Category Archives: Water microbiome

March 21, 2018

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A long digest today – lots of science on the gut, environment, and some interesting editorials on techniques, bioinformatics, and methodologies applied to microbiome studies.

General microbiome

[pre print] Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – The PLOS ONE Editors – PLOS ONE

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy – Elisa Banchi – PLOS ONE

Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome – Zachary S. Ballard – ACS Nano

Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease – Catherine A. Lozupone – mSystems

Making Millennial Medicine More Meta – Peter J. Turnbaugh – mSystems

Pregnancy and early life

Neonatal intestinal dysbiosis in necrotizing enterocolitis – Naomi-Liza Denning – Molecular Medicine

Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units – Zhi-Hui Zou – Annals of Clinical Microbiology and Antimicrobials

* The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial – Valerie J. Flaherman – The Journal of Pediatrics

Multi-site human microbiome

The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It – Heather Armstrong – Cancers

Human oral microbiome

Salivary microbial profiles in relation to age, periodontal, and systemic diseases – Ronaldo Lira-Junior – PLOS ONE

Human respiratory microbiome

Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective – Georgios D. Kitsios – mSystems

Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies – Emily K. Cope – mSystems

Human gut microbiome

The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome – Christopher John Kiely – Gut Microbes

Species Level Description of the Human Ileal Bacterial Microbiota – Heidi Cecilie Villmones – Nature

* Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates – Francesco Multinu – mSphere

* Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

In this issue: Effect of gut microbiome on mucosal immunity and enteric diseases – Kumar, Himanshu – International Reviews of Immunology

Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis – Dragos Ciocan – Nature

Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention – Sara L. Revolinski – Infection Control and Hospital Epidemiology

* Of Microbes and Minds: A Narrative Review on the Second Brain Aging – Riccardo Calvani – Frontiers in Medicine

Microbiome: Viral hormones activate human insulin signalling – Ashley York – Nature

Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy – Yiming Wang – Frontiers in Immunology

* Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study – Carmen Losasso – Frontiers in Microbiology

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies – Melanie Tramontano – Nature

Animal experiments

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Low dose brain estrogen prevents menopausal syndrome while maintaining the diversity of the gut microbiomes in estrogen-deficient rats – Sunmin Park – American Journal of Physiology-Endocrinology and Metabolism

Oral supplementation of Bifidobacterium longum strain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability – Yuko Makioka – Bioscience, Biotechnology, and Biochemistry

Animal microbiome

Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok – Martha Zakrzewski – Nature

Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats – Joseph P. Receveur – Microbial Ecology

Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system – Marina Ezcurra – Biogerontology

Plant, root, and soil microbiome

[pre print] Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ pre prints

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application – A. N. Naliukhin – Eurasian Soil Science

Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification – Jun Lou – PeerJ

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions – Alfonso Méndez-Bravo – PLOS ONE

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields – Xuhong Song – PLOS ONE

Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6 – Betina Cecilia Agaras – PLOS ONE

Water and extremophile microbiome

Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: a full-scale study – Joonyeob Lee – Bioresource Technology

Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities – Tiago R. Silva – Polar Biology

Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought – Debra A. Davis – Microorganisms

Diversity and assembly patterns of activated sludge microbial communities: A review – Yu Xia – Biotechnology Advances

Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide – Michal Sposob – Process Biochemistry

Metagenomic Exploration of Microbial Signatures on Periyar River Sediments from the Periyar Tiger Reserve in the Western Ghats – Aparna Chakkamadathil Rajeev – Genome Announcements

Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes – Ian Hewson – PLOS One

Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands – Xiao Huang – Water Research

Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting – Tatiana Robledo-Mahón – Journal of Environmental Management

* Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? – S. K. Schmidt – Antonie van Leeuwenhoek

Rapid alterations to marine microbiota communities following an oil spill – Brad J. Gemmell – Ecotoxicology

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica – Aritri Sanyal – Microbiological Research

Built environment

Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms – John A. Handley – Frontiers in Microbiology

Food microbiology

Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections – Anthony Opeyemi Ayeni – Journal of Dietary Supplements

Probiotics / prebiotics

Polyphenols’ Gut Microbiota Metabolites: Bioactives or Biomarkers? -Francisco A. Tomas-Barberan – Journal of Agriculture and Food Chemistry

* A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial – Nazarii Kobyliak – Journal of Gastrointestinal and Liver Diseases

Bioinformatics

Species classifier choice is a key consideration when analysing low-complexity food microbiome data – Aaron M. Walsh – Microbiome

Data and Statistical Methods To Analyze the Human Microbiome – Levi Waldron – mSystems

* Discovery of enzymes for toluene synthesis from anoxic microbial communities – Beller HR – Nature

Techniques

Community Assembly Processes of the Microbial Rare Biosphere – Xiu Jia – Trends in Microbiology

* Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration – Jing Cheng – Computational Systems Biology

[Patent] Spectrometric Analysis of Microbes – Zoltan Takats

* Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics – Stefan A. Boers – European Journal of Clinical Microbiology & Infectious Diseases

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle – Jair C. Ferreira – PLOS One

Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics – Casey M. Theriot – mSystems

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research – Nicole A. Hynson – mSystems

Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions – Jillian M. Petersen – mSystems

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies – Isabelle Laforest-Lapointe – mSystems

Microbes on the market 

DuPont Expands Microbiome Research Program, Adds Second Partnership with Fermentation Specialist

Science, publishing, and career

Biocodex Microbiota Foundation Awards Grants to Two Innovative Researchers in the Microbiome Field

Early-Career Systems Microbiology Scientists – Jack A. Gilbert – mSystems

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Self-employed people happier and more engaged at work, study finds

Health Care Spending in the United States and Other High-Income Countries

Ancient DNA Is Rewriting Human (and Neanderthal) History

Sturdy Insulator Made of Wood

How exercise in old age prevents the immune system from declining

March 20, 2018

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Still short and sweet. Highlights include combining bacterial and archaeal membranes, a reference catalog for the rumen microbiome and your gut microbiome keeping you awake at night, but really?

