February 15, 2018

An especially interesting article on engineered bacteria in the treatment of colon cancer today: Chun Loong Ho and colleagues engineered an E. coli strain to bind to colon cancer cells and constitutively secrete an enzyme that can turn dietary derived glucosinolates (from cruciferous vegetables) into cancer fighting isothiocynates. Mice exposed to carcinogens and fed both the engineered bacteria and broccoli developed fewer and smaller colorectal tumors than exposed mice who were fed 1) neither bacteria or brocoli, 2) only bacteria, or 3) only broccoli.  Engineered probiotics anyone?

Also : A cultured community developed from wastewater that can reduce the greenhouse gas N2O to Nand help mitigate global warming; the majority of Daphnia microbiomes are not passed from parent to offspring but absorbed from the surrounding environment; and the impacts of CRISPR-Cas9 selection pressure on phage evolution.

Events and jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

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General microbiome

Review: The genome, microbiome and evolutionary medicine – Robert C. Brunham – cmaj

Pregnancy and early life

Survey of Staphylococcus aureus in a general pediatric population and focus on isolates with three clinically relevant toxin-encoding genes – Anne Filleron – World Journal of Pediatrics

Human skin microbiome

Review: Impact of Skin Microbiome on Attractiveness to Arthropod Vectors and Pathogen Transmission – Niels O. Verhulst – Skin and Arthropod Vectors

Human gut microbiome

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers – Xi Mei Zhang – Biomedical and Environmental Sciences

The microbiome in chronic kidney disease patients undergoing hemodialysis and peritoneal dialysis – Liliana Simões-Silva – Pharmacological Research

Review: Intestinal Microbiome Shifts, Dysbiosis, Inflammation, and Non-alcoholic Fatty Liver Disease – Emma T. Saltzman – Frontiers in Microbiology

Does Low-Protein Diet Influence the Uremic Toxin Serum Levels From the Gut Microbiota in Nondialysis Chronic Kidney Disease Patients? – Ana Paula Black – Journal of Renal Nutrition

The Effect of Oligofructose-Enriched Inulin on Faecal Bacterial Counts and Microbiota-Associated Characteristics in Celiac Disease Children Following a Gluten-Free Diet: Results of a Randomized, Placebo-Controlled Trial – Natalia Drabińska – Nutrients

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo – bioRxiv

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Animal experiments

Influence of Eimeria falciformis Infection on Gut Microbiota and Metabolic Pathways in Mice – Guangping Huang – Infection and Immunity

The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance – Teizo Yoshimura – The Journal of Immunology

Animal microbiome

*Good Daphnia parents do not control the offspring microbiome – Angela E. Douglas – Journal of Animal Ecology

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens – Sanjay Kumar – PLOSone

Review: The Microbial Zoo in the C. elegans Intestine: Bacteria, Fungi and Viruses – Hongbing Jiang – Viruses

Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes – Isabel S. Keller – Evolution

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats – Guido Bonthond – PeerJ

Effect of ginkgo extract supplementation on in vitro rumen fermentation and bacterial profiles under different dietary conditions – Seongjin Oh – Animal Science Journal

Review: Animal host–microbe interactions – Bethany J. Hoye – Journal of Animal Ecology

Plant, root, and soil microbiome

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium – Xin Wang – Journal of Soils and Sediments

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters – Emine Gozde Ozbayram – Microorganisms

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community – Felix Moronta-Barrios – Microorganisms

Water and extremophile microbiome

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro – The ISME Journal

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea – Jin Zhou – Microbial Ecology

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea – Yuzhi Wu – Extremophiles

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system – Caroline Souffreau – Environmental Microbiology

Chemical and Microbial Quality of Groundwater in Siloam Village, Implications to Human Health and Sources of Contamination – John Ogony Odiyo – International Journal of Environmental Research and Public Health

Microbial Ecology

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies – Mari Pent – Environmental Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Resistome

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes – Wenguang Xiong – BMC Microbiome

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Probiotics / prebiotics

Effect of VSL#3 Probiotic in a Patient with Glycogen Storage Disease Type Ia and Irritable Bowel Disease-like Disease – Miguel Carnero-Gregorio – Probiotics and Antimicrobial Proteins

New Insight into Biofilm Formation Ability, the Presence of Virulence Genes and Probiotic Potential of Enterococcus sp. Dairy Isolates – Nikola Popović – Frontiers in Microbiology

Effectiveness and Safety of a Probiotic-Mixture for the Treatment of Infantile Colic: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial with Fecal Real-Time PCR and NMR-Based Metabolomics Analysis – Maria Elisabetta Baldassarre – Nutrients

Fecal Microbiome Transplants

Long-term follow-up of the effects of fecal microbiota transplantation in combination with soluble dietary fiber as a therapeutic regimen in slow transit constipation – Xueying Zhang – Science China Life Sciences

