July 18, 2019

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Have a nice Thursday! Today in this Digest, we have papers with clinical implications for the use of microbiota in disease analysis; for example: a paper presenting a model for the use of gut microbiota for disease classification, or an article showing the impact of microbiota in cardiometabolic risk. Today we have several papers about animal microbiome or studies in animal models, including an interesting article showing a relationship between wasp adaptation and their microbiota. And, of course, more papers!

 

Human and General Microbiome

* Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data – Sohyun Bang – Scientific Reports

* Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry – Sandra J. Guzmán-Castañeda – Gut Microbes 

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes – Natalia Gutiérrez – mSystems

The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji – Laura K. Boelsen – Microbiome

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients – Azadeh Saffarian – mBio

A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro – Zachary D. Moye – Journal of Food Protection

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli – Chunhua Zhao – npj Biofilms and Microbiomes

Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners – Emanuel Vamanu – Genes

Research Highlight: Microbiota supplements to improve metabolic health – Anna Kriebs – Nature Reviews Endocrinology

Review: Ketogenic Diet and Microbiota: Friends or Enemies? – Antonio Paoli – Genes

Review: Supporting a Healthy Microbiome for the Primary Prevention of Eczema – Sofia Szari – Clinical Reviews in Allergy & Immunology

A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans – Shengqin Wang – BioMed Research International

 

Animal Models / Animal Experiments

* Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps – Edward J. van Opstal – mBio

The microbiota protects from viral-induced neurologic damage through microglia-intrinsic TLR signaling – D Garrett Brown – eLife

Pregnancy and lactation interfere with the response of autoimmunity to modulation of gut microbiota – Qinghui Mu – Microbiome

Polysaccharide A-Dependent Opposing Effects of Mucosal and Systemic Exposures to Human Gut Commensal Bacteroides Fragilis in Type 1 Diabetes – M. Hanief – Diabetes

Heart failure developed after myocardial infarction does not affect gut microbiota composition in the rat – Renata Maria Lataro – Gastrointestinal and Liver Physiology

Effect of chrysin on changes in intestinal environment and microbiome induced by fructose-feeding in rats – Nelson Andrade – Food & Function

Microbiota of periodontal pockets and root canals in induced experimental periodontal disease in dogs – Cícero R. Gadê‐Neto – Journal of Investigative and Clinical Dentistry

Frontline Science: Abnormalities in the gut mucosa of non-obese diabetic mice precede the onset of type 1 diabetes – Mariana Camila Gonçalves Miranda – Journal of Leukocyte Biology

Early Feeding Regime of Waste Milk, Milk, and Milk Replacer for Calves Has Different Effects on Rumen Fermentation and the Bacterial Community – Rong Zhang – Animals

 

Beneficial Compounds and Microbes

Modified apple polysaccharide regulates microbial dysbiosis to suppress high-fat diet-induced obesity in C57BL/6J mice – Yuhua Li – European Journal of Nutrition

Mulberry leaves ameliorate obesity through enhancing brown adipose tissue activity and modulating gut microbiota – Yao Sheng – Food & Function

 

Plant Microbiome

Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains – Anna Koprivova – PNAS

 

Environmental Microbiome

An RNA-based quantitative and compositional study of ammonium-oxidizing bacteria and archaea in Lake Taihu, a eutrophic freshwater lake – Tong-tong Liu – FEMS Microbiology Ecology

Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy – Lucia Cavalca – Frontiers in Microbiology

July 15, 2019

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Today we have covered several interesting studies including the effect of drugs such as levofloxacin and penconazole, vitamin E, and raw potato starch on the microbiome composition. Microbial diversity of bharals (Pseudois nayaur) is also explored under wild and captive conditions. Additionally, researchers from Gordon’s group have investigated the interactions between therapeutic diet, microbiota development, and growth recovery. Hope readers will enjoy today’s digest.

