December 31, 2019

Posted on December 31, 2019 by JP Cardenas

This is the last Microbiome Digest post from 2019! As part of the MD team, I want to say: Thank you very much for follow this blog. Have a great 2020, better than the 2019. The best for you!

Cheers as well to Dr. Elies Bik (the MD founder) and all the other member of the MD team. -JPC

Human and General Microbiome

Review: Microbiota impacts on chronic inflammation and metabolic syndrome – related cognitive dysfunction – María Arnoriaga-Rodríguez – Reviews in Endocrine and Metabolic Disorders

Review: A Review of the Brain-Gut-Microbiome Axis and the Potential Role of Microbiota in Alzheimer’s Disease – Sun, Miao – Journal of Alzheimer’s Disease

Meta-Analysis: The lacking effects of prebiotic products on decreasing adiposity parameters in overweight and obese individuals: a systematic review and meta-analysis – Hua Qu – Current Medicinal Chemistry

Review: Autoimmune Hepatitis-Immunologically Triggered Liver Pathogenesis-Diagnostic and Therapeutic Strategies – Elisabeth Suche – Journal of Immunology Research

Review: A Comprehensive Review and Update on the Pathogenesis of Inflammatory Bowel Disease – Qingdong Guan – Journal of Immunology Research

Review: Advances in Gut Microbiota of Viral Hepatitis Cirrhosis – Yixuan Wang – BioMed Research International

Review: Mechanisms of gastrointestinal microflora on drug metabolism in clinical practice – Chaonan Sun – Saudi Pharmaceutical Journal

Review: Gut microbiome and response to checkpoint inhibitors in non-small cell lung cancer-A review – Misako Nagasaka – Critical Reviews in Oncology/Hematology

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek – npj Biofilms and Microbiomes

Faecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection: Experience with Lyophilized Oral Capsules – E. Reigadas – Journal of Hospital Infection

Vaginal microbiome diversity and preterm birth: results of a nested case-control study in Peru – Freida Blostein – Annals of Epidemiology

Disordered cutaneous microbiota in systemic lupus erythematosus – Cancan Huang – Journal of Autoimmunity

Transfer of skin microbiota between two dissimilar autologous microenvironments: A pilot study – Benji Perin – PLoS ONE

Animal Microbiome

Alleviating chronic kidney disease progression through modulating the critical genus of gut microbiota in a cisplatin-induced Lanyu pig model – Ya-Jane Lee – Journal of Food and Drug Analysis

Microbiota changes in a pediatric acute lymphocytic leukemia mouse model – Yajing Song – MicrobiologyOpen

Impact of chronic exposure to trichlorfon on intestinal barrier, oxidative stress, inflammatory response and intestinal microbiome in common carp (Cyprinus carpio L.) – Xulu Changa – Environmental Pollution

Glucocorticoid and dietary effects on mucosal microbiota in canine inflammatory bowel disease – Todd Atherly – PLoS ONE

Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation – Josefine Hantschel – PLoS ONE

Involvement of the gut microbiota and barrier function in glucocorticoid induced osteoporosis – Jonathan D Schepper – ASBMR

Food Microbiome

Exploring functional core bacteria in fermentation of a traditional Chinese food, Aspergillus-type douchi – Huilin Yang – PLoS ONE

High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? – Elena Kamilari – International Journal of Food Science

Beneficial Microbes and Compounds

Blueberry Attenuates Liver Fibrosis, Protects Intestinal Epithelial Barrier, and Maintains Gut Microbiota Homeostasis – Zhiqiang Yan – Canadian Journal of Gastroenterology and Hepatology

Cortex Phellodendri extract’s anti-diarrhea effect in mice related to its modification of gut microbiota – Baoyang Xu – Biomedicine & Pharmacotherapy

Environmental and Water Microbiome

Tossed ‘good luck’ coins as vectors for anthropogenic pollution into aquatic environment – Alejandro Martínez – Environmental Pollution

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao – Water Research

Enterococci Isolated from Trout in the Bukovec Water Reservoir and Čierny Váh River in Slovakia and Their Safety Aspect – Andrea Lauková – BioMed Research International

Bioinformatics / Databases

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species – Serena Manara – Genome Biology

Sufficient dimension reduction for compositional data – Diego Tomassi – Biostatistics

Cultivated Escherichia coli diversity in intestinal microbiota of Crohn’s disease patients and healthy individuals: Whole genome data – Maria Siniagina – Data in Brief

December 27, 2019

Posted on December 27, 2019 by xinhuang7

Today’s Digest brings you a report linking gut microbiota and metabolites, a study on dishwasher rubber as a bacterial reservoir, a news piece for your guide to probiotics, and many more. If we don’t see you again in 2019, Happy New Year! May 2020 bring much success and happiness!