Bioinformatics

Identification of fungi in shotgun metagenomics datasets – Paul D. Donovan – PLOSone

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies – Ahmed A. Metwally – BMC Microbiome

Biotechnology

*Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention – Chun Loong Ho – Nature Biomedical Engineering

*Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 – Pan Tao – Science Advances

Waste and Pollution

*Life on N2O: deciphering the ecophysiology of N2O respiring bacterial communities in a continuous culture – Monica Conthe – The ISME Journal

Metagenomic analysis of microbial community and function involved in cd-contaminated soil – Gang Feng – BMC Microbiology

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Microbes in the news

Humpback microbiome linked to seasonal, environmental changes – Phys.org

 

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February 8, 2018

Many interesting articles today: the geographical location of habitat has a stronger impact on the fecal microbiome of lemurs than sex, age, or species;  the mechanism for pathobiont-dependent inflammatory bowel disease involves microbiota reactive T cells; highly active antiretroviral therapy can restore gut microbiome diversity in AIDS patients; host immunity can interact with skin microbiota composition as shown in two species of giant salamander; the development of the small intestine microbiome in silka deer; and the gut microbiome of preterm infants that are breastfed develops normally.

Events and jobs

FEMS Project: Volunteer for the Opportunities Board Taskforce

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General microbiome

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists – A. B. F. Ivens – Molecular Ecology

Pregnancy and early life

Maternal antibiotic exposure during pregnancy and hospitalization with infection in offspring: a population-based cohort study – Jessica Eden Miller – International Journal of Epidemiology

*Intestinal microbiota development and gestational age in preterm neonates – Katri Korpela – Scientific Reports

Human oral microbiome

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population – Gao, Xiaowei MM – Medicine

Human vaginal microbiome

Commentary: The implausible “in vivo” role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota – Gilda Tachedjian – Microbiome

Human gut microbiome

Microbiome–host systems interactions: Protective effects of propionate upon the blood–brain barrier – Lesley Hoyles – bioRxiv

*Alterations in the gut microbiota of patients with acquired immune deficiency syndrome – Youlian Zhou – Journal of Cellular and Molecular Medicine

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons – Amy Wallis – Microbiome

Review: Diet and microbiota linked in health and disease  – T. Requena – Food And Function

Review: The role of gut microbiota and IL-23/IL-17 pathway in ankylosing spondylitis immunopathogenesis: New insights and updates – Farhad Babaie – Immunology Letters

Dissertation: Interaction of Cocoa Powder with Intestinal Microbiota – Zuyin Li – Louisiana State University


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Animal experiments

*c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont – Mo Xu – Nature

Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity – Prasant Kumar Jena – The FASEB Journal

High-fat diet stimulates the gut pathogenic microbiota and maintains hepatic injury in antibiotic-treated rats – Sooad Al-Daihan – Cellular and Molecular Biology

Review: Searching for the gut microbial contributing factors to social behavior in rodent models – Brittany D. Needham – Developmental Neurobiology

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria – Evelyne Mann – Frontiers in Microbiology


Animal microbiome

*Occupancy strongly influences faecal microbial composition of wild lemurs – Alexander Umanets – FEMS Microbiology Ecology

*Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders – Obed Hernández-Gómez – Molecular Ecology

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities – Christine P. Zolnik – Tick and Tick-borne Diseases

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning – Zhipeng Li – Frontiers in Microbiology

Exploring coral microbiome assemblages in the South China Sea – Lin Cai – Scientific Reports

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea – Esther Rubio-Portillo – Frontiers in Microbiology

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties – Elodie Denet – PLOSone

Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.) – Xiaofeng Xia – Frontiers in Microbiology

Effects of predation stress and food ration on perch gut microbiota – Yinghua Zha – Microbiome

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability – Jason A. Rothman – Microbial Ecology


Plant, root, and soil microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain – Yu Shi – Microbiome

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities – Li Zhaolei – Ecotoxicology and Environmental Safety

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils – Mira Mutschlechner – FEMS Microbiology Ecology

Diversity and metabolic potential of the microbiota associated with a soil arthropod – Simon Bahrndorff – Scientific Reports

Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China – Jia Liu – Journal of Soils and Sediments

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate – Larisa Cortes-Tolalpa – Applied Microbiology and Biotechnology

Commentary: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Review: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? – Christina Hazard – New Phytologist

Review: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection


Water and extremophile microbiome

Ultra-rare marine microbes contribute to key sulfur related ecosystem functions – Dimitri Kalenitchenko – Molecular Ecology

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea – Keon Hee Kim – Applied Biological Chemistry

Built environment

Airborne microbial communities in the atmospheric environment of urban hospitals in China – Xin-Lei Gao – Journal of Hazardous Materials


