Category Archives: Pregnancy and birth

July 28, 2018

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Have a good weekend! For this Saturday, we have more than 60 articles! 

Including: A set of reviews about mother, delivery and neonate microbiome; relationship between microbiome and cancer and Alzheimer; microbiome in primate models, reviews about pathogens and more…

 

Human and General Microbiome

Review: Gut Mycobiota and Fungal Metabolites in Human Homeostasis – Izabella Mogilnicka – Current Drug Targets

Review: Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome – Mary Ni Lochlainn – Nutrients

Review: The interplay between neutrophils and microbiota in cancer – Carolyne K. Smith – Journal of Leukocyte Biology

Review: Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut – Siavash Atashgahi – Frontiers in Physiology

Review: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? – Sharon Y. Geerlings – Microorganisms

Review: Considering gut microbiota disturbance in the management of Helicobacter pylori infection – Loris R. Lopetuso – Expert Review of Gastroenterology & Hepatology

Microbiome Analyses for Toxicological Studies – Jacquelynn Benjamino – Current Protocols in Toxicology

Editorial: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention – Giannattasio A. – Annals of Nutrition and Metabolism

Review: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health – Arboleya S. – Annals of Nutrition and Metabolism

Review: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development – Francino M.P.  – Annals of Nutrition and Metabolism

Review: Intervention for Dysbiosis in Children Born by C-Section – Francavilla R. – Annals of Nutrition and Metabolism

Review: Gut Microbiota Composition in Healthy Japanese Infants and Young Adults Born by C-Section – Nagpal R. – Annals of Nutrition and Metabolism

Review: Dysbiosis in Children Born by Caesarean Section – Salas Garcia M.C. – Annals of Nutrition and Metabolism

 

Human Gut

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? – Aguayo, Sebastian –  Journal of Alzheimer’s Disease

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma – Zhigang Ren – Gut

A Multi-omic Association Study of Trimethylamine N-Oxide – Ohad Manor – Cell Reports

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults – Chad W. MacPherson – Scientific Reports

Cost-effectiveness analysis of ribotype-guided fecal microbiota transplantation in Chinese patients with severe Clostridium difficile infection – Minghuan Jiang – PLoS ONE

Microbiota Quality and Mitochondrial Activity Link with Occurrence of Muscle Cramps in Hemodialysis Patients using Citrate Dialysate: A Pilot Study – Durand P.-Y. – Blood Purification

Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women – S. Mörkl – European Journal of Nutrition

Analysis of the Enteric Microbiome: First Tentative Steps Towards a Comprehensive Work-up of Prostate Cancer? – Ilaria Cavarretta – European Urology

 

Human Respiratory Tract

Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients – Georgios D. Kitsios – Frontiers in Microbiology

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients – Laura Iaffaldano – Scientific Reports

 

Newborn and Mother Microbiome

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study – Naruaki Imoto – Journal of Perinatology

 

Human Urinary/Reproductive Tract

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection – Christina Balle – Scientific Reports

Introduction: Microbes in the female reproductive function, do they matter? – Carlos Simon – Fertility and Sterility

 

Human Skin

Relations between epidermal barrier dysregulation and staphylococci-dominated microbiome dysbiosis in atopic dermatitis – Can Altunbulakli – Atopic Dermatitis Research

 

Animal Microbiome / Animal Experiments

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – Scientific Reports

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana) – Hui Zhu – Microbes and Environments

An orally administered oral pathobiont and commensal have comparable and innocuous systemic effects in germ-free mice – Keisuke Sato – Journal of Periodontal Disease

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model – Shuai Chen – Food and Nutrition

Early-life stress leads to sex-dependent changes in pubertal timing in rats that are reversed by a probiotic formulation – Caitlin S. M. Cowan – Developmental Psychobiology

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway – Emilie U. Andersen-Ranberg – Microorganisms

Gut microbiota influences Alzheimer’s disease pathogenesis by regulating acetate in Drosophila model – Yan Kong – Future Microbiology

Elevated Seawater Temperatures Decrease Microbial Diversity in the Gut of Mytilus coruscus – Yi-Feng Li – Frontiers in Physiology

Microbiome-metabolomics Analysis of the Impacts of Long-term Dietary Advanced Glycation End Products Consumption on the C57BL/6 Mouse Fecal Microbiota and Metabolite Perturbation – Wanting Qu – Journal of Agricultural and Food Chemistry

Papio spp. Colon microbiome and its link to obesity in pregnancy – XuanJi Li – Journal of Medical Primatology

Combination of Aronia, Red Ginseng, Shiitake Mushroom and Nattokinase Potentiated Insulin Secretion and Reduced Insulin Resistance with Improving Gut Microbiome Dysbiosis in Insulin Deficient Type 2 Diabetic Rats – Hye Jeong Yang – Nutrients

Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial – Jacqueline C. Whittemore​ – PeerJ

Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice – Liang Qiu – Food and Function

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood – Yanjie Guo – Food and Function

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity – Xue-Song Zhang – eLife

Clostridium butyricum Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-Like Behavior in Mice via the Gut-Brain Axis – Jing Sun – Journal of Agricultural and Food Chemistry

 

Food Microbiome

Analysis of Fish Commonly Sold in Local Supermarkets Reveals the Presence of Pathogenic and Multidrug-Resistant Bacterial Communities – Ama Okyere – Microbiology Insights

Short communication: Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp – Jinxin Jie – Journal of Food Science and Technology

 

Beneficial Microbes and Compounds

Review: Probiotics against airway allergy: host factors to consider – Irina Spacova – Disease Model and Mechanisms

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics – Jonna Sandberg – European Journal of Nutrition

Letter: Effect of Metformin or Chinese Herbal Formula in Patients with Type 2 Diabetes Mellitus and Hyperlipidemia: A Reassessment – Venu Gopal Jonnalagadda – mBio

Coreopsis Tinctoria Modulates Lipid Metabolism by Decreasing Low-Density Lipoprotein and Improving Gut Microbiota – Ren Z. – Cellular Physiology and Biochemistry

 

Pathogen Research

Review: Recent insights into Shigella – Stephen Baker – Current Opinion in Infectious Diseases