General microbiology

Preprint: The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes – Maria A. Sierra et al. – bioRxiv

A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships – Suyeon Kim et al. – BMC Genomics

Antimicrobial resistance

Preprint: Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment – Morteza Roodgar et al. – bioRxiv

Human oral microbiome

Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities – Sayaka Katagiri et al. – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens – Alessia Santoro et al. – Current Medicinal Chemistry

Human gut microbiome

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi – Siddhika Pareek et al. – npj Biofilms and Microbiomes

Review: The influence of dietary patterns on gut microbiome and its consequences for nonalcoholic fatty liver disease – Qing-Song Zhang et al. – Trends in Food Science and Technology

** Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic et al. – Nature Communications

Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination – Jacob A. Cram et al. – PLoS One

Preprint: The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu & Yuanqing Fu et al. – bioRxiv

Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer – Yang Guo et al. – Gut

Human gut-microbiome-brain axis

The relationship between the gut microbiome and mild cognitive impairment in patients without dementia: a cross-sectional study conducted in Japan – Naoki Saji et al. – Scientific Reports

Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice – Juan Maldonado Weng et al. – Molecular Neurodegeneration

Metabolomics

Tech Note: Boost that metabolomic confidence – Vivien Marx – Nature Methods

The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics

Animal experiments

Allergic inflammation alters the lung microbiome and hinders synergistic co-infection with H1N1 influenza virus and Streptococcus pneumoniae in C57BL/6 mice – Kim S. LeMessurier et al. – Scientific Reports

Jatrorrhizine Balances the Gut Microbiota and Reverses Learning and Memory Deficits in APP/PS1 transgenic mice – Sheng Wang et al. – Scientific Reports

The impact of gut microbiota manipulation with antibiotics on colon tumorigenesis in a murine model – Jae Gon Lee et al. – PLoS One

Maternal milk and fecal microbes guide the spatiotemporal development of mucosa-associated microbiota and barrier function in the porcine neonatal gut – Hongbin Liu et al. – BMC Biology

Built environment microbiome

** The dishwasher rubber seal acts as a reservoir of bacteria in the home environment – Jerneja Zupančič et al. – BMC Microbiology

Plant, root and soil microbiome

Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective – Helga E.Balázs et al. – Applied Soil Ecology

Towards simple tools to assess functional effects of contaminants on natural microbial and invertebrate sediment communities – Stéphane Pesce et al. – Environmental Science and Pollution Research

Core rhizosphere microbiomes of dryland wheat are influenced by location and land-use history – Daniel C Schlatter et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

Single molecule sequencing reveals response of manganese-oxidizing microbiome to different biofilter media in drinking water systems – Xin Zhao et al. – Water Research

Prokaryotic Population Dynamics and Viral Predation in a Marine Succession Experiment Using Metagenomics – Jose M. Haro-Moreno et al. – Frontiers in Microbiology

Phages and viruses

News & Views: Phages build anti-defence barriers – Eugene V. Koonin & Mart Krupovic – Nature Microbiology

Microbes in the news

The Best Thing That Happened This Week: Dogs Rule Because They Drool – Sandy Hingston – Philadelphia Magazine

** A guide to the best probiotics – Louisa Richards/Katherine Marengo – Medical News Today

Having a Dog as a Child Is Tied to a Lower Risk of Schizophrenia as an Adult – Nicholas Bakalar – New York Times

Expanding virophage diversity – DOE/Joint Genome Institute

Microbes on the market

Carbiotix to partner with Italian university on neuroinflammation project – Nathan Gray – Nutraingredients

Human Microbiome Market is Expected to Touch US$ 1888.9 Mn by 2026 – Sheila Shipman – News Cast Report

The next frontier – Aaron Massecar – Today’s Veterinary Business

December 23, 2019

Posted on December 23, 2019 by Svetlana Ugarcina Perovic

In today’s digest read about the subway microbiome (from surface and air samples collected at 16 subway stations in Oslo, Norway), role of Staphylococcus epidermidis in healthy maturation of the nasal microbiome, effect of storage and time on urinary microbiome, and more. Happy Holidays!