Jobs

Research Associate, Microbiology – Kintai Therapeutics – Cambridge, MA

Partners with relevant publications are needed – Faculty of Agriculture, Ain Shams University – Egypt

Biomedical Scientist or Trainee Biomedical Scientist (Microbiology) – York Teaching Hospital, UK

General microbiology

Identification of Biofilm Inhibitors by Screening Combinatorial Libraries of Metal Oxide Thin Films – Michal M. Dykas et al. – Applied Materials and Interfaces

** Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane – Antonella Caforio et al. – PNAS, USA

Press: Scientists engineer new life form with mixed Bacteria and Archaea membrane – Tibi Puiu – ZME Science

Preprint: Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling – Arnau Domenech et al. – bioRxiv

Animal microbiome

** Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection – Rekha Seshadri et al. – Nature Biotechnology

Press: A reference catalog for the rumen microbiome – Joint Genome Institute, DOE

Water and extremophile microbiome

Preprint: Growth arrest in the active rare biosphere – Bela Hausmann et al. – bioRxiv

Phages and viruses

Preprint: Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection – Maxine Zylberberg et al. -bioRxiv

Technology

Essay: Which experimental systems should we use for human microbiome science? – Angela E. Douglas – PLoS Biology

Preprint: Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior – Haitao Chen et al. – bioRxiv

Microbes in the news

Could the Microbiome Treat Side Effects of Stem Cell Transplants? – Alexander Burik – Labiotech

Rapid Starch Increases, Decreases in Horse Diets Upset Gut Microbiome – Kristen M. Janicki – the Horse

** Could it be your gut keeping you awake at night? – Kate Leaver – the Guardian

Molecular cuisine for gut bacteria – ScienceDaily

Bacteria churn out a million potential protein drugs – KATRINA KRÄMER – ChemistryWorld

Bacteria that can kill wild sheep and goats has never turned up in Alaska — until now – Zaz Hollander – Anchorage Daily News

News Bites: New molecule able to kill drug-resistant bacteria, FDA approves at-home breast cancer risk test – Chu Meiyi – MIMS Today

Non-antibiotic drugs promote antibiotic resistance – The Economist

Microbes on the market

Microbiome Therapeutics Market Overview with Qualitative analysis, Competitive landscape & Forecast 2023 – Healthcare Journal

March 15, 2018

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A few interesting articles in early life human microbiome, plus:
A comparison between Staphylococcus epidermidis commensal and pathogenic lineages from the skin of healthy individuals living in North American and India; A new tool to reconstruct microbial genome-scale metabolic models (GSMMs) from their genome sequence; The seasonal changes in Amazon rainforest soil microbiome are associated with changes in the canopy; A specific class of chemicals secreted by birds modulates their feather microbiome; chronic stress alters gut microbiota and triggers a specific immune response in a mouse model of colitis; and evidence that the short chain fatty acids profile in the gut reflects the impact of dietary fibre on the microbiome using the PolyFermS continuous intestinal fermentation model.

Pregnancy and early life

*Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium – Terhi Tapiainen – Pediatric Research

*Bifidobacterium longum subsp infantis CECT7210 supplemented formula reduces diarrhoea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research

*Gut microbiota in adolescents and the association with fatty liver: The EPOCH study – Maggie A Stanislawski – Pediatric Research

Review: Does Dysbiosis in Intestinal Microbiome Plays a Role in Children with Relapsing Idiopathic Nephrotic Syndrome? – Crespo-Salgado J. – American Journal of Nephrology

Gut Microbiota Dysbiosis in Children with Relapsing Idiopathic Nephrotic Syndrome – Tsuji S – American Journal of Nephrology

Human skin microbiome

*Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates – Shikha Sharma – Frontiers in Microbiology

Human oral microbiome

Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis – Misato Muro – Folia Microbiologica

Supragingival and subginival microbiota from patients with poor oral hygiene submitted to radiotherapy for head and neck cancer treatment – Elerson Gaetti-Jardim Jr – Archives of Oral Biology

Human nearly-sterile sites

PrePrint: Transcriptome analysis in whole blood reveals increased microbial 1 diversity in schizophrenia – Loes M Olde Loohuis – bioRxiv

Human gut microbiome

Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome – Pierre H. H. Schneeberger – Parasites and Vectors

FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects – Williams Turpin – Gut Microbes

Bacterial growth, flow, and mixing shape human gut microbiota density and composition – Markus Arnoldini – Gut Microbes

Complementary effects of cereal and pulse polyphenols and dietary fiber on chronic inflammation and gut health – Joseph M. Awika – Food & Function

Roseburia intestinalis alleviates experimental colitis pathology by inducing anti-inflammatory responses – Zhaohua Shen – Gastroenterology and Hepatology

Targeting gut microbiota in hepatocellular carcinoma: probiotics as a novel therapy – Murphy L. Y. Wan – Hepatobiliary Surgery and Nutrition

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients – Matthew K. Doherty – mBio

Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection
Kevin Rey – Transplantation

Review: Multiple hit infection and autoimmunity: the dysbiotic microbiota–ACPA connection in rheumatoid arthritis – Lazaros I Sakkas – Current Opinion in Rheumatology

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In vitro experiments

*Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS) – Sophie A. Poeker – Scientific Reports

Animal experiments

Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka – Cell Reports

Fructose liquid and solid formulations differently affect gut integrity, microbiota composition and related liver toxicity: a comparative in vivo study – Raffaella Mastrocola – Journal of Nutritional Biochemistry

NLRX1 Modulates Immunometabolic Mechanisms Controlling the Host–Gut Microbiota Interactions during Inflammatory Bowel Disease – Andrew Leber – Frontiers in Immunology

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota that Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice – Myreen E. Tomas – Antimicrobial Agents and Chemotherapy

The Lung Microbiota of Healthy Mice are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Interactions between stress and sex in microbial responses within the microbiota-gut-brain axis to stress in a mouse model – Matthew C.B. Tsilimigras – Psychosomatic Medicine

*Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response – Xinghua Gao – PNAS

Modulation of inflammatory arthritis by gut microbiota through mucosal inflammation and autoantibody generation – Widian K. Jubair – Arthritis & Rheumatology

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers – Helen M. Golder

Animal microbiome

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity – Kevin D. Kohl – Integrative Zoology

*Chemical regulation of body feather microbiota in a wild bird – Staffan Jacob – Molecular Ecology

Plant, root, and soil microbiome

Bacterial community changes in response to oil contamination and perennial crop cultivation – Lijuan Yan – Environmental Science and Pollution Research

