Category Archives: Metagenomics & Bioinformatics

August 15, 2019

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Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

August 10, 2019

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This weekend, read about the role that gut microbes play in inflammation, microbes in the placenta-maternal interface, BactMAP R package, and more. Happy reading!

General microbiome

High proportions of bacteria and archaea across most biomes remain uncultured – Andrew D. Steen – The ISME Journal

Isolation of an archaeon at the prokaryote-eukaryote interface – Hiroyuki Imachi – bioRxiv

Urinary microbiome

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males – Borna Kassir – Urology

Gut microbiome

*Review: The intestinal microbiota fuelling metabolic inflammation – Herbert Tilg – Nature Reviews Immunology

Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight – Gabriela K Fragiadakis – bioRxiv

Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs – Katharine M. Ng – bioRxiv

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan – Muhammad Iftikhar Khan – bioRxiv

Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls – Dongmei Ai – PeerJ

Specific changes in faecal microbiota are associated with familial Mediterranean fever – Samuel Deshayes – Annals of the Rheumatic Diseases

Pregnancy and early life

*Functional characterization of Ralstonia insidiosa, a bona fide resident at the maternal-fetal interface – Lindsay A. Parnell – bioRxiv

The association between caesarean section delivery and later life obesity in 21-24 year olds in an Urban South African birth cohort – Eniola Sogunle – bioRxiv

Water and extremophile microbiome

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments – Satoshi Hiraoka – bioRxiv

Metabolically-active obligate aerobes in anoxic (sulfidic) marine sediments – Sabyasachi Bhattacharya – bioRxiv

Plant microbiome

Shared mycorrhizae but distinct communities of other root-associated microbes on co-occurring native and invasive maples – Tonia DeBellis – PeerJ

Non-target Effects of Trichoderma on Plants and Soil Microbial Communities – Monika Jangi – Plant Microbe Interface

Bioinformatics

*BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy data – Renske van Raaphorst – bioRxiv

Podcast

The placental microbiome, and advances in artificial intelligence – Nick Howe and Noah Baker – Nature Podcast

August 1, 2019

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Happy Thursday! Today’s digest includes fungi abundance in paddy fields, the microbial quality of treated wastewater, and the oral microbiome of cats. Enjoy!

Animal microbiome

The feline cutaneous and oral microbiota are influenced by breed and environment – Older – PLoS One

Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis – Paludo – PLoS One

Preprint: Effects of the copper IUD on composition of the vaginal microbiota in the olive baboon – Eastman – bioRxiv

Plant, root, and soil microbiome

Nitrogen fertilization altered arbuscular mycorrhizal fungi abundance and soil erosion of paddy fields in the Taihu Lake region of China – Zhang – Environmental Science and Pollution Research

Reconciling disparate responses to grazing in the arbuscular mycorrhizal symbiosis – van Der Heyde – Rhizosphere

Redox-driven shifts in soil microbial community structure in the drawdown zone after construction of the Three Gorges Dam – Wang – Soil Ecology Letters

Water and extremophile microbiome

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and cold – Lezcano – Astrobiology

Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain – Knapik – Scientific Reports

Built environment

How does urban wastewater treatment affect the microbial quality of treated wastewater? – Lopez – Process Safety and Environmental Protection

Identifying microbial community evolution in membrane bioreactors coupled with anaerobic side-stream reactor, packing carriers and ultrasonication for sludge reduction by linear discriminant analysis – Zheng – Bioresource Technology

Food microbiology

Preprint: Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico – Rocha-Arriaga – bioRxiv

Bioinformatics

Preprint: µbialSim: constraint-based dynamic simulation of complex microbiomes – Popp and Centler – bioRxiv

July 27, 2019

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Have a nice weekend! Today, in this Digest, it is worth to remark a study in mice showing the impact of microbiome composition on muscle loss, in addition to a paper presenting the new version of QIIME, one of the most utilized microbiome analysis software available. 