General microbiome

The emergence of microbiome centres – Jennifer B. H. Martiny – Nature Microbiology

Subway microbiome

*The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities– Jostein Gohli – Microbiome

Gut microbiome

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut– Pichet Praveschotinunt – Nature Communications

Urinary microbiome

*The urinary microbiota composition remains stable over time and under various storage conditions – Caspar Bundgaard-Nielsen – bioRxiv

Vaginal microbiome

Review: Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species – Joana Castro – Trends in Microbiology

Nasal microbiome

*Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production – Qian Liu – Cell Host & Microbes

Animal microbiome

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China – Chunlai Wang – mSystems

Animal experiments

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice– Dian Eurike Septyaningtrias – Neuroscience Research

Plant/root/soil microbiome

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities – S. Emilia Hannula – mBio

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland– Jie Yang – Scientific Reports

Water microbiome

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge– Chenbing Ai – Microorganisms

Viruses

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves – Victor Golyaev – Scientific Reports

Bioinformatics

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise – Valentina Peona – bioRxiv

Transcriptome assembly from long-read RNA-seq alignments with StringTie2– Sam Kovaka – Genome Biology

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework – Guo Liang Gan – BMC Bioinformatics

The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data – Yue Wang – mSystems

December 20, 2019

Posted on December 20, 2019 by xinhuang7

This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!

Events

BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.

Danone North America Announces 2019-2020 Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Danone North America

Current Issue of The ISME Journal

The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain

General microbiology

Depletion of microbiome-derived molecules in the host using Clostridium genetics – Chun-Jun Guo et al. – Science

Microbial carbon limitation ‐ the need for integrating microorganisms into our understanding of ecosystem carbon cycling – Jennifer L. Soong et al. – Global Change Biology

High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology

Antimicrobial resistance

** Significant reduction of vancomycin resistant E. faecium in the Norwegian broiler population coincided with measures taken by the broiler industry to reduce antimicrobial resistant bacteria – Roger Simm et al. – PLoS One

Preprint: Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination – Sophia David et al. – bioRxiv

Human skin microbiome

The diversity and abundance of fungi and bacteria on the healthy and dandruff affected human scalp – Sally G. Grimshaw et al. – PLoS One

Human oral microbiome

** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications

Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American

Human respiratory microbiome

The upper-airway microbiota and loss of asthma control among asthmatic children – Yanjiao Zhou et al. – Nature Communications

Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity

Press: Asthma severity linked to microbiome of upper airway – MedicalXpress

Human gut microbiome

Differences in the intestinal microbiome of healthy children and patients with newly diagnosed Crohn’s disease – Kinga Kowalska-Duplaga et al. – Scientific Reports

Obesity and disease severity magnify disturbed microbiome-immune interactions in asthma patients – David Michalovich et al. – Nature Communications

Functional Associations between Gut Microbiome and Bone Health Status in Post-Menopausal Women: A Cross-Sectional Study – Bolaji Lilian Ilesanmi-Oyelere et al. – Proceedings

The microbiota composition of the offspring of patients with gestational diabetes mellitus (GDM) – Valentina Ponzo et al. – PLoS One

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption – Jeffery& Das et al. – Gastroenterology

Human vaginal microbiome

Characterization of vaginal microbiota in women with preterm labor with intra-amniotic inflammation – Teresa Cobo et al. – Scientific Reports

Human gut-microbiota-brain axis

Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition

Cancer microbiome

Preprint: Growth rate alterations of human colorectal cancer cells by 157 gut bacteria – Rahwa Taddese et al. – bioRxiv

Metabolomics

Metabolomics analysis of human acute graft-versus-host disease reveals changes in host and microbiota-derived metabolites – David Michonneau et al. – Nature Communications

** Integrated univariate, multivariate and correlation-based network analyses reveal metabolite-specific effects on bacterial growth and biofilm formation in necrotizing soft tissue infections – MUHAMMAD AFZAL et al. – Journal of Proteome Research

The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics

Animal experiments

Circadian misalignment alters insulin sensitivity during the light phase and shifts glucose tolerance rhythms in female mice – Li-Xin Zhong et al. – PLoS One