Integrated network analysis reveals the importance of microbial interactions for maize growth – Jiemeng Tao – Applied Microbiology and Biotechnology

*Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology – Erika Buscardo – Scientific Reports

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant – Jitendra Keshridf – Applied Microbiology and Biotechnology

Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture – Linkun Wu – International Journal of Molecular Sciences

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions – Xiaoyun Wang – Microbial Biotechnology

Water and extremophile microbiome

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Microbial Ecology

Mycotoxin: Its Impact on Gut Health and Microbiota – Winnie-Pui-Pui Liew – Frontiers in Cellular and Infection Microbiology

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Probiotics / prebiotics

Effect of an Enterococcus faecium probiotic on specific IgA following live Salmonella Enteritidis vaccination of layer chickens – Breno C. B. Beirão – Avian Pathology

Effect of a Protein Supplement on the Gut Microbiota of Endurance Athletes: A Randomized, Controlled, Double-Blind Pilot Study – Diego Moreno-Pérez – Nutrients

Fecal Transplants

Fecal transplants in spondyloarthritis and uveitis: ready for a clinical trial? – Rene Y Choi – Current Opinion in Rheumatology

Phages and viruses

Together Forever: Bacterial–Viral Interactions in Infection and Immunity – Zhenda Shi – Viruses

Bioinformatics

*Towards predicting the environmental metabolome from metagenomics with a mechanistic model – Daniel R. Garza – Nature Microbiology

Phylogenetic convolutional neural networks in metagenomics – Diego Fioravanti – BMC Bioinformatics

Waste and Pollution

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Techniques

Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis – Jocelyn Sietsma Penington – Scientific Reports

Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay – J R Bowers – Medical Mycology

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March 14, 2018

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Today’s Digest adds to the growing literature of microbiome research. Highlights include the synergistic relationship between fungi and an invasive plant, enteral nutrition may help maintain the gastrointestinal function of critically ill patients, and the NCI calls for advancing epidemiologic research on the human microbiome.

Jobs

Student Trainee Microbiology Student Trainee Usda Pathways Internship Program Job in SAINT LOUIS, MO – Opening from 3/12-3/16, 2018

General microbiology

Antibiotic-induced population fluctuations and stochastic clearance of bacteria – Jessica Coates et al. – eLife

Press: Biophysicists discover how small populations of bacteria survive treatment – Science Daily

Preprint: Division of labor during biofilm matrix production – Anna Dragos et al. – bioRxiv

Isolation and characterization of two novel groups of kanamycin-resistance ColE1-like plasmids in Salmonella enterica serotypes from food animals – Chin-Yi Chen et al. – PLoS One

Human nasal microbiome

Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities – Yaqi You et al. – PLoS One

Human oral microbiome

In vitro: pH changes of mixed biofilms of Streptococcus mutans and Candida albicans after exposure to sucrose solutions in vitro – Thamires Priscila Cavazana et al. – Archives of Oral Biology

Human lung microbiome

Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis – Lisa A. Carmody et al. – PLoS One

Human gut microbiome

** Review: Effects of enteral nutrition on gastrointestinal function in patients who are critically ill – Michael Schörghuber and Sonja Fruhwald – The Lancet Gastroenterology & Hepatology

An overview on the interplay between nutraceuticals and gut microbiota – Adrian Catinean et al. – PeerJ

Animal experiments

Aronia berry (Aronia mitschurinii ‘Viking’) inhibits colitis in mice and inhibits T cell tumour necrosis factor-α secretion – Derek A. Martin et al. – Journal of Functional Foods

Mouse: Diet, Genetics, and the Gut Microbiome Drive Dynamic Changes in Plasma Metabolites – Shiho Fujisaka et al. – Cell Reports

Animal microbiome

Pathology and bacteria related to digital dermatitis in dairy cattle in all year round grazing system in Brazil – Tiago F. Moreira et al. – PLoS One

Food microbiology

The potential use of leaf extracts of two Newtonia (Fabaceae) species to treat diarrhoea – K.E. Motlhatlego et al. – South African Journal of Botany

Editorial: The interactions between food components and human nutrition – Charles Brennan – International Journal of Food Science & Technology

Plant, root and soil microbiome

** The unspecificity of the relationships between the invasive Pennisetum setaceum and mycorrhizal fungi may provide advantages during its establishment at semiarid Mediterranean sites – G. Rodríguez-Caballero et al. – Science of the Total Environment

Review: Environmental and public health related risk of veterinary zinc in pig production – Using Denmark as an example – John Jensen et al. – Environment International

Hydrophobins contribute to root colonization and stress responses in the rhizosphere-competent insect pathogenic fungus Beauveria bassiana – Soumya Moonjely et al. – Microbiology

Perspective: Tracing the role of human civilization in the globalization of plant pathogens – Alberto Santini et al. – ISME

Water and extremophile microbiome

Review: Surface water flooding, groundwater contamination, and enteric disease in developed countries: A scoping review of connections and consequences – L. Andrade et al. – Environmental Pollution

Domestic wastewater treatment and power generation in continuous flow air-cathode stacked microbial fuel cell: Effect of series and parallel configuration – Edson Baltazar Estrada-Arriaga et al. – Journal of Environmental Management

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches – Samuel P. Parker et al. – Ecosphere

Phages and viruses

Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India) – Vijayan Jasna et al. – PLoS One

Bioinformatics

A Bayesian Semiparametric Regression Model for Joint Analysis of Microbiome Data – Juhee Lee and Marilou Sison-Mangus – Frontiers in Microbiology

A systems pharmacology model for inflammatory bowel disease – Violeta Balbas-Martinez et al. – PLoS One

Microbes in the news

** Of Microbes and Men: Advancing Epidemiologic Research on the Human Microbiome – Victoria Fisher – National Cancer Institute

Opinion: Inflammatory bowel disease: complexity and variability need integration – Claudio Fiocchi – Frontiers in Medicine

Stress: How social conflict alters gut bacteria – Maria Cohut – Medical News Today

High-Fiber Generates Gut Bacteria Good for Type 2 Diabetes – Becky McCall – Medscape

New pathway may lead to improved probiotic products – Tim Lundeen – Feedstuffs

Probiotic potential: Specific gut microbes could cut severity of parasitic infections in developing countries – Nathan Gray – NUTRAingredients

Wandering Gut Bacteria Could Be Behind Conditions Like Lupus – Abby Norman – Futurism

