022

Have a nice weekend! Today, the Digest contains several reviews.

Highlights!

Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake – Zachary C Holmes – Microbiome → A three-way crossover study showed that prebiotic personalization regimens can be beneficial in different manners to different people; this study showed that people with low fiber intake received more effect from those interventions.

Human and General Microbiome

Differential Gut Microbiota Compositions Related With the Severity of Major Depressive Disorder – Qi Zhong – Frontiers in Cellular and Infection Microbiology

Phospholipid metabolites of the gut microbiota promote hypoxia-induced intestinal injury via CD1d-dependent γδ T cells – Yuyu Li – Gut Microbes

Gut bacteria interact directly with colonic mast cells in a humanized mouse model of IBS – Chiko Shimbori – Gut Microbes

Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents – Jonathan Thorsen – Annals of the American Thoracic Society

Minireview: Role of microbial secreted proteins in gut microbiota-host interactionsBoris Vidal-Veuthey – Frontiers in Cellular and Infection Microbiology 

Review: A Bibliometric Analysis of Research on the Links Between Gut Microbiota and Atherosclerosis – Ya Wang – Frontiers in Cardiovascular Medicine

Review: Microbiota-derived metabolites as drivers of gut-brain communication – Hany Ahmed – Gut Microbes

Review: Female reproductive dysfunctions and the gut microbiota – Sangappa B Chadchan – Journal of Molecular Endocrinology

Systematic Review: A Bibliometric Review on Gut Microbiome and Alzheimer’s Disease Between 2012 and 2021 – Alejandro I Trejo-Castro – Frontiers in Aging Neuroscience

Systematic Review: Disturbances of Vaginal Microbiome Composition in Human Papillomavirus Infection and Cervical Carcinogenesis: A Qualitative Systematic Review – Ming Wu – Frontiers in Oncology

Beneficial Microbes and Compounds

Review: Bacterial-fungal metabolic interactions within the microbiota and their potential relevance in human health and disease: a short review – Alexia Lapiere – Gut Microbes

Animal Model Microbiome

Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides difficile Colonization in a Mouse Model of Colitis – Madeline R Barron – mBio

Non-Model Animal Microbiome

Comparative and functional analyses of fecal microbiome in Asian elephants – Guiding Li – Antonie van Leeuwenhoek

Bioinformatics and Microbiome Analysis Techniques

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake – Luke R Thompson – GigaScience

July 5, 2022

Highlights!

A volatile from the skin microbiota of flavivirus-infected hosts promotes mosquito attractiveness – Hong Zhang – Cell → The production of acetophenone, a potent attractant for mosquitoes, is induced by Flavivirus by a microbiota-based mechanism. This finding shows an interesting example of the interplay between certain viral agents and the microbiota to influence host susceptibility to interact with other species. 

Human and General Microbiome

Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut – Yifei Shen – Advanced Science

Interaction of n-3 polyunsaturated fatty acids with host CD36 genetic variant for gut microbiome and blood lipids in human cohorts – Zelei Miao – Clinical Nutrition 

A weight-loss model based on baseline microbiota and genetic scores for selection of dietary treatments in overweight and obese population – Amanda Cuevas-Sierra – Clinical Nutrition

Beneficial Microbes and Compounds

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model – Jingyi Yuan – Applied Microbiology and Biotechnology

A synbiotics, long chain polyunsaturated fatty acids, and milk fat globule membranes supplemented formula modulates microbiota maturation and neurodevelopment – Tomás Cerdó – Clinical Nutrition

Animal Model Microbiome

Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice – Tian Tian – Journal of Advanced Research

C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [clostridium] scindens in mice – Sean H Adams – Physiological Reports

A single respiratory tract infection early in life reroutes healthy microbiome development and affects adult metabolism in a preclinical animal model – Soner Yildiz – NPJ Biofilms and Microbiomes

Non-Model Animal Microbiome

Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis – Laura Baldassarre – Nature Communications

Dysbiosis and Predicted Functions of the Dental Biofilm of Dairy Goats with Periodontitis – Ana Carolina Borsanelli – Microbial Ecology

Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria – Anna Voulgari-Kokota – Scientific Reports

Plant and Soil Microbiome

Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area – Gargi Das – Current Microbiology

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning – Kendra E Walters – The ISME Journal

Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.) – Davide Francioli – Scientific Reports

Bioinformatics and Microbiome Analysis

MB-SupCon: Microbiome-based predictive models via Supervised Contrastive Learning – Sen Yang – Journal of Molecular Biology

July 2, 2022

Have a nice weekend!

Highlights!

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

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

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

Human and General Microbiome

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

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

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

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

Beneficial Microbes and Compounds

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

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

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

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

Animal Microbiome

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

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

Plant Microbiome

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

Environmental Microbiome

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

Microbiome Analysis Techniques and Tools

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

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

March 25, 2022

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