Review: Cholera: recent updates – Ana A. Weil – Current Opinion in Infectious Diseases

 

Soil and Plant Microbiome

Microbial community assembly differs across minerals in a rhizosphere microcosm – Thea Whitman – Environmental Microbiology

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome – Eric J. N. Helfrich – Nature Microbiology

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts – Ming-Yi Chou – Scientific Reports

 

Methods

Methodology: A two-stage microbial association mapping framework with advanced FDR control – Jiyuan Hu – Microbiome

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods – Jyotsna Talreja Wassan – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Generalized Linear Models with Linear Constraints for Microbiome Compositional Data – Jiarui Lu – Biometrics

Analyzing differences between microbiome communities using mixture distributions – Konstantin Shestopaloff – Statistics in Medicine

Pathomimetic modeling of human intestinal diseases and underlying host-gut microbiome interactions in a gut-on-a-chip – Woojung Shin – Methods in Cell Biology

 

Other

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems – Magdalena Calusinska – Biotechnology for Biofuels

 

July 20, 2018

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Happy Friday! Today’s digest includes the bacterial diversity of bat guano, cyanobacterial blooms in oil-contaminated sediments, and the shrimp gut microbiome. Also, an NPR interview with astrophysicist Adam Frank about how to be a savvy consumer of science news.

Pregnancy and early life

Maternal peripartum antibiotic exposure and the risk of postpartum depression – Jordan R. Murphy – Research in Nursing and Health

Review: Breast milk, formula, the microbiome and overweight – Elisabetta Mueller – Nature Reviews Endocrinology

Human vaginal microbiome

Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome – Somaieh Afiuni-Zadeh – Scientific Reports

Human gut microbiome

Review: The Gut Microbiota and Healthy Aging: A Mini-Review – Sangkyu Kim – Gerontology

Animal experiments

Western diet feeding influences gut microbiota profiles in apoE knockout mice – Baoning Liu – Lipids in Health and Disease

Animal microbiome

Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano – Marian P. De Leon – PLoS One

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota – Zhiyuan Yao – AMB Express

In ovo microbial communities: a potential mechanism for the initial acquisition of gut microbiota among oviparous birds and lizards – Brian K. Trevelline – Biology Letters

Plant, root, and soil microbiome

Plant diversity and density predict belowground diversity and function in an early successional alpine ecosystem – Dorota L. Porazinska – Ecology

Water and extremophile microbiome

Cyanobacterial blooms in oil-contaminated subtidal sediments revealed by integrated approaches – Cuixiao Xie – Environmental Microbiology Reports

ddPCR applied on archived Continuous Plankton Recorder samples reveals long-term occurrence of class 1 integrons and a sulphonamide resistance gene in marine plankton communities – Andrea Di Cesare – Environmental Microbiology Reports

Structure of Microbial Communities of the Sediments of Alkaline Transbaikalia Lakes with Different Salinity – S. V. Zaitseva – Microbiology

Diversity of Heterotrophic Halophilic Bacteria Isolated from Coastal Solar Salterns, Bulgaria and Their Ability to Synthesize Bioactive Molecules with Biotechnological Impact – I. Boyadzhieva – Microbiology

Diversity of Prokaryotes in Planktonic Communities of Saline Sol-Iletsk lakes (Orenburg Oblast, Russia) – E. A. Selivanova – Microbiology

Pre-Print: Genetic evidence for two carbon fixation pathways in symbiotic and free-living bacteria: The Calvin-Benson-Bassham cycle and the reverse tricarboxylic acid cycle – Maxim Rubin Blum – BioRxiv

Science, publishing, and career

Track the fate of postdocs to help the next generation of scientists – Nature

How To Be A Savvy Consumer Of Science News – NPR’s All Things Considered

Non-microbiology picks

Jupiter has 10 more moons we didn’t know about — and they’re weird – Nature

July 19, 2018

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An all-around Digest today features newly discovered Wolbachia in Anopheles mosquitoes that can lead to probiotic therapy for malaria, a novel mechanism for the plants to control rhizosphere microbiota, growth and defense, and fascinating art produced entirely by microbes. Enjoy!

General microbiology

Review: Large noncoding RNAs in bacteria – Kimberly A. Harris & Ronald R. Breaker – Microbiology spectrum

Bioremediation and microbial metabolism of benzo(a)pyrene – E M Ostrem Loss & J H Yu – Molecular Microbiology

Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses – Fábio Campioni et al. – Scientific Reports

Preprint: Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen – Alicia Fajardo-Lubian et al. – bioRxiv

Pregnancy and early life

Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester – María Florencia Zacarías et al. – PLoS One

Mini-Review: Antibiotics and lactation: An overview of relative infant doses and a systematic assessment of clinical studies – J.J. van Wattum et al. – Basic & Clinical Pharmacology & Toxicology

Human respiratory microbiome

Characterisation of the nasal microbiota in granulomatosis with polyangiitis – Rennie L Rhee et al. – Annals of the Rheumatic Diseases

Human skin microbiome

Human skin commensals augment Staphylococcus aureus pathogenesis – Emma Boldock et al. – Nature Microbiology

Human oral microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen et al. – Scientific Reports

Human gut microbiome

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages – Chris M Rands et al. – Environmental Microbiology

Review: Recent advances in probiotics as live biotherapeutics against gastrointestinal diseases – Kota RK et al. – Current Pharmaceutical Design

Review: Microbiota–Host Crosstalk: A Bridge Between Cardiovascular Risk Factors, Diet, and Cardiovascular Disease – Jacques Amar – American Journal of Hypertension

Human built environment microbiome

β-Lactam and Fluoroquinolone-Resistant Enterobacteriaceae Recovered from the Environment of Human and Veterinary Tertiary Care Hospitals – Dimitria A. Mathys et al. – Vector-Borne and Zoonotic Diseases

Metabolomics

Quantitative metabolomics comparison of traditional blood draws and TAP capillary blood collection – Alexis Catala et al. – Metabolomics

Functional genetic discovery of enzymes using full-scan mass spectrometry metabolomics – Amy A. Caudy et al. – Biochemistry and Cell Biology