Model Can Predict Which Bacteria will Engraft after FMT – Rachel Lutz – MD Magazine

Can Coral Microbes Protect Reefs From Climate Change? – Amelia Urry – NewsDeeply

Study: Several important vaginal metabolites elevated in smokers – Bob Kronemyer – Modern Medicine

Doctors collect viruses from pond and employ them to combat a man’s antibiotic resistance infection in man’s heart – Mark Kaufman – Mashable

Making good bacteria more resilient – Gali Weinreb – Globes

Study links decline of ‘good’ bacteria in infants to higher long-term increases in pH of poo – Tim Cutcliffe – NUTRAingredients

Microbes on the market

German biotech company wants to turn old PCs into gold – Jeremy Gray – Handelsblatt Global – European Business & Finance News

 

March 13, 2018

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In today’s digest it was quite hard to pick just few papers, since there are many, many interesting papers. From mentioned reviews I would recommend the one by H. Bokhari on the exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens and the one by J. R. Bober on engineering probiotics and microbes for biomedical applications. From other papers I would like to highlight the one by M. Mehrshad and enigmatic SAR202 cluster, the one by A. C. Lehours and biogeographic patterns of aerobic anoxygenic phototrophic bacteria and the one by E. M. Llufrio and how fluorescence activated cell sorting introduces oxidative stress and alters the metabolic state of cells. Don’t forget to check on news, where you can read about metagenomic clustering powered by supercomputers, while in general science section there is an interesting article by B. Barros on ‘scientific knowledge percolation process’ or how scientific information diffuse into the social sphere.

General microbiome

Review: Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens – Habib Bokhari – Critical Reviews in Microbiology

The aryl hydrocarbon receptor as a moderator of host-microbiota communication – Limin Zhang – Current Opinion in Toxicology

Pregnancy and early life

The Role of the Microbiome in the Developmental Origins of Health and Disease – Leah T. Stiemsma – Pediatrics

Human gut microbiome

 

Translocation of a gut pathobiont drives autoimmunity in mice and humans – S. Manfredo Vieira – Science

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome – Laura-Isobel McCall – PLOS One

How to Increase the Butyrate-Producing Capacity of the Gut Microbiome: Do IBD Patients Really Need Butyrate Replacement and Butyrogenic Therapy? – Stanislav Sitkin – Journal of Crohn’s and Colitis

Effect of Faecal Microbiota Transplantation for Treatment of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis of Cohort Studies – Tuo chen –  Journal of Crohn’s and Colitis

Animal experiments 

Supplementation of Bacillus subtilis based probiotic reduces heat stress-related behaviors and inflammatory response in broiler chickens – W C Wang – Journal of Animal Science

Comparisons of bacterial and Archaeal Communities in the Rumen and a Dual-Flow Continuous Culture Fermentation System using Amplicon Sequencing – I J Salfer – Journal of Animal Science

The Microbiome Regulates Pulmonary Responses to Ozone in Mice – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology

Bifidobacteria exert species-specific effects on constipation in BALB/c mice – Linlin Wang – Food & Function

Animal microbiome 

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing – Carmen Ventura – Current Microbiology

Metagenomic insights into lignocellulose-degrading genes through Illumina-based de novo sequencing of the microbiome in Vietnamese native goats’ rumen – Thi Huyen Do – The Journal of General and Applied Microbiology

Plant, root, and soil microbiome

Colonization of Eggplant by Endophytic Bacteria Antagonistic to Ralstonia solanacearum, the Bacterial Wilt Pathogen – Gauri A. Achari – Proceedings of the National Academy of Sciences, India Section B: Biological Sciences

Landscape scale factors affecting prevalence of Escherichia coli in surface soil include land cover type, edge interactions, and soil pH – Nicholas Dusek – Applied and Environmental Microbiology

Nigericin and grisorixin methyl ester from the Algerian soil-living Streptomyces youssoufiensis SF10 strain: a computational study on their epimeric structures and evaluation of glioblastoma stem cells growth inhibition – Nassima Leulmi – Natural Product Research

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification – Haifeng Qian – Pesticide Biochemistry and Physiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás  – Frontiers in Microbiology

Resveratrol as a growth substrate for bacteria from the rhizosphere – Zohre Kurt – Applied and Environmental Microbiology

Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits – Jonathan W. Leff – The ISME Journal

Diversity of microbial communities potentially involved in mercury methylation in rice paddies surrounding typical mercury mining areas in China – Xin Liu – Microbiology Open

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Volatile compounds from beneficial or pathogenic bacteria differentially regulate root exudation, transcription of iron transporters, and defense signaling pathways in Sorghum bicolor – Erasto Hernández-Calderón –  Plant Molecular Biology

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root–rhizosphere interactome – Etienne Yergeau – The ISME Journal

Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community – Xi-Hui Xu – Journal of Hazardous Materials

Water and extremophile microbiome 

Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes – Anne-Catherine Lehours – Scientific Report

Mercury-methylating bacteria are associated with zooplankton: a proof-of-principle survey in the Baltic Sea –  Elena Gorokhova – bioRxiv

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community – Laura Gómez-Consarnau – bioRxiv

Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows – Songlin Liu – Microbiology Open

Chapter 17 – Rhizosphere Metabolite Profiling: An Opportunity to Understand Plant-Microbe Interactions for Crop Improvement -Amit Verma – Crop Improvement Through Microbial Biotechnology

Chapter 22 – Plant-Microbe Interaction and Genome Sequencing: An Evolutionary Insight – Krishna K. Sharma – Crop Improvement Through Microbial Biotechnology

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management – Domenico Savio – Wiley Interdisciplinary Reviews: Water

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments – Kathleen M. Scott – Environmental Microbiology

Data Article: Bioinformatics delimitation based on sequence data of the psychrophilic and psychrotolerant actinobacteria isolated from the Polar Frontal waters of the Antarctic Ocean – Palaniappan Sivasankar – Data in Brief

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity – Kai Tang – Frontiers in Microbiology

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling – Maliheh Mehrshad – The ISME Journal

The widespread dissemination of integrons throughout bacterial communities in a riverine system – Gregory C. A. Amos – The ISME Journal

Expression profiling of host and virus during a coccolithophore bloom provides insights into the role of viral infection in promoting carbon export – Uri Sheyn – The ISME Journal