Polysaccharide from Rosa roxburghii Tratt fruit attenuates hyperglycemia, hyperlipidemia and regulates colon microbiota in diabetic db/db mice – Lei Wang et al. – Journal of Agricultural and Food Chemistry

Animal microbiome

Review: Beneath the surface: community assembly and functions of the coral skeleton microbiome – Francesco Ricci et al. – Microbiome

Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis – Qifan Zeng et al. – Microbiome

Microbial diversity within the digestive tract contents of Dezhou donkeys – Guiqin Liu et al. – PLoS One

An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome – Wesley T. Loo et al. – PLoS One

Plant, root and soil microbiome

Endophytic Microbiome of Biofuel Plant Miscanthus sinensis (Poaceae) Interacts with Environmental Gradients – Chao-Li Huang et al. – Microbial Ecology

Short-term nitrogen fertilization affects microbial community composition and nitrogen mineralization function in an agricultural soil – Ouyang & Norton – Applied and Environmental Microbiology

Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology

Water and extremophile microbiome

Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock – Stephanie A. Napieralski et al. – PNAS

Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments – Changchun Yan et al. – Science of the Total Environment

Seasonal Variability of Conditionally Rare Taxa in the Water Column Bacterioplankton Community of Subtropical Reservoirs in China – Pascaline Nyirabuhoro et al. – Microbial Ecology

Phages and viruses

Diversity, evolution, and classification of virophages uncovered through global metagenomics – David Paez-Espino et al. – Microbiome

Discordant transmission of bacteria and viruses from mothers to babies at birth – Rabia Maqsood et al. – Microbiome

Technology

Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities – Ilia G. Halatchev et al. – Microbiome

Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports

** A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science

Enrichment of specific microbial communities by optimum applied voltages for enhanced methane production by microbial electrosynthesis in anaerobic digestion – Flores-Rodriguez & Min – Bioresource Technology

Bioinformatics

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools – Xiaofang Jiang et al. – PLoS One

** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology

Microbes in the news

Exposure to UVB light may lead to beneficial changes in the human gut microbiome: Study – Danielle Masterson – Nutraingredients

Mayo Clinic researchers look at post menopause as key factor in endometrial cancer – Eurekalert

In mice, a high-fat, high-sugar diet remodels the microbiome and endocannabinoid system – ASM – EurekAlert

Prescient Metabiomics and CoreBiome collaborating to develop breakthrough colon cancer screening test – P&T Community

The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World

Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG

Coculturing of Mosquito‐Microbiome Bacteria Promotes Heme Degradation in Elizabethkingia anophelis – Jack Ganley et al. – ChemBioChem

** Mining metagenomics: A faster and more efficient method to compare metagenomes – Chinese Academy of Sciences – Phys.org

Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine

Is There a Link Between Migraine and the Gut Microbiome? – Sally Robertson – News Medical

Non-microbiology pick

Preprint: Grant reviewer perceptions of the quality and effectiveness of panel discussion – Stephen A Gallo et al. – bioRxiv

December 6, 2019

Posted on December 6, 2019 by Tulika Arora

Today’s post is about metabolic networks of the human gut microbiota with host, how aging affects microbial world in humans, microbiome in honey bee and lifestyle dependent gut microbiota gradients in diverse Indian population. Have a nice weekend!

General microbiome

Review: Metabolic networks of the human gut microbiota – Susannah Selber-Hnatiw – Microbiology

Review: Cannabinoids and the Microbiota‐Gut‐Brain‐Axis: Emerging Effects of Cannabidiol and Potential Applications to Alcohol Use Disorders – Hollis C. Karoly – Alcoholism Clinical and Experimental Research

Review: The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging – Oscar Salvador Barrera-Vázquez – Journal of Gerontology

Review: Nanotechnology intervention of the microbiome for cancer therapy – Wantong Song – Nature Nanotechnology

Commentary: Gut microbiome influences exercise response – Claire Greenhill – Nature Reviews Endocrinology

Human microbiome

Bacterial DNA induces the formation of heat-resistant disease-associated proteins in human plasma – Victor Tetz – Scientific Reports

Lifestyle induced microbial gradients: An Indian perspective – Rashmi Singh – Frontiers in Microbiology

Microbiota, type 2 diabetes and non-alcoholic fatty liver disease: protocol of an observational study – Benedetta M. Motta – Journal of Translational Medicine