Animal experiments

Dietary L-Arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut microbiota in Broiler Chickens Challenged by Clostridium perfringens – Beibei Zhang et al. – Frontiers in Microbiology

Dissertation: Recent Evolution of Host Genetic Control of Microbiota in Cichlid Fishes and Humans – Kaitlin Patricia Coyle – North Carolina State University

Mouse: Gut Microbiota-Stimulated Innate Lymphoid Cells Support b-Defensin 14 Expression in Pancreatic Endocrine Cells, Preventing Autoimmune Diabetes – Michela Miani et al. – Cell Metabolism

Mouse: In vitro probiotic properties of vaginal Lactobacillus fermentum MG901 and Lactobacillus plantarum MG989 against Candida albicans – Chang-Ho Kang et al. – European Journal of Obstetrics & Gynecology and Reproductive Biology

Betaine Improves Intestinal Functions by Enhancing Digestive Enzymes, Ameliorating Intestinal Morphology, and Enriching Intestinal Microbiota in High-salt stressed Rats – Haichao Wang et al. – Nutrients

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract – Xiaoxi B. Lin et al. – The ISME Journal

Differences Between the Intestinal Lumen Microbiota of Aberrant Crypt Foci (ACF)-Bearing and Non-bearing Rats – Xiuli Xiao et al. – Digestive Diseases and Sciences

Mouse: A selective gut bacterial bile salt hydrolase alters host metabolism – Lina Yao et al. – eLife

Diabetes-Associated Alterations in the Cecal Microbiome and Metabolome are Independent of Diet or Environment in the UC Davis Type 2-Diabetes Mellitus Rat Model – Brian D. Piccolo et al. – American Journal of Physiology-Endocrinology and Metabolism

Animal microbiome

Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition – Yanliang Bi et al. – BMC Microbiology

The cecal microbiome of commercial broiler chickens varies significantly by season – Brian B Oakley et al. – Poultry Science

American beaver: Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome – Zachary Armstrong et al. – The ISME Journal

High Gut Microbiota Diversity Provides Lower Resistance against Infection by an Intestinal Parasite in Bumblebees – Kathrin Näpflin & Paul Schmid-Hempel – The American Naturalist

Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens – Yue Shang et al. – Poultry Science

Arrival date and microorganisms in barn swallows – Z. Al Rubaiee et al. – Journal of Avian Biology

* Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds – Sabarni Biswas, Asok K. Biswas & Bratati De – Plant Signaling & Behavior

* Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota – Lingfei Hu et al. – Nature Communications

Water and extremophile microbiome

Abstract: Exploring the relative importance of surficial cyanobacteria communities versus physical, chemical and bioloigical processes at depth on sulfur cycling in two microbial mat environments – Maya Gomes et al. – Caltech Authors

Temperature driven changes in benthic microbial diversity influences biogeochemical cycling in coastal sediments – Natalie Hicks et al. – Frontiers in Microbiology

Resistance and Recovery of Methane-Oxidizing Communities depends on Stress Regime and History; a Microcosm Study – Henri van Kruistum et al. – Frontiers in Microbiology

Enterococci Concentrations in a Coastal Ecosystem are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources – Derek Rothenheber & Stephen Jones – Applied and Environmental Microbiology

Agulhas Current properties shape microbial community diversity and potential functionality – Sandra Phoma et al. – Scientific Reports

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N. Enke et al. – Nature Communications

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays – Manel Ben Abdallah et al. – Extremophiles

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size – Laura Frère et al. – Environmental Pollution

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative – Mark V. Brown et al. – Scientific Data

Microbes in space

The influence of bioregenerative life‐support system (BLSS) dietary structure and lifestyle on the gut microbiota: A 105‐day ground‐based space simulation in Lunar Palace 1 – Zikai Hao et al. – Environmental Microbiology

Probiotics, Prebiotics and Synbiotics

Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review – Aïda Bafeta et al. – Annals of Internal Medicine

Lactobacillus acidophilus and Clostridium butyricum ameliorate colitis in murine by strengthening the gut barrier function and decreasing inflammatory factors – Y. Wang et al. – Beneficial Microbes

Technology

Review: Interkingdom microbial consortia mechanisms to guide biotechnological applications – Shu Zhang et al. – Microbial Biotechnology

Establishing a mucosal gut microbial community in vitro using an artificial simulator – LinShu Liu et al. – PLoS One

Bioinformatics

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome – Jun Miyoshi et al. – PeerJ

Preprint: Macroecological relationships in the dynamics of gut microbiota – Brian W. Ji et al. – bioRxiv

Microbes in the news

Designer microbiomes – Alfie Gleeson & Abigail Sawyer – BioTechniques

* You need to see this award-winning artwork made entirely from microbes – Irish News

Disgusting Things You Never Knew Your Pets Are Bringing Into Your Home – Amanda Harding – Cheat Sheet

Scientific education

Preprint: Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course – Sarah Ly et al. – bioRxiv

11 July, 2018

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Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

July 8, 2018

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Today’s Microbiome Digest blog comes up with the current research articles on the microbiome of GIT, Respiratory, UT, Vagina, Infant, Oral, Marine, Plant-Soil and Animal- Bird. It also features the articles on the bioremediation, pre/pro-biotics, nutrient and dietary effects on microbiome, the potential prognosis, biofilm reduction and multi-omics study of pregnancy cohort, role of Environmental Contaminants(ECs), spore-forming bacteria, attenuation of colitis score, systematic repercussions by antibiotics, glucocorticoid signaling, TMAO, drug-induced liver injury (DILI), neurotransmitter interactions, effect of glycation of fish proteins, NOD2-IBD, Carbapenemase-producing Enterobacteriaceae (CPE).

Have a look and enjoy SUNDAY!