General microbiome

Review: The impact of microbiome in urological diseases: a systematic review – Joseph K. M. Li – International Urology and Nephrology

Impact of Pristine Graphene on Intestinal Microbiota Assessed Using a Bioreactor-Rotary Cell Culture System – Mohamed H. Lahiani – ACS Applied Materials & Interfaces

Review: Host–microbial dialogues in atopic dermatitis – Tetsuro Kobayashi – International Immunology

Human gut microbiome

A sparse covarying unit that describes healthy and impaired human gut microbiota development – Arjun S. Raman – Science

Effects of microbiota-directed foods in gnotobiotic animals and undernourished children – Jeanette L. Gehrig – Science

Insights: Gut Microbiota and Short Chain Fatty Acids: Influence on the Autonomic Nervous System – Jessica Bruning – Neuroscience Bulletin

Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder – Aaron J. Stevens – Scientific Reports

Characterization of gut microbiota, bile acid metabolism, and cytokines in intrahepatic cholangiocarcinoma – Xiaodong Jia – Hepatology

Effect of Synbiotic Supplementation in a Very‐Low‐Calorie Ketogenic Diet on Weight Loss Achievement and Gut Microbiota: A Randomized Controlled Pilot Study – Carolina Gutiérrez‐Repiso – Molecular Nutrition and Food Research

Animal microbiome / Animal experiments

Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of d-Galactose-Induced Aging Rats Fed with High-Fat Diet – Lee-Ching Lew – Probiotics and Antimicrobial Proteins

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence – Ling-cong Kong – Scientific Reports

Comparison of gut microbiota diversity between wild and captive bharals (Pseudois nayaur) – Xiangwen Chi – BMC Veterinary Research

The effects of desynchronosis on the gut microbiota composition and physiological parameters of rats – Ksenia M. Klimina – BMC Microbiology

Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia – Lisanne M. M. Gommers – The FASEB Journal

The role of commensal microbes in the lifespan of Drosophila melanogaster – Hye-Yeon Lee – Aging

The effect of levofloxacin on the lung microbiota of laboratory rats – Sade M. B. Finn – Experimental Lung Research

Impacts of penconazole and its enantiomers exposure on gut microbiota and metabolic profiles in mice – Zhiyuan Meng – Journal of Agricultural and Food Chemistry

Evaluation of the impact of in ovo administered bacteria on microbiome of chicks through 10 days of age – K M Wilson – Poultry Science

Vitamin E (α-tocopherol) consumption influences gut microbiota composition – Yukyung Choi – International Journal of Food Sciences and Nutrition

CRTAM Shapes the Gut Microbiota and Enhances the Severity of Infection – Araceli Perez-Lopez – The Journal of Immunology

Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach – Stefano Levi Mortera – Journal of Proteomics

Bacillus subtilis Strain DSM 29784 Modulates the Cecal Microbiome, Concentration of Short-Chain Fatty Acids, and Apparent Retention of Dietary Components in Shaver White Chickens during Grower, Developer, and Laying Phases – Mohamed Neijat – Applied and Environmental Microbiology

Effect of raw potato starch on the gut microbiome and metabolome in mice – So-Jung Bang – International Journal of Biological Macromolecules

Edgeworthia gardneri (Wall.) Meisn. water extract improves diabetes and modulates gut microbiota – Zhiwen Zhang – Journal of Ethnopharmacology

Plant, root, and soil microbiome

Review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales – Regina L. Wilpiszeski – Applied and Environmental Microbiology

Water and extremophile microbiome

Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities – Prinpida Sonthiphand – Environmental Science and Pollution Research

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges – Rachel Samson – Science of The Total Environment

Techniques

Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs – Massimo Milan – Food Chemistry

Microbiome news

The Gut Microbiome Can Be a Boon or a Bane for Cardiovascular Health – SHAWNA WILLIAMS

The human microbiome is a treasure trove waiting to be unlocked

13 July, 2019

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Good morning everyone!

Today’s digest is kind of diverse (as always), with great papers about women microbiome, sardines gut microbiome, a great review about soil aggregates and, corals microbiomes and much more. Be sure to read the first paper right down here- The Conceptual Ecology of the Human Microbiome. Have a great weekend!