Antibiotic exposure and the risk of colorectal adenoma and carcinoma: systematic review and meta‐analysis of observational studies – Leigh N. Sanyaolu – Colorectal Disease

Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes – Ki Wook Kim – Pediatric Diabetes

Animal experiments

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera) – Michelle A. Taylor – PlosOne

Seven-day Green Tea Supplementation Revamps Gut Microbiome and Caecum/Skin Metabolome in Mice from Stress – Eun Sung Jung – Scientific Reports

Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization travel – Raies A. Mir – PlosOne

Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening – Zhen Tan – PlosOne

SOD1 deficiency alters gastrointestinal microbiota and metabolites in mice – Haruka Sagi – Experimental Gerontology

Plant, soil, root microbiome

Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere – Michael D. Jochum – PlosOne

Arctic tundra soil bacterial communities active at subzero temperatures detected by stable isotope probing – Preshita S. Gadkari – FEMS Microbiology Ecology

Techniques

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces – Richard W. Hagan – American Journal of Physical Anthropology

Microbes in the news

How Microbiomes Affect Fear – Quanta Magazine

Rainforest Dwellers and Urbanites Have Consistently Different Microbiomes – Scientific American

Human Microbiome Modulators Market is Furbishing worldwide with Bayer, BioGaia, Chr. Hansen Holding, DowDuPont – News Description

December 4, 2019

Posted on December 3, 2019 by Kiran

Highlights: Microbiome of human milk, AMON to integrate microbiome and metabolome data, soil microbiomes, skin microbiome based news and many more!

General microbiome

The fight for glycans in reproductive tract microbial ecology – MIH Pishchany – AJOG

Microbiota, a Third Player in the Host–Plasmodium Affair – D Mukherjee – Trends in Parasitology

Pregnancy and early life

Baby’s First Microbes: The Microbiome of Human Milk – MC Collado – How Fermented Foods Feed a Healthy Gut Microbiota

Human respiratory microbiome

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis – ID Boeck – mSphere

Animal microbiome

Next generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis) – MJ Foysal – Letters in Applied Microbiology

Plant, root, and soil microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – M Weil – bioRxiv

The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation – R Bartelme – bioRxiv

Rhizosphere: a home for human pathogens – R Sharma – Plant Biotic Interactions

Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes – SD Mandal – Environmental Monitoring and Assessment

Soil bacterial and fungal communities exhibit distinct long-term responses to disturbance in temperate forests – ED Osburn – Frontiers in Microbiology

Decomposition of mixtures of cover crop residues increases microbial functional diversity – SM Drost – Geoderma

Techniques

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data – M Shaffer – BMC Bioinformatics

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity – GS Watts – PLoS Computational Biology

Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes – BO Oyserman – bioRxiv

Microbes in the news

Korean beauty makers join the rush towards new skin gold mine of microbiome – Pulse

Mode of Delivery May Alter Microbiome, But Study Finds No Link to Later GI Issues – Gastro Endo News

Smart Skin care – Cosmetics Design Europe

The Dynamic Microbiome – Gen Eng News

microRNA Found in Gut Microbiome May Unlock Future Therapeutic Approach for MS – Multiple Sclerosis News Today

A Matchmaker for Microbiomes – Identifying Relationships of Microbes and Metabolites – Scitech Daily

November 30, 2019

Posted on November 30, 2019 by JP Cardenas

Have a nice weekend! In this Digest, we have a set of reviews about the gut-brain axis, covering associations between microbiota and neurological diseases, as well as a set of reviews about the connection between the microbiome and the immune system. We have also a paper about the microbiome from people living in high-altitude environments, and of course, several papers more.

Human and General Microbiome

Gut microbiota composition in Himalayan and Andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment – Andrea Quagliariello – Journal of Anthropological Sciences

Microbiological evidences for gastric cardiac microflora dysbiosis inducing the progression of inflammation – Ruijing Yan – Journal of Gastroenterology and Hepatology

Review: Targeting the gut microbiota for the treatment of irritable bowel syndrome – Charles C. Herndon – The Kaohsiung Journal of Medical Sciences

Review: The Gut Microbiome and Treatment-Resistance in Schizophrenia – Mary V. Seeman – Psychiatric Quarterly

Review: The Role of the Gut Microbiota in the Pathogenesis of Parkinson’s Disease – Dongming Yang – Frontiers in Neurology