 

Human and General Microbiome

Pearls: Microbiome evolution during host aging – Francisco Daniel Davila Aleman – PLOS Pathogens

Review: The structure and function of the human small intestinal microbiota: Current understanding and future directions – Arthur J. Kastl, Jr – Cellular and Molecular Gastroenterology and Hepatology

Review: The impact of tumor and gut microbiotas on cancer therapy; Beneficial or detrimental? – Yalda Hekmatshoar – Life Sciences 

Review: Gut Microbiota in Phytopharmacology: A Comprehensive Overview Of Concepts, Reciprocal Interactions, Biotransformations And Mode Of Actions – Priyankar Dey – Pharmacological Research

Review: The role of the skin microbiota in acne pathophysiology – S. Ramasamy – British Journal of Dermatology

Review: Study Insights into Gastrointestinal Cancer through the Gut Microbiota – Fanli Kong – BioMed Research International

Review: Contribution of Aging, Obesity, and Microbiota on Tumor Immunotherapy Efficacy and Toxicity – Regina E. M. Baiden-Amissah – International Journal in Molecular Sciences

TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides – Jos P.H. Smits – Journal of Investigative Dermatology

The Gut Microbiota in Collagenous Colitis Shares Characteristics With Inflammatory Bowel Disease-Associated Dysbiosis – Adam Carstens – Clinical and Translational Gastroenterology

Changes in oral microbial profiles associated with oral squamous cell carcinoma vs leukoplakia – Kengo Hashimoto – Journal of Investigative and Clinical Dentistry

Probiotics modulate the gut microbiota composition and immune responses in patients with atopic dermatitis: a pilot study – Zhifeng Fang – European Journal of Nutrition

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease –  – Caihua Wang – Mediators of Inflammation

Rectal Swabs from Critically Ill Patients Provide Discordant Representations of the Gut  Microbiome Compared to Stool Samples – Katherine Fair – mSphere 

Measurement of gut microbial metabolites in cardiometabolic health and translational research – Wei‐Kai Wu – Rapid Communications in Mass Spectrometry

 

Animal Microbiome and Animal Experiments

The gut microbiota influences skeletal muscle mass and function in mice – Shawon Lahiri – Science Translational Science

Intestinal Clostridium species lower host susceptibility to enterohemorrhagic Escherichia coli O157:H7 infection – Yukako Koyanagi – Pathogens and Disease

Preparation and characterization of selenium enriched-Bifidobacterium longum DD98, and its repairing effects on antibiotic-induced intestinal dysbacteriosis in mice – Hui Zhu – Food and Function 

The Ruminal Microbiome and Metabolome Alterations Associated with Diet-Induced Milk Fat Depression in Dairy Cows – Hongbo Zeng – Metabolites

 

Water Microbiome

Insights into the antibiotic resistance dissemination in a wastewater effluent microbiome:  bacteria, viruses and vesicles matter – Lucia Maestre‐Carballa – Environmental Microbiology

 

Built Environment Microbiome

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data – Alejandro R. Walker – Biology Direct 

 

Plant Microbiome

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom-Forming Microcystis aeruginosa – Sara L. Jackrel – Molecular Ecology

Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) – Julian Taffner – Journal of Advanced Research

Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks – Birgit Wassermann – Microbiome

 

Bioinformatics

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 – Evan Bolyen – Nature Biotechnology

Friday, July 19th

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Happy Friday! Today’s digest includes the microbiome of plankton, viral diversity of ticks, and a review of microbiome engineering. Enjoy!

General microbiome

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems – Chuang – PNAS

Human nearly-sterile sites

Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma – Walker – Scientific Reports

Human gut microbiome

Review: Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes – Lam – Cell Host & Microbe

A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study – Frost – PLoS One

Animal experiments

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus – Tan – PLoS One

Animal microbiome

Cicadae pupa promotes metabolites synthesis of Isaria cicadae, a dominant species in cicada flowers microbiota – Chunyu – Journal of Agricultural and Food Chemistry

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice – Moeller – mSphere

Fecal microbiota of different reproductive stages of the central population of the lesser-long nosed bat, Leptonycteris yerbabuenae – Gaona – PLoS One

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection – Kolody – ISME

Plant, root, and soil microbiome

Preprint: Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity – Cobo-Diaz – BioRxiv

Water and extremophile microbiome

Impacts of continuous inflow of low concentrations of silver nanoparticles on biological performance and microbial communities of aerobic heterotrophic wastewater biofilm – Alizadeh – Journal of Agricultural and Food Chemistry

Phages and viruses

Preprint: Metagenomic exploration of viral diversity and virus-host interactions in a deep freshwater lake – Okazaki – BioRxiv

Preprint: Identification and evolution of avian endogenous foamy viruses – Chen – BioRxiv

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago – Sameroff – Scientific Reports

Bioinformatics

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences – Mallick – Nature Communications

Heterogeneity spacers in 16S rDNA primers improve analysis of mouse gut microbiomes via greater nucleotide diversity – Jensen – BioTechniques

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 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 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