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations – Sarahi L. Garcia – The ISME Journal

Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota – Lin-Xing Chen – The ISME Journal

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases – Andrea G. Bravo – The ISME Journal

Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef  – Michael P. Lesser – The ISME Journal

Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. – Mikhail A. Moldovan – Frontiers in Microbiology

Halotolerant Exiguobacterium profundum PHM11 Tolerate Salinity by Accumulating L-Proline and Fine-Tuning Gene Expression Profiles of Related Metabolic Pathways – Vikas K. Patel – Frontiers in Microbiology

The predictability of a lake phytoplankton community, over time-scales of hours to years – Mridul K. Thomas – Ecology Letters

Built environment

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting – Tingting Wang – Journal of Microbiology and Biotechnology

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems – Krishnaveni Venkidusamy – Frontiers in Microbiology

Inhibitors degradation and microbial response during continuous anaerobic conversion of hydrothermal liquefaction wastewater – Buchun Sia – Science of The Total Environment

Food microbiology

Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation – Francesca De Filippis – Food Microbiology

Staphylococcus aureus undergoes major transcriptional reorganization during growth with Enterococcus faecalis in milk – Gabriela NogueiraViçosa – Food Microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts – Food Microbiology

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Qian Li – Food Microbiology

Microbial diversity and chemical analysis of the starters used in traditional Chinese sweet rice wine – Haiying Cai –  Food Microbiology

Structure of association networks in food bacterial communities – Eugenio Parente – Food Microbiology

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures – Ganyu Gu – Food Microbiology

Probiotics / prebiotics

Effective identification of Lactobacillus casei group species: genome-based selection of the gene mutL as the target of a novel multiplex PCR assay – Benedetta Bottari – Microbiology

Phages and viruses

A Holistic Assessment of the Risks and Benefits of the Synthesis of Horsepox Virus – Diane Di Euliis – mSphere

Biotechnology

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song – Bioresource Technology

Review: Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications – Josef R. Bober – Annual Review of Biomedical Engineering

Techniques

Sorting Cells Alters Their Redox State and Cellular Metabolome – Elizabeth M. Llufrio – Redox Biology

Microbes in the news 

Ibuprofen Counters Key Bacteria in Lungs of CF Patients, Study Shows

Bacteria in your intestines can trigger autoimmune diseases

A game changer: Metagenomic clustering powered by supercomputers

Science, publishing, and career

Scientific knowledge percolation process and social impact: a case study on the biotechnology and microbiology perceptions on Twitter – Beatriz Barros – Science and Public Policy

March 12, 2018

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Today we have  interesting reviews by Thomas S.B. about gut microbiome and by F. Newberry about microbiome and virome contribution to myalgic encephalomyelitis/chronic fatigue syndrome. Another highlight for viruses is a commentary by Y.Z. Zhang on how metagenomics has changed our understanding of RNA viruses. Check these recommendations as well as many other articles in today’s digest.

General microbiome

Analysis: Microbiome Research in a Social World – Diana Crow – Cell

Commentary: The Past and Future Biology of the Human Microbiome in an Age of Extinctions – Martin J. Blaser – Cell

Perspective: Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life – Cindy J. Castelle – Cell

Review: The Biology of CRISPR-Cas: Backward and Forward – Frank Hille – Cell

Human skin microbiome

The Microbiome in Dermatology – Shenara Musthaq – Clinics in Dermatology

Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process – Hye-Jin Kim – Science Advances

Human nearly-sterile sites 

Review: Altered microbiome in chronic kidney disease: systemic effects of gut-derived uremic toxins – Wei Ling Lau – Clinical Science

Human urinary microbiome

Microbial metagenome of urinary tract infection – Ahmed Moustafa – Scientific Reports

Human gut microbiome

Neuroinflammation, Gut Microbiome, and Alzheimer’s Disease – Li Lin – Molecular Neurobiology

Gut microbiota and its implications in small bowel transplantation – Chenyang Wang – Frontiers of Medicine

Festschrift for Ronan O’Connell: pouchitis, ulcerative colitis and the microbiome – Aonghus Lavelle – Irish Journal of Medical Science (1971 -)

Lipid nanoparticles to counteract gastric infection without affecting gut microbiota – Catarina Leal Seabraa – European Journal of Pharmaceutics and Biopharmaceutics

Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children – Xingcui Wanga – International Immunopharmacology

Gut Microbiota Signature in Heart Failure Defined From Profiling of 2 Independent Cohorts – Martin Kummen – Journal of the American College of Cardiology

Toxin profile of fecal Clostridium perfringens strains isolated from children with autism spectrum disorders – Góra Bartłomiej – Anaerobe

Exploration of fecal microbiota transplantation in the treatment of refractory diarrhea after renal transplantation  – Bo Gu – Transplantation Proceedings

Review: The Human Gut Microbiome: From Association to Modulation – Thomas S.B. Schmidt – Cell

Animal experiments

Gut microbiota mediates diurnal variation of acetaminophen induced acute liver injury in mice – Shenhai Gong – Journal of Hepatology

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches – Ramesh J. Pandit – Systematic and Applied Microbiology

Animal microbiome 

Understanding the Intestinal Microbiome in Health and Disease – Marcio Carvalho Costa – Veterinary Clinics of North America: Equine Practice

The association between gut microbiome, sex, age and body condition scores of horses in Maiduguri and its environs – Esther Solomon Mshelia – Microbial Pathogenesis

Plant, root, and soil microbiome

Phenolic compounds as antioxidants and chemopreventive drugs from Streptomyces cellulosae strain TES17 isolated from rhizosphere of Camellia sinensis – Riveka Rani – Microbiome

A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant – Katherine Lavelle – Applied and Environmental Microbiology

Simultaneous application of two herbicides and green compost in a field experiment: Implications on soil microbial community – C. García-Delgado – Applied Soil Ecology

Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century – Mikhail V. Semenov – Applied Soil Ecology

Water and extremophile microbiome

Brief Communication: Potential for primary productivity in a globally-distributed bacterial phototroph – E. D. Graham – The ISME Journal

Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae – Melissa Y Chen – Molecular Ecology

The sponge holobiont in a changing ocean: from microbes to ecosystems – L. Pita – Microbiome

Microbiome dynamics in a large artificial seawater aquarium – Nastassia V. Patin – Applied and Environmental Microbiology

Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria – Isabelle Raymond-Bouchard – FEMS Microbiology Ecology

Built environment

Phenol removal performance and microbial community shift during pH shock in a moving bed biofilm reactor (MBBR) – Hao Zhou – Journal of Hazardous Materials

Evaluation of process performance, energy consumption and microbiota characterization in a ceramic membrane bioreactor for ex-situ biomethanation of H2 and CO2 – Natalia Alfaro – Bioresource Technology

Food microbiology

Assessing the functionality and genetic diversity of lactococcal prophages – Philip Kelleher – International Journal of Food Microbiology

The bacterial biota of laboratory-reared edible mealworms (Tenebrio molitor L.): From feed to frass – Andrea Osimani – International Journal of Food Microbiology

Phages and viruses

Review: Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? – Fiona Newberry –  Clinical Science

Commentary: Using Metagenomics to Characterize an Expanding Virosphere – Yong-Zhen Zhang – Cell

Techniques

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga

Microbes in the news 

Virus from a pond treats man with antibiotic-resistant infection

Manipulating gut microbes may reduce intestinal parasitic infections

Study Shows Gut Bacteria Can Spread to Other Organs And Trigger Disease

Social stress leads to changes in gut bacteria

Could Our Gut Be the Source of a New Generation of Drugs?

Microbes and art

This watercolour painting was created by artistic bacteria

 

March 11, 2018

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Events and jobs

EVEN seminar: Weakest link in water quality control: Drinking water biofilm in premise plumbing – INSTAAR, CU Boulder

General microbiome

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes – Aura Ferreiro, Cell

Egalitarianism in Biofilms – Dawen Gao, Microbial Ecology

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds – Hui Wang, Frontiers in Microbiology

Human multi-site microbiome

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis – Raphaël Enaud, Microorganisms

Human gut microbiome

Gut Microbiota Alteration After Long-Term Consumption of Probiotics in the Elderly – Renyuan Gao, Probiotics and Antimicrobial Proteins

Sex differences in gut microbiota in patients with major depressive disorder – Chen JJ, Neuropsychiatric Disease and Treatment

Oral microbiome

Influence of periodontal treatment on subgingival and salivary microbiotas – Daniel Belstrøm, Journal of Periodontology

Microbiome at sites of gingival recession in children with Hutchinson–Gilford progeria syndrome – Seyed Hossein Bassir, Journal of Periodontology

Subgingival microbial profile of obese women with periodontal disease – Carina M. Silva-Boghossian, Journal of Periodontology

Animal experiments

The effect of probiotics and polysaccharides on the gut microbiota composition and function of weaned rats – Mengxia Wang, Food and Function

Cecal Versus Fecal Microbiota in Ossabaw Swine and Implications for Obesity – Matthew R Panasevich, Physiological Genomics

Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets – Kan Gao, Journal of Neurochemistry

Animal microbiome

Nutrient factories: Metabolic function of beneficial microorganisms associated with insects – Nana Y. D. Ankrah, Environmental Microbiology

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla) – Wei Huang, Applied Microbiology and Biotechnology

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs – Brandon J. Varela, Frontiers in Microbiology

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota – Na Zhao, Frontiers in Cellular and Infectious Microbiology

Plant, root, and soil microbiome

The Soil-Borne Legacy – Peter A.H.M. Bakker, Cell

Water and extremophile microbiome

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic – Omar Federico Ordoñez, Microbial Ecology

Occurrence of Legionella in Nonpotable Reclaimed Water – William J. Johnson, American Water Works Association

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China – Haihan Zhang, International Journal of Environmental Research and Public Health

Food microbiome

Microbial community and physicochemical dynamics during the production of ‘Chicha’, a traditional beverage of Indigenous people of Brazil – Ludmila Vilela Resende, World Journal of Microbiology and Biotechnology

Techniques

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton – Emma K. Wear, Environmental Microbiology

Microbes in the news

Pitting Viruses Against Bacteria To Combat The Antibiotic Crisis – SciFri

March 10, 2018

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Many interesting perspectives from a recent mSystems issue, along with plenty of plant/soil articles!

Events and jobs
Group Leader R&D | (Microbiology/Biomarkers), 8685 – Stratacuity: Proven Scientific Placement  Company – Boston, Massachusetts

General microbiome
Preprint: Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – bioRxiv

Preprint/Review: Host genetics and microbiome associations from the lens of genome wide association studies – Omer Weissbrod – PeerJ

Review: Studying microbial functionality within the gut ecosystem by systems biology – Bastian Hornung – BMC Genes and Nutrition

Perspective: Making Millennial Medicine More Meta – Peter J. Turnbaugh – MSystems

Perspective: Spatial Analyses of Specialized Metabolites: The Key to Studying Function in Hosts – Melissa M. Galey – MSystems

Pregnancy and early life
Development of the Human Mycobiome over the First Month of Life and across Body Sites – Tonya L. Ward – mSystems

The potential of gut microbiota and fecal volatile organic compounds analysis as early diagnostic biomarker for necrotizing enterocolitis and sepsis in preterm infants – Daniel Johannes Cornelis Berkhout – Expert Review of Gastroenterology & Hepatology

Review: Factors Affecting the Immunity to Respiratory Syncytial Virus: From Epigenetics to Microbiome. – Wendy Fonseca – Frontiers In Immunology

Human respiratory microbiome
The Nasal Microbiome in Asthma. – Mina Fazlollahi – The Journal Of Allergy And Clinical Immunology

Human oral microbiome
Review: Metatranscriptome of the Oral Microbiome in Health and Disease. – J Solbiati – Journal Of Dental Research

Human vaginal microbiome
The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case control study – Jacob D Pierson – Pathogens and Disease

Human gut microbiome
Preprint: Gut microbiota density influences host physiology and is shaped by host and microbial factors – Eduardo Contijoch – bioRxiv

Review: Gender Differences in the Gut Microbiome and How These Affect Cardiovascular Diseases – Adriana Cabal – Gender Differences in the Pathogenesis and Management of Heart Disease

Microbial ecology
Perspective: A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology – Kevin D. Kohl – mSystems

Animal experiments
Rapid environmental effects on gut nematode susceptibility in rewilded mice. – Jacqueline M Leung – Plos Biology