Editorial: Interactions of the microbiota with the mucosal immune system – Calum C. Bain – Immunology

Review: Understanding immune-microbiota interactions in the intestine – Philip P. Ahern – Immunology

Review: The interaction of intestinal microbiota and innate lymphoid cells in health and disease throughout life – Stephanie C. Ganal‐Vonarburg – Immunology

Review: Immunological mechanisms underpinning faecal microbiota transplantation for the treatment of inflammatory bowel disease – M. N. Quraishi – Clinical and Experimental Immunology

Review: Population Genetics in the Human Microbiome – Nandita R. Garud – Trends in Genetics

Review: Gut Microbiota And The Use Of Probiotics In Constipation In Children And Adolescents: Systematic Review – Daiane Oliveira Vale San Gomes – Revista Paulista de Pediatria

Review: The gut microbiota modulates both browning of white adipose tissue and the activity of brown adipose tissue – José María Moreno-Navarrete – Reviews in Endocrine and Metabolic Disorders

Decoding Microbiome Research for Clinical Psychiatry – Jane A. Foster – The Canadian Journal of Psychiatry

Lactobacillus iners Is Associated with Vaginal Dysbiosis in Healthy Pregnant Women: A Preliminary Study – Nengneng Zheng – BioMed Research International

Human Endometrial Microbiota at Term of Normal Pregnancies – Claudia Leoni – Genes (MDPI)

Helicobacter pylori Infection Aggravates Dysbiosis of Gut Microbiome in Children With Gastritis – Lu Yang – Frontiers in Cellular and Infection Microbiology

The Effect of Gut Microbiome Composition on Human Immune Responses: An Exploration of Interference by Helminth Infections – Ivonne Martin – Frontiers in Genetics

Metagenome-wide association study of the alterations in the intestinal microbiome composition of ankylosing spondylitis patients and the effect of traditional and herbal treatment – RunYue Huang – Journal of Medical Microbiology

Gut Microbiota and Cardiometabolic Risk Factors in Hemodialysis Patients: A Pilot Study – Annabel Biruete – Topics in Clinical Nutrition

Habitual animal fat consumption in shaping gut microbiota and microbial metabolites – Yi Wan – Food and Function

Animal Microbiome and Animal Experiments

Division of labor in honey bee gut microbiota for plant polysaccharide digestion – Hao Zheng – PNAS

Exploring interactions between xenobiotics, microbiota, and neurotoxicity in zebrafish – Luísa B. Bertotto – NeuroToxicology

The Skin Microbiota of Eleutherodactylus Frogs: Effects of Host Ecology, Phylogeny, and Local Environment – Liza Garcia-Recinos – Frontiers in Microbiology

The intestinal microbiota of lake anchovy varies according to sex, body size, and local habitat in Taihu Lake, China – Min Jiang – Microbiology Open

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition – Nicholas M. Fountain‐Jones – Journal of Animal Ecology

Immunodeficiency Promotes Adaptive Alterations of Host Gut Microbiome: An Observational Metagenomic Study in Mice – Shuyu Zheng – Frontiers in Microbiology

Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics – Jie Han – Scientific Reports

Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome – Rafael J. Vivero – Scientific Reports

Ochratoxin A induces liver inflammation: involvement of intestinal microbiota – Wence Wang – Microbiome

Toxicity, Pharmacokinetics, and Gut Microbiome of Oral Administration of Sesterterpene MHO7 Derived from a Marine Fungus – Wei Tian – Marine Drugs

Bioinformatics

AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data – M. Shaffer – BMC Bioinformatics

Managing batch effects in microbiome data – Yiwen Wang – Briefings in Bioinformatics

Review: Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities – Duo Jiang – Frontiers in Genetics

Methods

Exploring the chemical space of the human microbiome – Lei Tang – Nature Methods

Other

Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples – Birgit Wassermann – Frontiers in Microbiology

Year in Review: Big data and tiny proteins: shining a light on the dark corners of the gut microbiome – Suzanne Devkota – Nature Reviews Gastroenterology & Hepatology

November 26, 2019

Posted on November 26, 2019 by JP Cardenas

Have a nice day! Today in this Digest, we have papers about the microbiome and colorectal carcinoma and autism spectrum disorder, as well as studies about skin microbiota. We have also a set of papers about the effect of diet or probiotics in different animal systems, as well as some studies in insects.