Human microbiome

**From June 2019, but a must-read nonetheless: The Conceptual Ecology of the Human Microbiome, Morar and Bohannan, Q. R. Biology

Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine, Wouter A. A. de Steenhuijsen Piters, Nature Communications

Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection, Simone Filardo, mSystems

Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli, Chunhua Zhao, MPMI

Secondary bile acid ursodeoxycholic acid (UDCA) alters weight, the gut microbiota, and the bile acid pool in conventional mice, Jenessa A. Winston, bioRxiv

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome, Cristina Alcon-Giner, bioRxiv

Animal microbiome

A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians, Lu Wu, mSystems

Contribution of gut microbiota to metabolism of dietary glycine betaine in mice and in vitro colonic fermentation, Ville M. Koistinen, Microbiome

Coral bacterial community structure responds to environmental change in a host-specific manner, Maren Ziegler, Nature Communications

Soil microbiome

**Mini-review: Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales, Regina L. Wilpiszeski , AEM

Continuous monoculture shapes root and rhizosphere fungal communities of corn and soybean in soybean cyst nematode-infested soil, Noah Strom, Phytobiomes

Engineered root bacteria release plant-available phosphate from phytate, Christine N. Shulse, AEM

Diversity and Characterization of Oomycetes Associated with Corn Seedlings in Michigan, J. A. Rojas, Phytobiomes

Environmental microbiome

Diverse, abundant and novel viruses infecting “unculturable” but abundant marine bacteria, Zefeng Zhang, bioRxiv

Biocide resistance and transmission of Clostridium difficile spores spiked onto clinical surfaces from an American healthcare facility, Calie Dyer, AEM

Microbiome in the news

Lab Startup uBiome Laying Off About Half of Global Workforce

Microbiome Repairing Food for Malnourished Children Beats Current Therapy

July 9, 2019

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Today’s digest features an overview of the “microbiota–nutrient metabolism–epigenetics” axis, a study on the human bile microbiota, an interesting selection of probiotics studies, and more. Check out the new Everything Hertz podcast episode “Improving the scientific poster”. Happy reading/listening!

Gut microbiome

*Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism – Joan Miro-Blanch and Oscar Yanes – Frontiers in Genetics

Microbiome and type 1 diabetes – Heli Siljander – EBioMedicine

Framework for rational donor selection in fecal microbiota transplant clinical trials – Claire Duvallet – medRxiv

A calcium-rich multi-mineral intervention to modulate colonic microbial communities and metabolic profiles in humans: Results from a 90-day trial – Muhammad N. Aslam – medRxiv

*The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile – Natalia Molinero – Microbiome

Oral microbiome

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage – Irina M. Velsko – Microbiome

Respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Skin microbiome

Trait-based analysis of the human skin microbiome – Sharon Bewick – Microbiome

Probiotics

Intermittent Lactobacilli-containing Vaginal Probiotic or Metronidazole Use to Prevent Bacterial Vaginosis Recurrence: Safety and Preliminary Efficacy by Microscopy and Sequencing – Janneke H.H.M. van de Wijgert – medRxiv

Impact of spray‐drying on the pili of Lactobacillus rhamnosus GG – Shari Kiekens – Microbial Biotechnology

The Probiotic Mixture VSL#3 Reverses Olanzapine-Induced Metabolic Dysfunction in Mice – Navneet Dhaliwal – Psychiatric Disorders

Prophylactic Effects of Bifidobacterium adolescentis on Anxiety and Depression-Like Phenotypes After Chronic Stress: A Role of the Gut Microbiota-Inflammation Axis – Ying Guo – Frontiers in Behavioral Neuroscience

Water microbiome

Active eukaryotes in drinking water distribution systems of ground and surface waterworks – Jenni Inkinen – Microbiome

Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water – Luke E. Holman – bioRxiv

Plant/root/soil microbiome

Microscale interactions between immigrant bacteria and plant leaf microbiota as revealed by live imaging – Shifra Steinberg – bioRxiv

Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow – Alexander Crits-Christoph – bioRxiv

Bioinformatics

DeepMicrobes: taxonomic classification for metagenomics with deep learning – Qiaoxing Liang – bioRxiv

Misclassification of a whole genome sequence reference defined by the Human Microbiome – DJ Darwin R. Bandoy – medRxiv

CarboLogR: a Shiny/R application for statistical analysis of bacterial utilisation of carbon sources – Kevin Vervier – bioRxiv

Using collaboration networks to identify authorship bias in meta-analyses – Thiago C. Moulin and Olavo B. Amaral – medRxiv

Podcast

*Episode 87: Improving the scientific poster (with Mike Morrison) – Dan Quintana and James Heathers – Everything Hertz

A terrific interview with @mikemorrison about the Better Poster format and UX design principles in science.

July 8, 2019

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Good Morning! Highlights of today’s digest include several AACR Cancer Research meeting abstracts on microbiome profiling which are promising for development of early detection cancer or treatment-associated-toxicity biomarkers and novel probiotics that can prevent HPV infections-associated cancers and oropharyngeal cancers, development of non-invasive health monitoring tools for endangered humpback whales from East Australia, and re-assemblage of rhizosphere microbiome of medicinal Chinese ginseng or Sanqi. Finally, check out the news about development of a food supplement, expected to be commercialized by 2021 and suggested only to be used as a complementary approach -not a replacement of appropriate dietary habits, that involves a probiotic gut bacterium Akkermansia muciniphila to improve metabolism and metabolic factors in obesity, type II diabetes and inflammatory bowel diseases.

Human oral microbiome

Meeting Abstract: Mucositis, candidiasis, and associations with the oral microbiome in treatment naive patients with oropharyngeal cancer – Pierce et al. – AACR Cancer Research

Multi-site human microbiome

Meeting Abstract: The microbiota associated to cervical and anal HPV infections in a Hispanic population – Vazquez-Sanchez et al. – AACR Cancer Research

Animal microbiome

Review: Coral microbiome dynamics, functions and design in a changing world – van Oppen et al. – Nature Reviews Microbiology

Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales – Vendl et al. – FEMS Microbiology Ecology

Plant, root and soil microbiome

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion – Goss-Souza et al. – Microbial Ecology

Mycorrhizal frequency, physiological parameters, and yield of strawberry plants inoculated with endomycorrhizal fungi and rhizosphere bacteria – Mikiciuk et al. – Mycorrhiza

Negative plant-soil feedback driven by re-assemblage of the rhizosphere microbiome with the growth of Panax notoginseng – Zhu et al. – Frontiers in Microbiology

Water and extermophile microbiome

Microbial communities in a flow-through fish farm for lumpfish (Cyclopterus lumpus L.) during healthy rearing conditions – Roalkvam et al. – Frontiers in Microbiology

Probiotics / prebiotics

Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine – Trachsel et al. – Frontiers in Immunology

Phages and viruses

Virome capture sequencing does not identify active viral infection in unicentric and idiopathic multicentric Castleman disease – Nabel et al. – PLOS ONE

Wide distribution of phage that infect freshwater SAR11 bacteria – Chen et al. – BioRxiv

Techniques

Meeting Abstract: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes – Peck et al. – AACR Cancer Research

Microbes in the news

Microbiome Food Supplement Improves Metabolic Syndrome in Overweight People – Smith – Labiotech.eu Newsletter

July 6, 2019

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Today’s microbiome digest featuring a variety of research and review articles highlighting the role of gut microbiota-derived signals to the beta cells are necessary for proper insulin trafficking, a microfluidic chip designed by Roberta et. al. to mimic interactions between microorganisms and host tissue, the innovative role of exosomes in the pathogenesis of CRC, and a very interesting study in mice shows the host mitochondrial genotype influence the gut microbiota species diversity. Happy weekend. Enjoy reading.