EVENTS, JOBS, PhD POSITIONS:

EVENT – Third Annual Microbiome Symposium on September 24 , 8:00AM – 7:00PM at the Stanford Faculty Club

 

GASTRO-INTESTINAL MICROBIOME: 

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports 

Review – The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy – Desselberger U – Pathogens

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PLoS One

Absence of NOD2 receptor predisposes to intestinal inflammation by a deregulation in the immune response in hosts that are unable to control gut dysbiosis – Patrícia Reisde Souza – Immunobiology

Review – Outside the liver box: The gut microbiota as pivotal modulator of liver diseases – Annika Wahlström – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

 

RESPIRATORY MICROBIOME:

Review – Microbiome in the primary prevention of allergic diseases and bronchial asthma – B.Sozańska – Allergologia et Immunopathologia

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

URINARY TRACT MICROBIOME:

Review – Infections – The Urinary Tract Microbiome: The Answer to All Our Open Questions? – Giuseppe Magistro – European Urology focus

VAGINAL MICROBIOME:

Anti-HIV-1 Activity of Lactic Acid in Human Cervicovaginal Fluid – Tyssen D – mSphere

INFANT MICROBIOME:

Bifidobacterium longum subsp. infantis EVC001 stably restores the infant gut microbiome over the first year of life in breastfed infants – Jennifer Smilowitz – Pediatrics

Review – Does antibiotic choice for the treatment of suspected late-onset sepsis in premature infants determine the risk of developing necrotising enterocolitis? A systematic review – Josephine V.Seale – Early Human Developmment

ORAL MICROBIOME: 

Review – Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Fakhruddin KS – Oral Diseases

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin – Mann AE – Scientific Reports

Distinctions and associations between the microbiota of saliva and supragingival plaque of permanent and deciduous teeth – Shi W – PLoS One

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PLoS One

GENERAL HUMAN MICROBIOME:

Human-associated microbial populations as evidence in forensic casework – Frederike C.A – Forensic Science International: Genetics

Book chapter – Genomics and Drug-Metabolizing Enzymes and Its Application in Drug Delivery: Evaluating the Influence of the Microbiome – Sheeba Varghese Gupta

Effects of Substance Use and Sex Practices on the Intestinal Microbiome During HIV-1 Infection – Jennifer A Fulcher –The Journal of Infectious Diseases

Preview – Interactions between Clostridioides difficile and fecal microbiota in in vitro batch model: growth, sporulation and microbiota changes – Sabina Horvat – Frontiers in Microbiology

Review – Metagenomic and clinical microbiology – Sophie Amrane – Human Microbiome

Implants induce a new niche for microbiomes – Tim H. Jakobsen – Wiley Online Library

Short Communication Transmission of IMI-2 carbapenemase-producing Enterobacteriaceae from river water to human – Chrislène Laurens – Journal of Global Antimicrobial Resistance

Review – The hygiene hypothesis: immunological mechanisms of airway tolerance – Eline Haspeslagh – Current Opinion in Immunology

Microbiota affects the expression of genes involved in HPA axis regulation and local metabolism of glucocorticoids in chronic psychosocial stress – M. Vodička – Brain, Behavior, and Immunity

Review – The Role of Microbiota in Cardiovascular Risk: Focus on Trimethylamine Oxide – HusseinAl-Rubaye – Current Problems in Cardiology

 

HUMAN-MICROBE CROSS-TALK:

Gut Microbiota-Dependent Trimethylamine N-Oxide Predicts Risk of Cardiovascular Events in Patients With Stroke and Is Related to Proinflammatory Monocytes – Haghikia A – Arterioscler Thromb Vasc Biol.

Cutting Edge: Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – J Immunol

Critical Role for the Microbiota in CX3CR1+ Intestinal Mononuclear Phagocyte Regulation of Intestinal T Cell Responses – Myunghoo Kim – Immunity

 

MARINE/WATER MICROBIAL ECOLOGY:

Review – Ecology and evolution of seafloor and subseafloor microbial communities – WD Orsi – Nature Reviews Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurèle Vuillemin – Environmental Microbiology

Metagenomic analysis of basal ice from an Alaskan glacier – Kayani MUR – Microbiome

Patterns of Change in Metabolic Capabilities of Sediment Microbial Communities in River and Lake Ecosystems – Oest A1 – Int J Microbiol

Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver–Julesburg Basin – Natalie M Hull – Science of The Total Environment

 

PLANT or SOIL MICROBIOME:

Preview – New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes – Marie E. Kroeger – Frontiers in Microbiology

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Preview – Unravelling the composition of the root-associated bacterial microbiota of Phragmites australis and Typha latifolia – Laura Pietrangelo – Frontiers in Microbiology

 

BIOREMEDIATION:

Characterization and Dynamic Shift of Microbial Communities during Start-Up, Overloading and Steady-State in an Anaerobic Membrane Bioreactor – Nsanzumukiza Martin Vincent – Int. J. Environ. Res. Public Health

Review – Response of microbial communities to oil spill in the Gulf of Mexico: A review – Linda Adzigbli – Afr. J. Microbiol. Res

A two-staged system to generate electricity in microbial fuel cells using methane – Jaewook Myung – Chemical Engineering Journal

The influence of pressure on crude oil biodegradation in shallow and deep Gulf of Mexico sediments – Nguyen UT – PLoS One

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers – Robert E. Danczak – mSystems

Energy efficiency: Importance of indigenous microorganisms contained in the municipal solid wastes – S.Zahedi – Waste management

Systematic characterization and proposed pathway of tetracycline degradation in solid waste treatment by Hermetia illucens with intestinal microbiota – Minmin Cai – Environmental Pollution

 

NUTRITION or DIET and TREATMENTS:

Functional Effects of the Buckwheat Iminosugar d-Fagomine on Rats with Diet-Induced Prediabetes – Ramos-Romero S – Mol Nutr Food Res

Long-Term Genistein Consumption Modifies Gut Microbiota, Improving Glucose Metabolism, Metabolic Endotoxaemia and Cognitive Function in Mice Fed a High-Fat Diet – López P – Mol Nutr Food Res

Brown rice-specific γ-oryzanol as a promising prophylactic avenue to protect against diabetes mellitus and obesity disease in humans – Masuzaki H – J Diabetes Investig

Intestinal Inflammation in Chilean Infants Fed With Bovine Formula vs. Breast Milk and Its Association With Their Gut Microbiota – Ossa JC – Front Cell Infect Microbiol.