Human and General Microbiome

Resistant starch: impact on the gut microbiome and health – Peter DeMartino – Current Opinion in Biotechnology

Mucosal cancer-associated microbes and anastomotic leakage after resection of colorectal carcinoma – Kosuke Mima – Surgical Oncology

Mycobacterial immunomodulation and viral manipulation of neuronal copper efflux in the setting of sporadic Parkinson’s disease: A multi – hit, outside – in hypothesis of its pathogenesis – George D.Vavougios – Medical Hypotheses

Specificity of gut microbiota in children with autism spectrum disorder in Slovakia and its correlation with astrocytes activity marker and specific behavioural patterns – A.Tomova – Physiology & Behavior

Small intestinal bacterial overgrowth is associated with Diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance – Kang-Qi Wu – Scandinavian Journal of Gastroenterology

Probiotics of Diverse Origin and Their Therapeutic Applications: A Review – Monika Yadav – Journal of the American College of Nutrition

Variation of Gut Mucosal Microbiome With Anti-Saccharomyces cerevisiae Antibody Status in Pediatric Crohn Disease – Shivani Kansal – Journal of Pediatric Gastroenterology and Nutrition

Dataset of the microbiome composition in skin lesions caused by lumpy skin disease virus via 16s rRNA massive parallel sequencing – Sören Hansen – Data in Brief

Characterization of Skin Microbiome in Tinea Pedis – Xiaoping Liu – Indian Journal of Microbiology

Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants – Lahari Das – Indian Journal of Microbiology

Vertical selection for nuclear and mitochondrial genomes shapes gut microbiota and modifies risks for complex diseases – Youjie Zhang – Physiological Genomics

The relationship of gastric microbiota and Helicobacter pylori infection in pediatrics population – Ruixue Miao – Helicobacter

The impact of vitamin B12 deficiency on infant gut microbiota – Perran Boran – European Journal of Pediatrics

Novel Therapies for Treatment of Food Allergy – Sultan Albuhairi – Immunology and Allergy Clinics

Structural and Functional Bases of Genitourinary Syndrome of Menopause – A. K. Pichigina – Bulletin of Experimental Biology and Medicine

The role of bacteria and its derived metabolites in chronic pain and depression: Recent findings and research progress – Shan Li – International Journal of Neuropsychopharmacology

Microbial supernatants from Mobiluncus mulieris, a bacteria strongly associated with spontaneous preterm birth, disrupts the cervical epithelial barrier through inflammatory and miRNA mediated mechanisms – Carolynn M. Dude – Anaerobe

Overview of prospects for inflammation pathways in autism spectrum disorders – H.Turbé – L’Encéphale

Animal Microbiome and Animal Experiments

The effect of nitrite and sulfide on the antioxidant capacity and microbial composition of the intestines of red swamp crayfish, Procambarus clarkii – Kun Guo – Fish & Shellfish Immunology

Feed supplementation with inulin on broiler performance and meat quality challenged with Clostridium perfringens: Infection and prebiotic impacts – Andréia Guaragni – Microbial Pathogenesis

Strain specific stress-modulating effects of candidate probiotics: a systematic screening in a mouse model of chronic restraint stress – Lotta K. Stenman – Behavioural Brain Research

Effects of the solubility of yeast cell wall preparations on their potential prebiotic properties in dogs – Stephanie de Souza Theodoro – PLoS One

The microbiota of Drosophila suzukii influences the larval development of Drosophila melanogaster – Gabrielle M. Solomon – PeerJ

Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies – Rittik Deb – PeerJ

Kestose supplementation exerts bifidogenic effect within fecal microbiota and increases fecal butyrate concentration in dogs – Kaori Ide – Journal of Veterinary Medical Science

Interactions between host and gut microbiota in domestic pigs: a review – Yadnyavalkya Patil – Gut Microbes

Absorptive transport of amino acids by the rat colon – Yuxin Chen – Gastrointestinal and Liver Physiology

Video: Visualization of Candida albicans in the Murine Gastrointestinal Tract Using Fluorescent In Situ Hybridization – Jessica N. Witchley – JoVE

Video: Infecting Mice with Malassezia spp. to Study the Fungus-Host Interaction – Florian Sparber – JoVE

Plant and Soil Microbiome

Assisted phytoremediation of chromium spiked soils by Sesbania Sesban in association with Bacillus xiamenensis PM14: A biochemical analysis – Bashir Ud Din – Plant Physiology and Biochemistry

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds – Sanderson Tarciso Pereira de Sousa – Ecotoxicology and Environmental Safety

November 23, 2019

Posted on November 23, 2019 by Svetlana Ugarcina Perovic

In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – PlosOne

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees

November 20, 2019

Posted on November 20, 2019 by xinhuang7

Today’s Digest brings you a comprehensive on microbial recovery after antibiotics, a series of studies in Blood on microbial changes after bone marrow transplant, how global ecological factors can drive soil microbiota evolution, and much more. Enjoy!