General microbiome

Review: Translating Recent Microbiome Insights in Otitis Media into Probiotic Strategies – Marianne F. L. van den Broek – Clinical Microbiology Reviews

Research Highlight : Microbiota guides insulin trafficking in beta cells – Ozren Stojanović – Cell Research

Human gut microbiome

Human-gut-microbiome on a chip – Roberta Poceviciute – Nature Biomedical Engineering

Gut microbial profile is altered in biliary atresia – Junfeng Wang – Biliary and Pancreatic

The specific use of alginate from Laminaria japonica by Bacteroidesspecies determined its modulation of the Bacteroides community – Chunging Ai – Food & Function

Lactose and Bovine Milk Oligosaccharides Synergistically Stimulate B. longum subsp. longum Growth in a Simplified Model of the Infant Gut Microbiome – Louise M.A. Jakobsen – Journal of proteome research

Review: Probiotics and constipation: mechanisms of action, evidence for effectiveness and utilisation by patients and healthcare professionals – Eirini Dimidi – Proceedings of the Nutrition Society

In Vitro Digestion and Fermentation of Three Polysaccharide Fractions from Laminaria japonica and Their Impact on Lipid Metabolism-Associated Human Gut Microbiota – Jie Gao – Journal of Agricultural and Food Chemistry

Review: Role of intestinal microbiota and metabolites in inflammatory bowel disease – Li-Na Dong – Chinese Medical Journal

Review: The malignant role of exosomes in the communication among colorectal cancer cell, macrophage and microbiome – Jinjie Wu – Carcinogenesis

Human respiratory microbiome

Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status – Tao Ding – mBio

Animal microbiome / Animal experiments

Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis – Terje Klemetsen – MicrobiologyOpen

Protein and carbohydrate intakes alter gut microbial community structure in crickets: A Geometric Framework approach – Soon Hwee Ng – FEMS Microbiology Ecology

Caulerpa lentillifera polysaccharides enhance the immunostimulatory activity in immunosuppressed mice in correlation with modulating gut microbiota – Yujiao Sun – Food & Function

Diet Consisting of Balanced Yogurt, Fruit and Vegetables Modifies the Gut Microbiota and Protects Mice Against Nonalcoholic Fatty Liver Disease – Chao‐Yue Kong – Molecular Nutrition Food Research

Unraveling the effects of the gut microbiota composition and function on horse endurance physiology – Sandra Plancade – Scientific Reports

Inulin and metformin ameliorate polycystic ovary syndrome via anti-inflammation and modulating gut microbiota in mice – Jing Xue – Endocrine Journal

Antiretroviral therapy administration in healthy rhesus macaques is associated with transient shifts in intestinal bacterial diversity and modest immunological perturbations – Alexandra M. Ortiz – Journal of Virology

Microbiota-Driven Tonic Interferon Signals in Lung Stromal Cells Protect from Influenza Virus Infection– Konrad C.Bradley – Cell Reports

Microbial and metabolomic remodeling by a formula of Sichuan dark tea improves hyperlipidemia in apoE-deficient mice – Lingzhi Li – PLOS ONE

Effect of chronic and acute heat challenges on fecal microbiota composition, production and thermoregulation traits in growing pigs – M Le Sciellour – Journal of Animal Science

Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) – José Francisco Lima-Barbero – Journal of Animal Science

L. plantarum, L. fermentum, and B. breveBeads Modified the Intestinal Microbiota and Alleviated the Inflammatory Response in High-Fat Diet–Fed Mice – Qingshen Sun – Probiotics and Antimicrobial Proteins

Host mitochondria influence gut microbiome diversity: A role for ROS – Tal Yardeni – Science Signaling

Potential effects of rapeseed peptide Maillard reaction products on aging-related disorder attenuation and gut microbiota modulation in D-galactose induced aging mice – Shudong He – Food & Function

The piglet mycobiome during the weaning transition: a pilot study – Katie L Summers – Journal of Animal Science

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions – R. John Wallace – Science Advances

Microbiome in news

Dairy cow microbiome could yield the key to eco-friendly agriculture 

July 3, 2019

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Today’s Digest is short with a few articles from Scientific Reports and bioRxiv, spanning six areas, with two highlights added. Enjoy!