Trigonelline inhibits intestinal microbial metabolism of choline and its associated cardiovascular risk – Anwar S – J Pharm Biomed Anal

Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota – Pierre H.H.Schneeberger – International Journal for Parasitology: Drugs and Drug Resistance

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Glycation of fish protein impacts its fermentation metabolites and gut microbiota during in vitro human colonic fermentation – Yuhong Yang – Food Research International

Correlation between microbiota and flavours in fermentation of Chinese Sichuan Paocai – YangshengXiao – Food Research International

Review – Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome – Giovana Jamar – Food Research International

Review – Microbiota of milk powders and the heat resistance and spoilage potential of aerobic spore-forming bacteria – Faizan A.Sadiq – International Diary Journal

Review – The debate over neurotransmitter interaction in aspartame usage – Arbind Kumar Choudhary – Journal of Clinical Neuroscience

 

METHODS:

Reevaluating approaches to cystic fibrosis pulmonary exacerbations – Schechter MS – Pediatr Pulmonol

Review – Bioresponsive drug delivery systems in intestinal inflammation: State-of-the-art and future perspectives – Niranjan G.Kotla – Advance Drug Delivery Reviews

Rapid analysis of photoautotroph microbial communities in soils by flow cytometric barcoding and fingerprinting – László Menyhárt – Applied Soil Ecology

Degradation studies of modified inulin as potential encapsulation material for colon targeting and release of mesalamine – MichaelWalz – Carbohydrate Polymers

Review – Advances in drug-induced cholestasis: Clinical perspectives, potential mechanisms and in vitro systems – M. LeonorFernández-Murga – Food and Chemical Toxicology

 

ANIMAL and BIRD MICROBIOME:

Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China – Liao F – Microbiology Open

Gut microbiota correlates with fiber and apparent nutrients digestion in goose – Guojun Liu – Poultry Science

Feeding sows resistant starch during gestation and lactation impacts their faecal microbiota and milk composition but shows limited effects on their progeny – Julie Leblois – PLoS One

Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli – J. Pollock – Journal of Animal Science

 

ANIMAL EXPERIMENTS:

Aryl hydrocarbon receptor/IL-22/Stat3 signaling pathway is involved in the modulation of intestinal mucosa antimicrobial molecules by commensal microbiota in mice – Wang J – Innate Immun.

Oral infection of mice with Fusobacterium nucleatum results in macrophage recruitment to the dental pulp and bone resorption – Larry Johnson – Biomedical Journal

Preview – Fecal Microbiota Transplantation is Associated with Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease – Megan C. Niederwerder – Frontiers in Microbiology

Oral treatment with Lactobacillus rhamnosus 64 during the early postnatal period improves the health of adult rats with TNBS-induced colitis – Stanislava Stanojević – Journal of Functional Foods

Antibiotic-induced dysbiosis effects on the murine gastrointestinal tract and their systemic repercussions – Caio PupinRosa – Life Sciences

 

MICROBIOLOGY:

N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli – Sicard JF – Gut Pathog

Benzoyl Peroxide Inhibits Quorum Sensing and Biofilm Formation by Gardnerella vaginalis 14018 – Ammar Algburi – Infectious Diseases in Obstetrics and Gynecology

 

PRE/PRO – BIOTICS:

Review : Benefaction of probiotics for human health: A review – George Kerry R – J Food Drug Anal

Review – Role of prebiotics in regulation of microbiota and prevention of obesity – Grethel T.Choque Delgado – Food Research International

Effects of the Administration of Probiotics on Fecal Microbiota Diversity and Composition in Healthy Individuals – Choong-Kyun Noh – J Neurogastroenterol Motil

 

METABOLOMICS:

Microbiome-related metabolite changes in gut tissue, cecum content and feces of rats treated with antibiotics – C.Behr – Toxicology and Applied Pharmacology

 

MULTI-OMICS PICKS:

Multiomics Modeling of the Immunome, Transcriptome, Microbiome, Proteome, and Metabolome Adaptations During Human Pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

July 6, 2018

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Today’s digest includes the spleen microbiome of wild mammals, the microbial phylogenetic diversity of natural clay, and the effects of non-nutritive sweeteners on the mouse gut microbiome. It also includes Nature’s picks for June’s best science images.

Pregnancy and early life

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner – Sara N. Lundgren – Microbiome

Human skin microbiome

Skin commensal bacteria S. epidermidis promote survival of melanocytes bearing UVB‐induced DNA damage, while bacteria P. acnes inhibit survival of melanocytes by increasing apoptosis – Zhenping Wang – Photodermatology, Photoimmunology, and Photomedicine

Human gut microbiome

Review: Gut microbiota‐immune‐brain interactions in chemotherapy‐associated behavioral comorbidities – Kelley R. Jordan – Cancer

Involvement of T helper 17 cells in inflammatory arthritis depends on the host intestinal microbiota – Heather Evans‐Marin – Arthritis and Rheumatology

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas – Bhabatosh Das – Scientific Reports

Animal experiments

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice – Qiao-Ping Wang – PLoS One

Effects of naturally-produced lovastatin on feed digestibility, rumen fermentation, microbiota and methane emissions in goats over a 12-week treatment period – Su Chui Len Candyrine – PLoS One

Perinatal short-chain fructooligosaccharides program intestinal microbiota and improve enteroinsular axis function and inflammatory status in high-fat diet-fed adult pigs – Cindy Le Bourgot – FASEB

Bifidobacterium bifidum TMC3115 Can Characteristically Influence Glucose and Lipid Profile and Intestinal Microbiota in the Middle-Aged and Elderly – Ke Wang – Probiotics and Antimicrobial Proteins

Isoquercetin and inulin synergistically modulate the gut microbiome to prevent development of the metabolic syndrome in mice fed a high fat diet – Si Tan – Scientific Reports

Animal microbiome

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria – Yan Ge – PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Inês S. Pais – PLoS Biology

Plant, root, and soil microbiome

Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K) – Sakshi Sharma – Archives of Microbiology

Bioinformatics

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Development of outbred CD1 mouse colonies with distinct standardized gut microbiota profiles for use in complex microbiota targeted studies – Marcia L. Hart – Scientific Reports

Non-microbiology picks

Astronauts, atmospheres and axolotls — June’s best science images – Nature

June 26, 2018

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Today’s Microbiome Digest cover the topics on bioinformatics; methods and models; trials and therapies; infection and immunity; microbiome of human gut, human vagina, insect, animals, plant, marine; food and nutrition; bioremediation and metabolomics.