Calcineurin B in CD4+ T Cells Prevents Autoimmune Colitis by Negatively Regulating the JAK/STAT Pathway – Andrea Mencarelli – Frontiers In Immunology

Green tea extract and black tea extract differentially influence cecal levels of short-chain fatty acids in rats – Tomonori Unno – Food Science and Nutrition

Animal microbiome
Detailed ecological associations of triatomines revealed by metabarcoding and next-generation sequencing: implications for triatomine behavior and Trypanosoma cruzi transmission cycles. – Eric Dumonteil – Scientific Reports

Comparative Metagenomic Profiling of Viromes Associated with Four Common Mosquito Species in China – Han Xia – Virologica Sinica

Preprint: Two novel strains of Torulaspora delbrueckii isolated from the honey bee microbiome and their use in honey fermentation – Joseph P. Barry – bioRxiv

16S rRNA metagenomic analysis of the symbiotic community structures of bacteria in foregut, midgut, and hindgut of the wood-feeding termite Bulbitermes sp. – Yue Ming Chew – Symbiosis

Plant, root, and soil microbiome
Towards a Natural History of Soil Bacterial Communities – Jennifer B.H. Martiny – Trends in Microbiology

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. – Binu M Tripathi – The Isme Journal

Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil – Kelly Campos Guerra Pinheiro de Goes – Brazilian Journal of Microbiology

Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity – Ulas Karaoz – mBio

Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome – Dmitri Mavrodi – Frontiers in Plant Science

Specialized core bacteria associate with plants adapted to adverse environment with high calcium contents. – Fei Li – Plos One

Diversity of the Bacterial Microbiome in the Roots of Four Saccharum Species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers In Microbiology

Long-Term Harvest Residue Retention Could Decrease Soil Bacterial Diversities Probably Due to Favouring Oligotrophic Lineages – Yaling Zhang – Microbial Ecology

Trichoderma-Inoculated Miscanthus Straw Can Replace Peat in Strawberry Cultivation, with Beneficial Effects on Disease Control – Jane Debode – Frontiers In Plant Science

Heterologous Expression of Secreted Bacterial BPP and HAP Phytases in Plants Stimulates – Lia R Valeeva – Frontiers In Plant Science

Perspective: Metabolomics and Agriculture: What Can Be Done? – Rodolpho Martin do Prado – MSystems

Perspective: Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology – Marnix H. Medema – mSystems

Soil Inoculation with Bacillus spp. Modifies Root Endophytic Bacterial Diversity, Evenness, and Community Composition in a Context-Specific Manner – Kiran R. Gadhave – Microbial Ecology

Book: Advances in Soil Microbiology: Recent Trends and Future Prospects – Tapan Kumar Adhya:
Many chapters may be of interest, including:

Water and extremophile microbiome
Persistent nitrogen limitation of stream biofilm communities along climate gradients in the arctic. – Maria Myrstener – Global Change Biology

Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding – Rippin Martin – FEMS Microbiology Ecology

Archaeal community compositions in tilapia pond systems and their influencing factors – Limin Fan – World Journal of Microbiology and Biotechnology

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. – Rafael R C Cuadrat – Frontiers In Microbiology

Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands – Kaarle J. Parikka – Polar Biology

An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies – Riley E. Steele – Microbial Ecology

Built environment
The classroom microbiome and asthma morbidity in children attending three inner-city schools. – Peggy S Lai – The Journal Of Allergy And Clinical Immunology

Decomposition of lignocellulose and readily degradable carbohydrates during sewage sludge biodrying, insights of the potential role of microorganisms from a metagenomic analysis – Lu Cai – Chemosphere

Illumina MiSeq Sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates – Xuehui Xie – Chemosphere

Food microbiology
An Ultrahigh-Performance Liquid Chromatography-Time-of-Flight Mass Spectrometry Metabolomic Approach to Studying the Impact of Moderate Red-Wine Consumption on Urinary Metabolome – Adelaida Esteban-Fernández – Journal of Proteome Research

Probiotics / prebiotics / antibiotics
Fate of antibiotic and metal resistance genes during two-phase anaerobic digestion of residue sludge revealed by metagenomic approach. – V Richarte – Environmental Science And Pollution Research International

Intra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential. – Jason W Arnold – Frontiers In Microbiology

Phages and viruses
Deciphering the Human Virome with Single-Virus Genomics and Metagenomics – Maria José de la Cruz Peña – Viruses

Urinary Virome perturbations in kidney transplantation – Neil Mercer – Frontiers in Microbiology

Preprint: Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity – Mariann Landsberger – bioRxiv

Preprint: Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity – Adair L Borges – bioRxiv

Bioinformatics
From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool – Simone Rampelli – Viral Metagenomics

Techniques
Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion. – Diane Plouchart – Plos One

Review: Electrochemical Probes of Microbial Community Behavior – Hunter J. Sismaet – Annual Review of Analytical Chemistry

Antibiotic-Responsive Bioart: Exploring DIYbio as a Design Studio Practice – Stacey Kuznetsov – ACM

Microbes in the news
Four stories of antibacterial breakthroughs – Natasha Gilbert – Nature

How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

Hacking a Cow’s Gut Bacteria Could Make More Meat, Less Pollution – Chelsea Gohd – Futurism

High-Fiber Diet Shifts Gut Microbes, Lowering Blood Sugar in Diabetics – Ashley Yeager – The Scientist

March 9, 2018

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Have a nice Friday! Today we have interesting papers about nasal/oral microbiota, some papers about studies in pathogens (including the use of bacteriophages for selective inhibition of E. coli), DNA extraction studies in meconium, and more!