General microbiology

Preprint: Horizontal gene transfer drives the evolution of dependencies in bacteria – Akshit Goyal – bioRxiv

Antimicrobial resistance

Cross Journal Series: Health Policy and the Management of Antimicrobial Resistance in LMICs – BMC

** Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs – Katharine Michelle Ng et al. – Cell Host & Microbe

Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer – Ryan V Trexler & Terrence H Bell – FEMS Microbiology Letters

Natural products discovery and potential for new antibiotics – Olga Genilloud – Current Opinion in Microbiology

Engineering enzymatic assembly lines to produce new antibiotics – Kenan AJ Bozhüyük et al. – Current Opinion in Microbiology

Human gut microbiome

Antibiotic Exposures and Dietary Intakes Are Associated with Changes in Microbiota Compositions in Allogeneic Hematopoietic Stem Cell Transplant Patients – Chi L. Nguyen et al. – Blood

Impact of Antibiotics on Gut Microbiota Diversity and the Results of a Prospective Dietary Assessment in Patients with Multiple Myeloma Undergoing Autologous Hematopoietic Stem Cell Transplantation – Christopher D’Angelo et al. – Blood

** Impact of Gut Mycobiota Composition on Outcomes after Allogeneic Hematopoietic Cell Transplantation – Florent Malard et al. – Blood

Functional microbiome deficits associated with ageing: Chronological age threshold – Susana Ruiz‐Ruiz et al. – Aging Cell

Human gut-microbiome-brain axis

Review: Gut Microbiota: A Perspective for Psychiatrists – Rea K. et al. – Neuropsychobiology

Metabolomics

Review: Metabolomics biotechnology, applications, and future trends: a systematic review – Qiang Yang et al. – RSC Adv

Animal experiments

Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr−/− mice on a high-fat, high-cholesterol diet – Tom Houben et al. – Scientific Reports

Animal microbiome

Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load – William J Landesman et al. – FEMS Microbiology Ecology

Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity – Francisca H. I. D. Segers et al. – Ecology and Evolution

Plant, root and soil microbiome

The invasive potential of a hybrid species: insights from soil chemical properties and soil microbial communities – Feng Sun et al. – Journal of Plant Ecology

** The role of multiple global change factors in driving soil functions and microbial biodiversity – Matthias C. Rillig et al. – Science

Influence of sulfur fertilization on CuO nanoparticles migration and transformation in soil pore water from the rice (Oryza sativa L.) rhizosphere – Lijuan Sun et al. – Environmental Pollution

Water and extremophile microbiome

Effect of temperature on opportunistic pathogen gene markers and microbial communities in long-term stored roof-harvested rainwater – Xiaodong Zhang et al. – Environmental Research

Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure – Jin-Mei Xia et al. – Applied Microbiology and Biotechnology

Groundwater cable bacteria conserve energy by sulfur disproportionation – Hubert Müller et al. – The ISME Journal

Bioinformatics

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks – Attayeb Mohsen et al. – BMC Bioinformatics

Microbes in the news

New Etiology of Rheumatoid Arthritis Identified in the Gut Microbiome – Frieda Wiley – Rheumatology Network

Gut microbiome diversity associates with sleep quality in healthy adults – Allison Clark – Gut Microbiota For Health

Metagenomics Unlocks Unknowns of Diarrheal Disease Cases in Children – John Toon – GA Tech

Clues for predicting premature birth risk may be found in mother’s immune system, microbiome – Amanda Keener – Genetic Literacy Project

Study offers a bird’s eye view of a bird’s smell – Kaylie Connors – Great Lakes Echo

Microbes on the market

Lancôme brings microbiome hub to Hong Kong with DFS – Elena Dimama – DFNI

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: General Microbiome

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