 

EVENTS- JOBS – PhD POSITIONS:

Event – Organoids: Modelling Organ Development and Disease in 3D Culture – EMBO| EMBL Symposia

 

NEWS and VIEWS:

Pairing off: a bottom-up approach to the human gut microbiome– Clare Abreu – Molecular Systems Biology

 

BIOINFORMATICS:
Zero-inflated generalized Dirichlet multinomial regression model for microbiome compositional data analysis – Tang ZZ – Biostatistics

 

METHODS and MODELS:

Book Chapter – Methods for Microbiota Analysis: Sample Collection and Laboratory Methods – Saleh Ibrahim – The Microbiome in Rheumatic Diseases and Infection

Review: Culturing the human microbiota and culturomics – Lagier JC – Nature Reviews Microbiology

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny – Katelyn Brandt – Microbial Genomics

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis – Cartwright CP – Diagnostics Microbiology and Infectious Disease.

PATENT – SYSTEM AND METHODS FOR DEVELOPING AND USING A MICROBIOME-BASED ACTION COMPONENT FOR PATIENT HEALTH – Warren Tracy, Jantzen Tammi Gregory Katherine

 

TRIALS and THERAPIES:

Antimicrobial photodynamic therapy as a new approach for the treatment of vulvovaginal candidiasis: preliminary results – Aline Silva Sousa – Lasers in Medical Science

Review – Prevention of Cystitis: Travelling between the Imaginary and Reality – Vecchio M – Annals of Nutrition and Metabolism

 

INFECTIONS and IMMUNITY:

Book Chapter – The Impact of Infections on Reproduction and Fertility – VE Jones – Clinical Reproductive Science

Intestinal barrier disruption and dysregulated mucosal immunity contribute to kidney fibrosis in chronic kidney disease – Yang J – Nephrology Dialysis Transplantation

In Press: Treatment and Prevention of Recurrent Lower Urinary Tract Infections in Women: A Rapid Review with Practice Recommendations – Ariana l Smith – The Journal of Urology

Book Chapter – Immunology of the Microbiome: Implications for Rheumatoid Arthritis and Other Autoimmune Diseases – Daniel M Altmann – The Microbiome in Rheumatic Diseases and Infection

 

VAGINAL MICROBIOME:

Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. – Diop K – Microbiology Open

 

GUT MICROBIOME: 

Preview – Gut microbiota as a missing link between nutrients and traits of human – Hea-Jong Chung – Frontiers in Microbiology

Preview – The gut-brain axis, the human gut microbiota and their integration in the development of obesity – Edward S Bliss – Frontiers in Microbiology

Review – The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Ömrüm Aydin – Current Diabetes reports

Beneficial metabolic effects of 2’, 3’, 5’-tri-acetyl-N6-(3-hydroxylaniline) adenosine in multiple biological matrices and intestinal flora of hyperlipidemic hamsters– Tianqi Li – Journal of Proteome Research

 

ANIMAL MICROBIOME:

Preview – Dynamics of gut microbiota diversity during the early development of an avian host: evidence from a cross-foster experiment – Aimeric Teyssier – Frontiers in Microbiology

Enterococcus faecium WEFA23 from infant lessens high-fat-diet-induced hyperlipidemia via cholesterol 7-alpha-hydroxylase gene by altering the composition of gut microbiota in rats – Fuqing Huang – ScienceDirect

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Flancman R – PloS One

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing – Ramesh J Pandit – Microbiome

 

GENERAL MICROBIOME:

Review – Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines – Amrita Bhattacharjee – Clinical Science

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities – Yoko Uchida – Molecules

 

PLANT/ROOT/SOIL MICROBIOME:

Editorial – The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Colonization cues of leaf- and root-inhabiting bacterial microbiota of Atractylodes lancea derived in vitro and in vivo – Yong Jia – Plant and Soil

Preview – Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism – Yuanchan Luo – – Frontiers in Microbiology

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a HighSalinity Environment – Juan Ignacio Vílchez – GenomeAnnouncements

 

INSECT MICROBIOME:

Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition – DongZhu – Soil Biology and Biochemistry

 

SKIN MICROBIOME:

Book Chapter – Psoriasis and Psoriatic Arthritis – Madhura Castelino – The Microbiome in Rheumatic Diseases and Infection

 

MARINE MICROBIOME:
Metagenomics Sheds Light on the Ecology of Marine Microbes and Their Viruses – Felipe Hernandes Coutinho – Trends in Microbiology

 

NEONATAL/INFANT MICROBIOME:

Communication – Maternal Intrapartum Antibiotic Administration and Infantile Colic: Is there a Connection? – Leppälehto E – Neonatology

Review – Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health – Lu L – Current Pathobiology Reports

 

CROSS – POPULATION MICROBIOME:
Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults – Abhishek Jain – AMB Express

 

PHAGES/VIRUSES:

Genome Sequence of the Pseudomonas protegens Phage GP100 – Jordan Vacheron – GenomeAnnouncements

 

FOOD and NUTRITION:

Plasma and urine metabolite profiling reveals the protective effect of Clinacanthus nutans in an ovalbumin-induced anaphylaxis model: 1H-NMR metabolomics approach – Leng Wei Khoo – Journal of Pharmaceutical and Biomedical Analysis

Drivers that establish and assembly the lactic acid bacteria biota in cheeses – Marco Gobbetti – Trends in Food Science & Technology

The food safety of DP-356Ø43 soybeans on SD rats reflected by physiological variables and fecal microbiota during a 90-day feeding study – Zou S – Regul Toxicol Pharmacol

Fermented Soybean Suppresses Visceral Fat Accumulation in Mice – Kushida M – Molecular Nutrition and Food Research