General microbiology

Preprint: Single Nanoparticle Tracking Reveals Efficient Long-Distance Undercurrent Transport above Swarming Bacteria – Jingjing Feng et al. – bioRxiv

Human gut microbiome

Preprint (correlation not causation): Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes – Federico Baldini et al. – bioRxiv

Plant, root and soil microbiome

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems – Hanlin Zhang et al. – Scientific Reports

Water and extremophile microbiome

Diversity and extracellular enzyme activities of heterotrophic bacteria from sediments of the Central Indian Ocean Basin – Vijayshree S. Gawas et al. – Scientific Reports

Preprint: Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica – Megan Dillon et al. – bioRxiv

** Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring – Shingo Kato et al. – The ISME Journal

Phages and viruses

** Review: Phage Therapy in the Twenty-First Century: Facing the Decline of The Antibiotic Era; Is it Finally Time for The Age of the Phage? – Shayla Hesse and Sankar Adhya – Annual Review of Microbiology

Education

Preprint: Developing critical thinking in STEM education through inquiry-based writing in the laboratory classroom – Ah Jung Jeon et al. – bioRxiv

Preprint: Genetic research at the intersection of gender identity, sexual orientation, and mental health: community attitudes and recommendations for researchers – Taylor R Thomas et al. – bioRxiv

July 2, 2019

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This Tuesday, read about the fecal microbial transplantation for cardiometabolic syndrome treatment, oral microbiome of early stage Parkinson’s disease, Finnish Health and Early Life Microbiota (HELMi) project, and more. Happy reading!

General microbiome

Review: Defining Division of Labour in Microbial Communities – Samir Giri – JMB

Review: Selective pressures during chronic infection drive microbial competition and cooperation – Jiwasmika Baishya & Catherine A. Wakeman – Biofilms and Microbiomes

Gut microbiome

*Review: Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome – Avner Leshem – Frontiers in Immunology

Review: The Microbiome and Irritable Bowel Syndrome – A Review on the Pathophysiology, Current Research and Future Therapy – Pei Pei Chong – Frontiers in Microbiology

Alterations of the bile microbiome in primary sclerosing cholangitis – Timur Liwinski – BMJ Gut Microbiota

Selective and suppressive effects of antibiotics on donor and recipient bacterial strains in gut microbiota determine transmission efficiency of blaNDM-1-bearing plasmids – Lianwei Ye – Journal of Antimicrobial Chemotherapy

Pregnancy and early life

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve – Kattayoun Kordy – bioRxiv

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota – Mari Hagbø – Paediatric research

*Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort – Katri Korpela – BMJ Paediatrics

Oral microbiome

*The oral microbiome of early stage Parkinson’s disease and its relationship with functional measures of motor and non-motor function – Dragos Mihaila – PlosOne

Phages and viruses

What is (not) known about the dynamics of the human gut virome in health and disease – Leen Beller Jelle Matthijnssens – Current Opinion in Virology

Water and extremophile microbiome

Characterization of indigenous bacteria from radon-rich groundwater and their tolerance to physicochemical stress – T. Nayak – International Journal of Environmental Science and Technology

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes – Nachiket P. Marathe – Microbiome

Techniques

Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities – Shi Ming Tan – Biofilms and microbiomes

Bioinformatics

Use and abuse of correlation analyses in microbial ecology – Alex Carr – ISME Journal

Education

From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training – Annette McGrath – Plos Computational Biology

Ten quick tips for effective dimensionality reduction – Lan Huong Nguyen and Susan Holmes – Plos Computational Biology

July 1, 2019

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Today’s Monday digest is about microbiome changes in diseases such as Parkinson’s disease, schizophrenia, colorectal cancer and inflammatory bowel disease; review on importance of pig microbiota and impact of fecal storage protocols on microbial diversity and composition.