 

Human/General Microbiome

Review: Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease – Carmela Cosola – Pharmacological Research

Predictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicine – Christina Kraniotou – Journal of Proteomics

The Nasal Microbiome in Asthma – Mina Fazlollahi – Journal of Allergy and Clinical Immunology

Metatranscriptome of the Oral Microbiome in Health and Disease – J. Solbiati – Journal of Dental Research

Nasal Microbiota and Respiratory Tract Infections: The Role of Viral Detection – Insa Korten – American Journal of Respiratory and Critical Care Medicine

Short term dynamics of the sputum microbiome among COPD patients – Rohita Sinha – Plos One

The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study – Ravi Jain – International Forum of Allergy & Rhinology

The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV – Mara Farcasanu – Current HIV/AIDS Reports

Emerging Mechanisms of Innate Immunity and Their Translational Potential in Inflammatory Bowel Disease – Daniele Corridoni – Frontiers in Medicine

Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital – Victoria C. Ewan – Frontiers In Cellular And Infection Microbiology

Influence of Intestinal Indigenous Microbiota on Intrafamilial Infection by Helicobacter pylori in Japan – Takako Osaki – Frontiers in Immunology

Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies – Lisa F. Stinson – Frontiers in Microbiology

Minireview: Gut Microbiota: An Integral Moderator in Health and Disease – Qingqing Feng –   Frontiers in Microbiology

Activation of Notch-1 in oral epithelial cells by P. gingivalis triggers the expression of the antimicrobial protein PLA2-IIA – Ahmad Al-Attar – Mucosal Immunology

Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis – Jasmohan S. Bajaj –  JCI Insight

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting – Edward T. Morgan – Drug Metabolism and Disposition

 

Pathogen Research

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota – Tomasz Cieplak – Gut Microbes

Triclosan Enhances the Clearing of Pathogenic Intracellular Salmonella or Candida albicans but Disturbs the Intestinal Microbiota through mTOR-Independent Autophagy – Chao Wang – Frontiers In Cellular And Infection Microbiology

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung – Izabela Galvão – Frontiers in Immunology

Parasite-Vector Interaction of Chagas Disease: A Mini-Review – Ana Beatriz Bortolozo de Oliveira – The American Journal of Tropical Medicine and Hygiene – Current Issue

Bacillus subtilis spore with surface display of paramyosin from Clonorchis sinensis potentializes a promising oral vaccine candidate – Hengchang Sun – Parasites & Vectors

 

Animal Microbiome

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata – Antonino Malacrinò – Plos One

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates – Tasha Barr – Gut Microbes

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression – Wenfang Dai – Applied Microbiology And Biotechnology

Intestinal bacterial signatures of white feces syndrome in shrimp – Dongwei Hou – Applied Microbiology And Biotechnology

Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice – Shoji Yamada – Oncotarget

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

Physiological mechanisms of sustained fumagillin-induced weight loss – Jie An – JCI Insight

Gpr109a Limits Microbiota-Induced IL-23 Production To Constrain ILC3-Mediated Colonic Inflammation – Brinda Bhatt – The Journal in Immunology

Fuzhuan brick tea polysaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with modulation in the gut microbiota – Guijie Chen – Journal Of Agricultural And Food Chemistry

 

Extremophiles

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

 

Plant Microbiome

Disease-induced assemblage of a plant-beneficial bacterial consortium – Roeland L. Berendsen – The ISME Journal

March 7, 2018

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Human Microbiome

The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome: Results From a Randomized Crossover Intervention Study – Mette Schmedes – Molecular Nutrition & Food Research

Addendum – Invited: Gut Microbiota in Toxicological Risk Assessment of Drugs and Chemicals: The Need of Hour – Ganesan Velmurugan – Gut Microbes

Effects of different thickening agents on infant gut microbiota – C. A. González-Bermúdez – Food & Function

The Impact of Laparoscopic Sleeve Gastrectomy with Duodenojejunal Bypass on Intestinal Microbiota Differs from that of Laparoscopic Sleeve Gastrectomy in Japanese Patients with Obesity – Rieko Kikuchi – Clinical Drug Investigation

Perspective: Precision antimicrobial therapeutics: the path of least resistance? – Caitlin N. Spaulding – npj Biofilms and Microbiomes

Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes – Tyler J. Carrier – Nature Communications

Case report: Successful faecal microbiota transplant for recurrent Clostridium difficile infection delivered by colonoscopy through a diverted ileostomy in a patient with severe perianal Crohn’s disease – Jonathan Digby-Bell – BMJ Case Reports

Outlook: How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

Correspondence: Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis: a role for bifidobacteria and lactobacilli? – Borja Sánchez – Nature Reviews Gastroenterology & Hepatology

Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples – Roshonda B. Jones – Scientific Reports

Review: Gastrointestinal toxicity of immune checkpoint inhibitors: from mechanisms to management – Mark A. Samaan – Nature Reviews Gastroenterology & Hepatology

Reply: Probiotics, bile acids and gastrointestinal carcinogenesis – Wei Jia – Nature Reviews Gastroenterology & Hepatology

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid – Philipp Kirstahler – Scientific Reports

 

Animal microbiome

Performance, egg quality, nutrient digestibility, and excreta microbiota shedding in laying hens fed corn-soybean-meal-wheat-based diets supplemented with xylanase – X. J. Lei – Poultry Science

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources – Simona Rimoldi – Plos One

Sugary Kefir Strain Lactobacillus mali APS1 Ameliorated Hepatic Steatosis by Regulation of SIRT-1/Nrf-2 and Gut Microbiota in Rats – Yung-Tsung Chen – Molecular Nutrition & Food Research

Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice – Jacob E. Friedman – Hepatology Communications

Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats – Qian Zhang​ – PeerJ

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut – Aaron C. Ericsson – Scientific Reports

News & Views: The intestinal microbiome influences checkpoint blockade – Cynthia L Sears – Nature Medicine

News Feature: Gut checkpoint: A rising cancer treatment may get a boost from intestinal bacteria – Anna Azvolinsky – Nature Medicine

Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome – Yi Hu – Nature Communications

Research Highlight: Comparative genomics: Blood, guts and vampire bats – Linda Koch – Nature Reviews Genetics

 

Pathogen research

Serial Clustering of Late Onset Group B Streptococcal Infections in the Neonatal Unit – a Genomic Re-Evaluation of Causality – Elita Jauneikaite – Clinical Infectious Diseases

A multi-omic analysis reveals the role of fumarate in regulating the virulence of enterohemorrhagic Escherichia coli – Cheng-Ju Kuo – Cell Death & Disease

Occurrence of blaNDM Variants Among Enterobacteriaceae From a Neonatal Intensive Care Unit in a Northern India Hospital – Nayeem Ahmad – Frontiers in Microbiology

 

Food Microbes

Lactobacillus rossiae strain isolated from sourdough produces putrescine from arginine – Beatriz del Rio – Scientific Reports

 

Environmental Microbiology

Microbial diversity associated to the anaerobic sediments of a soda lake (Mono Lake, CA) – Patricia Rojas – Canadian Journal of Microbiology