Combined Use of C. butyricum Sx-01 and L. salivarius C-1-3 Improves Intestinal Health and Reduces the Amount of Lipids in Serum via Modulation of Gut Microbiota in Mice – Long M – Nutrients

Review – Dietary polyphenols: A novel strategy to modulate microbiota-gut-brain axis – Diana Serra – Trends in Food Science & Technology

 

METABOLOMICS:

Non-invasive urinary metabolomic profiles discriminate biliary atresia from infantile hepatitis syndrome – Wei-Wei Li – Metabolomics

Metabolomics of the amniotic fluid: Is it a feasible approach to evaluate the safety of Chinese medicine during pregnancy? – Jinjun Shan – Journal of Applied Toxicology

Article – A validated, fast method for quantification of sterols and gut microbiome derived 5α/β-stanols in human faeces by isotope dilution LC-high resolution MS – Schoett HF – Analytical Chemistry

 

BIOREMEDIATION:

Bioprospecting for microbes with potential hydrocarbon remediation activity on the northwest coast of the Yucatan Peninsula, Mexico, using DNA sequencing – Mariela Beatriz Reyes-Sosa – Science of The Total Environment

 

ANTIBIOTIC SUSCEPTIBILITY:
Skin and nasal vestibule colonisation by Staphylococcus aureus and its susceptibility to drugs in atopic dermatitis patients – Wrobel J – Annals of Agriculture and Environmental Medicine

 

 

June 25, 2018

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Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science

June 22, 2018

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Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes,  metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity – Kyla S. Ost – Annual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of D. magna to a bacterial pathogen – Marilou P. Sison-Mangus – Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo–Endometrium Synchrony at Implantation – Keiji Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei – American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study – Jovita D’souza – Advances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome

Review: Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria – Jiang S – Journal of Dental Research

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study –  Abigail L. Coughtrie – Journal of Medical Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

Human vaginal microbiome

Review: Pharmacology of Antiretrovirals in the Female Genital Track for HIV Prevention – Melanie R. Nicol – The Journal of Clinical Pharmacology

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis – Zhi-Luo Deng – mSphere 

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes/Metabolism Research and Reviews

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile – Thanissery R – Frontiers in Microbiology

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects – Tomohisa Takagi – Journal of Gastroenterology

Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota – Erin K. Crowley – Marine Drugs

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks – Microbiome

Review: Potential Role of the Gut Microbiome in ALS: A Systematic Review – Michelle L. Wright – Biological Research for Nursing

Animal experiments

Lack of liver steatosis in germ-free mice following hypercaloric diets – Stephan C. Bischoff – European Journal of Nutrition

 Plant, root, and soil microbiome

Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways – Gengwei Wu – Molecular Plant-Microbe Interactions

Correlation and Distribution of Xenobiotics Genes and Metabolic Activities with Level of Total Petroleum Hydrocarbon in Soil, Sediment and Estuary Water in the Niger Delta Region of Nigeria – U. O. Edet – Asian Journal of Biotechnology and Genetic Engineering

Review: Status and future of disease protection and grape berry quality alteration by microorganisms in viticulture – Misa Otoguro – Letters in Applied Microbiology

Editorial: The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Water and extremophile microbiome

Mini-Review: Future direction in marine bacterial agarases for industrial applications -Saeid Tamadoni Jahromi – Applied Microbiology and Biotechnology

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands) – M. Papale – Extremophiles

Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula – Vívian N. Gonçalves – Extremophiles 

A strong link between marine microbial community composition and function challenges the idea of functional redundancy – Pierre E. Galand – The ISME Journal

Probiotics / prebiotics

Gut Microbiota, Probiotics, and Sport: From Clinical Evidence to Agonistic Performance – Marco Pane – Journal of Clinical Gastroenterology

 Microbes in the news

‘Green’-feed: Industrial microbes could feed cattle, pigs, chicken

SMU researchers hope microbes will lead them to strike oil offshore

Scientists Reveal How Gut Microbes ‘Recover’ After Antibiotic Treatment

Celebrate your gut microbiota on the first World Microbiome day!

 Microbes on the market (news about biotech companies)

Human Microbiome Market – Global Industry Analysis, Size, Share, Growth, Trends, and Forecast 2018 – 2026

MaaT Pharma and Lutech Sign Licensing Agreement on Microbiome Therapy for Graft-vs-Host Disease

 

Ashok’s non-microbiology picks

The Rheumatoid Arthritis-Associated Citrullinome – Ronak Tilvawala – Cell Chemical Biology

Inflammation-Induced, STING-Dependent Autophagy Restricts Zika Virus Infection in the Drosophila Brain – Yuan Liu – Cell Host & Microbe

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells – Patrick Fernandes Rodrigues – Nature Immunology

A synaptic threshold mechanism for computing escape decisions – Dominic A. Evans – Nature

June 20, 2018

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This digest has a study on the human hair microbiome, lots of animal studies and experiments, the normal long list of soil/plant publications, some water/extremophile studies, and a few interesting bioinformatics articles.  Enjoy!

Events and jobs

There were some very cool events to check out from my employer, GENEWIZ, this past month.  Every year here there is a celebration with a number of different events called GENEWIZ Week.  Check out this past set of events below:

GENEWIZ Week

GENEWIZ Webinars – definitely check these cool talks out.  You can access past talks, like mine on Metagenomics from 2017, at GENEWIZ Webinars Archive and my past webinar here: Metagenomics for Biomarker Discovery: Precision Medicine Applications

GENEWIZ DNA Award Winners

GENEWIZ Scientist of the Day

General microbiome

[pre-print] Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs – Yingnan Gao – bioxRiv

Pregnancy and early life

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS ONE

Human respiratory microbiome

* The respiratory virome in chronic obstructive pulmonary disease – Marian Garcia-Nuñez – Future Medicine

TRANSPLANTING THE PULMONARY VIROME: DYNAMICS OF TRANSIENT POPULATIONS – Alicia B Mitchell – The Journal of Heart and Lung Transplantation