General microbiome

The pig microbiota and the potential for harnessing the power of the microbiome to improve growth and health – Nirosh D Aluthge – Journal of Animal Science

Microbial genes and pathways in inflammatory bowel disease – Melanie Schirmer – Nature Reviews Microbiology

Human microbiome

Changes in Gut Microbiome after Bariatric Surgery Versus Medical Weight Loss in a Pilot Randomized Trial – Clare J. Lee – Obesity Surgery

Microbiome Signatures Associated with Steatohepatitis and Moderate to Severe Fibrosis in Children With Nonalcoholic Fatty Liver Disease – Jeffrey B. Schwimmer – Gastroenterology

Altered gut microbiota and mucosal immunity in patients with schizophrenia – Ruihuan Xu – Brain Behavior and Immunity

Patients Eligible for Trials of Microbe-based Therapeutics do not Represent the Population With Recurrent Clostridioides difficile Infection – Colleen R. Kelly – Clinical Gastoenterology and Hepatology

A role for the mammalian female reproductive tract microbiome in pregnancy outcomes – Babiche A. Heil – Physiological Genomics

Altered intestinal microbiota associated with colorectal cancer – Hong Zhang – Frontiers of Medicine

Gut microbiota is associated with adiposity markers and probiotics may impact specific genera – Aline Corado Gomes – European Journal of Nutrition

Consistent alterations in faecal microbiomes of patients with primary sclerosing cholangitis independent of associated colitis – Malte Ruhlemann – Alimentary Pharmacology and Therapeutics

Altered gut microbiota and inflammatory cytokine responses in patients with Parkinson’s disease – Chin-Hsien Lin – Journal of Neuroinflammation

Animal experiments

Hypergravity disrupts murine intestinal microbiota – Corentine Alauzet – Scientific Reports

Dietary fructose-induced gut dysbiosis promotes mouse hippocampal neuroinflammation: a benefit of short-chain fatty acids – Jian-Mei Li – Microbiome

Gut microbiota depletion from early adolescence alters adult immunological and neurobehavioral responses in a mouse model of multiple sclerosis – Maryam Zeraati – Neuropharmacology

Enrichment of intestinal Lactobacillus by enhanced secretory IgA coating alters glucose homeostasis in P2rx7−/− mice – Lisa Perruzza – Scientific Reports

Plant, root, soil microbiome

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat – Ezgi Özkurt – BioRxiv

Emphasis on the deep or shallow parts of the tree provides a new characterization of phylogenetic distances – Julia Fukuyama – Genome Biology

Techniques

Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study – Shirin Moossavi – BMC Mirobiology

Microbes and the market

Microbiome Sequencing Market players include: Biolog Inc., CosmosID Inc., Illumina Inc., Metabiomics and Oxford Nanopore Technologies Ltd – News Exterior

Global Microbiome Drugs Market NEWS 2019 By Types Probiotics, Prebiotics, Small Molecules, Biological Drugs – Market Reports

 

June 29, 2019

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Happy Saturday! Today, in this Digest: a review about the relationship between hypertension and the gut (including the microbiome as a key player) and a systematic review of the associations between vaginal microbiota, HPV and cervical dysplasia. Today we have also several papers about bioinformatic tools, methods, and techniques associated with microbiome research, including the analysis of well-to-well contamination during microbiome research. And of course, many more papers!

 

Human or General Microbiome

Review: Hypertension as a Metabolic Disorder and the Novel Role of the Gut – Masami Tanaka – Current Hypertension Reports

Minireview: Antibiotics and immunotherapy in gastrointestinal tumors: Friend or foe? – Cong Yan – World Journal of Clinical Cases

Review: Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified – Giovanni Bruno – World Journal of Gastroenterology

Systematic Review: The vaginal microbiota, HPV and cervical dysplasia: a systematic review and network meta-analysis – Johanna Norenhag – BJOG

Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy – Azza Abdel-Gadir – Nature Medicine

Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study – Mary Ann Faucher - American Journal of Perinatology

Banking feces: a new frontier for public blood banks? – Simon Mark Dahl Jørgensen – Transfusion