Human skin microbiome

** Spatial and Environmental Variation of the Human Hair Microbiota – Lauren Brinkac – Scientific Reports

Human oral microbiome

Denture-Associated Oral Microbiome and Periodontal Disease Causing an Anaerobic Pyogenic Liver Abscess in an Immunocompetent Patient: A Case report and Review of the Literature – Muhammad Bader Hammami – Gastroenterology Research

Human gut microbiome

Changes in Gastric Microbiota during Gastric Carcinogenesis – Sun-Young Lee – KoreaMed Synapse

ADTU-05 Gut microbial composition in the migrant south-asian IBD population in UK – Mohammed Quraishi – BMJ Journals (Gut)

Gut Microbiota Dysbiosis and Diarrhea in Kidney Transplant Recipients – Lee JR – American Journal of Transplantation

The microbiome in autoimmune diseases – Fabrizio De Luca – Clinical and Experimental Immunology

Suppression of IL-17F, but not of IL-17A, provides protection against colitis by inducing Treg cells through modification of the intestinal microbiota – Ce Tang – Nature Immunology

* Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome – Laura Rindom Krogsgaard – Clinical and Translational Gastroenterology

Fecal microbiota transplantation for recurrent Clostridium difficile infection – Susy S. Hota – CMAJ

(not just human) The Expensive-Tissue Hypothesis in Vertebrates: Gut Microbiota Effect, a Review – Chun Hua Huang – International Journal of Molecular Sciences

Mediterranean Diet Score: Associations with Metabolic Products of the Intestinal Microbiome, Carotid Plaque Burden, and Renal Function – Michael Pignanelli – Nutrients

Animal experiments

Rumen Microbial Community of Saanen Goats Adapted to a High‐Fiber Diet in the Northeast of Iran – S.H. Ebrahimi – Iranian Journal of Applied Animal Science

Humic substances alter ammonia production and the microbial populations within a RUSITEC fed a mixed hay – concentrate diet – Stephanie A. Terry – Frontiers in Microbiology

Intestinal Microbiota Ecological Response to Oral Administrations of Hydrogen-Rich Water and Lactulose in Female Piglets Fed a Fusarium Toxin-Contaminated Diet – Weijiang Zheng – Toxins

Animal microbiome

Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam – Ton That Huu Dat​ – PeerJ Microbiology

Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal

Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives – Bosheng Chen – The ISME Journal

Aetiological Characterization of the Cutaneous Ulcer Syndrome in Papua New Guinea using Shotgun Metagenomics – Marc Noguera-Julian – Clinical Infectious Diseases

Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity – Tamsyn M. Uren Webster – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Influence of Belowground Herbivory on The Dynamics of Root and Rhizosphere Microbial Communities – Morgane Ourry – Frontiers of Ecological Evolution

* Plant species and heavy metals affect biodiversity of microbial communities associated with metal-tolerant plants in metalliferous soils – Sławomir Borymski – Frontiers in Microbiology

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence – Torres-Cortés Gloria – Frontiers in Plant Science

Influence of the Chemical Form of Antimony on Soil Microbial Community Structure and Arsenite Oxidation Activity – Kataoka T – Europe PMC

Recognizing Patterns: Spatial Analysis of Observed Microbial Colonization on Root Surfaces – Hannes Schmidt – Frontiers in Environmental Science

Microbial diversity of tobacco rhizosphere soil in different growth stages of marigold-tobacco intercropping system –  Xia TiYuan – Editorial Department of Southwest China Journal of Agricultural Sciences

Differences in rice rhizosphere bacterial community structure by application of lignocellulolytic plant-probiotic bacteria with rapid composting traits – Thounaojam Nevita – Ecological Engineering

Data on molecular identification, phylogeny and in vitro characterization of bacteria isolated from maize rhizosphere in Cameroon – Tchuisseu Tchakounté Gylaine Vanissa – Data in Brief

[pre-print] A comprehensive mycofloral diversity of pedosphere, phyllosphere and aerosphere of Som. (Persea bombycina Kost.) -Manjit Kumar Ray  – bioRxiv

Rhizosphere Microbiomes Modulated by Pre-crops Assisted Plants in Defense Against Plant-Parasitic Nematodes – Ahmed Elhady – Frontiers in Microbiology

The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth – Ye Xia – PLOS ONE

Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions – Lin Zhang – Environmental Microbiology

Water and extremophile microbiome 

Metagenomic insights into diazotrophic communities across Arctic glacier forefields – Maisie V. Nash – FEMS Microbiology Ecology

Microbial community shifts in response to acid mine drainage pollution within a natural wetland ecosystem – Oscar E. Aguinaga – Frontiers in Microbiology

Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis – Xinyi Cao – Scientific Reports

Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater – Lotta Purkamo – FEMS Microbial Ecology

Reduced arsenic availability and plant uptake and improved soil microbial diversity through combined addition of ferrihydrite and Trichoderma asperellum SM-12F1 – Hongxiang Zhang – Environmental Science and Pollution Research

Fungi from Admiralty Bay (King George Island, Antarctica) Soils and Marine Sediments – Lia Costa Pinto Wentzel – Microbial Ecology

Bioinformatics

When old metagenomic data meet newly sequenced genomes, a case study – Xin Li – PLOS ONE

PERFect: PERmutation Filtering test for microbiome data – Ekaterina Smirnova – Biostatistics

Ed’s non-microbiology picks

Photochemistry beyond the red limit in chlorophyll f–containing photosystems –  Dennis J. Nürnberg – Science

Research Finds Tipping Point for Large-scale Social Change

LACK OF PAID SICK LEAVE INCREASES POVERTY

Toxic toads could devastate Madagascar’s biodiversity – Science

Effects of 8-hour time restricted feeding on body weight and metabolic disease risk factors in obese adults: A pilot study – Kelsey Gabel – Nutrition and Healthy Aging

Forget in a Flash: A Further Investigation of the Photo-Taking-Impairment Effect – Julia S. Soares – Journal of Applied Research in Memory and Cognition

New discovery about the brain’s water system may prove beneficial in stroke

DNA repair processes are critical mediators of p53-dependent tumor suppression – Ana Janic – Nature Medicine

Astronomers find a galaxy unchanged since the early universe