Diet-microbiota-metabolite interaction networks reveal key players in inflammatory bowel disease – Yijie Weng – Journal of Digestive Diseases

The microbiome of calcium-based urinary stones – Ryan A. Dornbier – Urolithiasis

Scientometric analysis of the term “microbiota” in research publications (1999-2017): A second youth of a century-old concept – Lesya Baudoin – FEMS Microbiology Letters

Microbiome analysis as a platform R&D tool for parasitic nematode disease management – Glenn Hogan – The ISME Journal

Is the Oral Microbiome Associated with Blood Pressure in Older Women? – Joshua H. Gordon – High Blood Pressure & Cardiovascular Prevention

An untargeted fecal and urine metabolomics analysis of the interplay between the gut microbiome, diet and human metabolism in Indian and Chinese adults – Abhishek Jain – Scientific Reports

Gut Microbiota Alteration is Characterized by a Proteobacteria and Fusobacteria Bloom in Kwashiorkor and a Bacteroidetes Paucity in Marasmus – Thi-Phuong-Thao Pham – Scientific Reports

The effects of perineal disinfection on infant’s oral microflora after transvaginal examination during delivery – Hongping Li – BMC Pregnancy and Childbirth

Metagenomic analysis of bile salt biotransformation in the human gut microbiome – Promi Das – BMC Genomics

 

Animal Microbiome / Animal Experiments

Metagenomic assessment of the Cebus apella gut microbiota – Jenni Firrman – American Journal of Primatology

Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective – Marta Turon – mSystems

Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense – Sasha E. Greenspan – Proceedings of the Royal Society B

Intestinal microbiota contributes to altered glucose metabolism in simulated microgravity mouse model – Yifan Wang – The FASEB Journal

Impact of Low-dose Ionising Radiation on the Composition of the Gut Microbiota of Mice – Xiaodan Liu – Toxicological Sciences

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats – Melissa R. Ingala – Ecology and Evolution

 

Microbiome and Therapeutics (Compounds, Microbes or Procedures)

Review: Effects of Fish n-3 PUFAs on Intestinal Microbiota and Immune System – Cinzia Parolini – Marine Drugs

Review: Updates in Treatment of Recurrent Clostridium difficile Infection – Tanveer Singh – Journal of Clinical Medicine Research

Synbiotics suppress colitis-induced tumorigenesis in a colon-specific cancer mouse model – Yasufumi Saito – PLOS One

Roles of Chinese Medicine and Gut Microbiota in Chronic Constipation – Zhenyuan Xu – Evidence-Based Complementary and Alternative Medicine

Increasing the Dose and/or Repeating Faecal Microbiota Transplantation (FMT) Increases the Response in Patients with Irritable Bowel Syndrome (IBS) – Magdy El-Salhy – Nutrients

Interleukin-37 sensitize the elderly type 2 diabetic patients to insulin therapy through suppressing the gut microbiota dysbiosis – Tianyi Li – Molecular Immunology

Skin microbiome modulation induced by probiotic solutions – Bernhard Paetzold – Microbiome

Evaluation of Predation Capability of Periodontopathogens Bacteria by Bdellovibrio Bacteriovorus HD100. An in Vitro Study – Romeo Patini – Materials

 

Bioinformatics, Methods and Techniques

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research – Jeremiah J. Minich – mSystems

Associated commentary: A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses – Alan W. Walker – mSystems

redbiom: a Rapid Sample Discovery and Feature Characterization System – Daniel McDonald – mSystems

Review: Methods and basic concepts for microbiota assessment – Marcio Costa – The Veterinary Journal

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system – Vincent Somerville – BMC Microbiology

Robust biomarker discovery for microbiome-wide association studies – Qiang Zhu – Methods

A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis – Griet Debyser – Emerging Sample Treatments in Proteomics

metaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes – Caleb W. Easterly – Molecular & Cellular Proteomics

Review: The dark side of technological advances in analysis of microbial ecosystems – Mick Bailey – Journal of Animal Science and Biotechnology