Food microbiology

Effects of chitosan oligosaccharides on microbiota composition of silver carp (Hypophthalmichthys molitrix) determined by culture-dependent and independent methods during chilled storage – Shiliang Jia – International Journal of Food Microbiology

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Probiotics / prebiotics

Lactobacillus plantarum AN1 cells increase caecal L. reuteri in an ICR mouse model of dextran sodium sulphate-induced inflammatory bowel disease – Yasushi Yokota – International Immunopharmacology

Lactobacillus salivarius LA307 and Lactobacillus rhamnosus LA305 attenuate skin inflammation in mice – S. Holowacz – Beneficial Microbes

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions – M. Ray – Beneficial Microbes

Lactobacillus rhamnosus GG Affects Microbiota and Suppresses Autophagy in the Intestines of Pigs Challenged with Salmonella Infantis – Wei Zhang – Frontiers in Microbiology

Probiotic Use in Equine Gastrointestinal Disease – Angelika Schoster – Veterinary Clinics: Equine Practice

Review: The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Journal of the Science of Food and Agriculture

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits – Agnieszka Mika – Neuroscience Letters

Biotechnology

Effects of voltage on sulfadiazine degradation and the response of sul genes and microbial communities in biofilm-electrode reactors – Xiao-Li Yang – Ecotoxicology and Environmental Safety

Waste and Pollution

Biodegradation of n-alkanes on oil–seawater interfaces at different temperatures and microbial communities associated with the degradation – Synnøve Lofthus – Biodegradation

Techniques

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens – Stefanie U. Wetzels – PLOSone

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? – Ylva Lekberg – New Phytologist


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Microbes in the news

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets – Signe Dean – Science Alert

The discovery of a third form of flagella-mediated motility in symbiotic bacteria – Phys.org

Phage or foe? – In light of new evidence, we have to reassess the role of bacteriophages in microbial communities: are they always the enemy? – Lucía Fernández – npj Biofilms and Microbiomes

The effect of gut bacteria on bone health cannot be generalized – Randi Lundberg – Taconic

Here’s What You Need To Know About The Bacteria In Your Vagina
A microbiome doesn’t just exist in your gut – Sarah DiGiulio – Huffington Post

Understanding Microbial Communities Living On Amphibian Skin – Sofia Prado-Irwin – Science Trends

In the battle against cancer, microbes could be the answer – Nicola Davison – Wired


February 1, 2018

The publication of a Springer manual entitled Mechanisms underlying host-microbiome interactions in pathopysiology of human diseases contains multiple interesting articles today, including reviews on the gut microbiome and preterm infant gut development, colerectal cancer, and metabolic disease, as well as a useful review of statistical models for mouse and human microbiome data. In addition, a revisitation of gut enterotypes via metabolomics, decreased Akkermansia muciniphila in psoriasis,  the bacterial communities of fiddler crabs, the impact of different wavelengths of light on hot spring bacteria, and two articles on the uses of metabarcoding in both 16S and eukaryotic microbiota analysis.

Events and jobs

Microbiology Manager – Covance – Indianapolis, Indiana

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Pregnancy and early life

*Review: Impact of Microbes on the Intestinal Development of the Preterm Infant – Elizabeth Humphrey – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Multi-site human microbiome

Review: Good and Bad Farming: The Right Microbiome Protects from Allergy – Markus Johannes Ege – Allergy Prevention and Exacerbation

Human gut microbiome

*Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes – Manoj Kumar Verma – Scientific Reports

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – BMC Gasteroentrology

*The Akkermansia muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Review: The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer – Cheng-Bei Zhou – Critical Reviews in Microbiology

Editorial: Unveiling the gut virome in human health and diseases – Tao Zuo – International Journal of Clinical Virology

*Review: The Influence of the Microbiota on the Etiology of Colorectal Cancer – Melissa C. Kordahi – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*Review: Altered Microbiota and Their Metabolism in Host Metabolic Diseases – Beng San Yeoh –  In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Review: The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All? – Eva Untersmayr – Allergy Prevention and Exacerbation

*Review: Fecal Microbiota Transplants: Current Knowledge and Future Directions – Roxana Chis – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

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Animal experiments

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice – Ann Wells – Journal of Proteome Research

The Changes of Colonic Bacterial Composition and Bacterial Metabolism Induced by an Early Food Introduction in a Neonatal Porcine Model – Chao Shi – Current Microbiology

Animal microbiome

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

Transcriptional changes detected in fecal RNA of neonatal dairy calves undergoing a mild diarrhea are associated with inflammatory biomarkers – Fernanda Rosa – PLOSone

Tiny but mighty: The role of the rumen microbes in livestock production
K M Cammack – Journal of Animal Science

Effects of Spray-Dried Porcine Plasma on Fecal Microbiota in Nursery Pigs – Huyen Tran – Journal of Animal Science

Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows – Susakul Palakawong Na Ayudthaya – Biotechnology for Biofuels

Plant, root, and soil microbiome

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

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production – Reeta Goel – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 7. Springer

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire – Taylor K. Dunivin – PLOSone

Review: The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance – Msizi Mhlongo – Frontiers in Plant Science

Characterization of bacteria isolated from the Saffron (Crocus Sativus L.) rhizosphere – Majid Jami Al-Ahmadi – Journal of Horticultural Research

Review: Rhizoremediation – Plant Microbe Interactions in the Removal of Pollutants – Mehak Oberai – International Journal of Current Microbiology and Applied Sciences (IJCMAS)

Role of microbes in organic carbon decomposition and maintenance of soil ecosystem – Hina Khatoon – International Journal of Chemical Studies

Water and extremophile microbiome

Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing – Kazuhisa Okada – Scientific Reports

*Effect of light wavelength on hot spring microbial mat biodiversity – Akifumi Nishida – PLOSone

Microbial Ecology

Estimating taxon-specific population dynamics in diverse microbial communities – Benjamin J. Koch – Ecosphere

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains – Eric Hong Jian Wong – Scientific Reports

Resistome

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut – Lisa Ciesinski – PLOSone

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Probiotics / prebiotics

An Integrative Review on the Effect of Prebiotics, Probiotics, and Synbiotics on Infection After Colorectal Cancer Surgery – Sarah Williams Anderson – Aorn Journal

Phages and Viruses

Metagenomic Analysis of the Jinding Duck Fecal Virome – Lili Zhao – Current Microbiology

Bioinformatics

*Statistical Models and Analysis of Microbiome Data from Mice and Humans – Yinglin Xia – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases – Qingyu Chen – Journal of Data and Information Quality

Techniques

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving – Clinical Metabolomics

*16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer) – Clare Bird – PLOSone

*Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients – Ibrahim Hamad – PLOSone

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Microbes in the news

The Germ and the Gene: Gut Bacteria Research Takes a Step Forward – Ruairi MacKenzie – Technology Networks

These bacteria produce gold by digesting toxic metals – EurekaAlert

 

 

January 25, 2018

Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

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Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

Review: Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

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Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice  – Feifei Lin – Food and Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista – British Journal of Nutrition

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

*Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

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Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

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Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

 

December 26, 2017

Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!

Human oral microbiome

The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease

Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science

Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research

Human gut microbiome

Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery

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Animal experiments

Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports

*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish

*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe

In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology

*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience

Animal microbiome

Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere

*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology

Plant, root, and soil microbiome

Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis –  G. R. Nalin Rathnayake – Natural Product Research

Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition

Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry

The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum

Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition

Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology

Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition

Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects ­ A review – H. Etesami – Journal of soil science and plant nutrition

Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition

Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition

Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition

Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express

Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots –  Belinda C. Martin – Frontiers in Microbiology

Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition

Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes

Water and extremophile microbiome

Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology

Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology

Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles

Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles

Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology

Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology

Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography

Microbial Ecology

Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex

Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports

Built environment

Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one

Food microbiology

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology

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Probiotics / prebiotics

Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients

Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes

Phages and viruses

Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata –  Douglas Beattie – Frontiers in Marine Science

Bioinformatics

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics

Techniques

*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere –  Elena L. Peredo – Frontiers in Microbiology

A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads –  Rosemarie Wilton – Frontiers in Plant Science

Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology

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Microbes in the news

Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science

Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science

 

December 14, 2017

Two interesting articles on pregnancy and early life: the placentobiome, and the cervical microbiome, as well as articles on the circadian rhythms of the saliva microbiome, the microbiome of exposed rock,  and new techniques to sequence single bacterial and archaeal cells.

Events and jobs

Postdoctoral Research Scientist – Genomics and Metagenomics – Quadram Institute Bioscience – Norwich UK

Assistant Professor, Cell Biology, Molecular Biology or Microbiology – Albany College of Pharmacy and Health Sciences

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Pregnancy and early life

*Mother-to-newborn transmission of mycobacterial L-forms and Vδ2 T-cell response in placentobiome of BCG-vaccinated pregnant women – T. Dimova – Scientific Reports*

*Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions – Gislaine Curty – Scientific Reports

Multi-site human microbiome

Microbiome in PTEN hamartoma tumor syndrome – Victoria Byrd – Society for Endrocrinology

Human respiratory microbiome

The Alteration of Nasopharyngeal and Oropharyngeal Microbiota in Children with MPP and Non-MPP – Zhiwei Lu – Genes

Human skin microbiome

Review: Staphylococcus aureus and Atopic Dermatitis: A Complex and Evolving Relationship – Joan A. Geoghegan – Trends in Microbiology

Human oral microbiome

*Timing of food intake impacts daily rhythms of human salivary microbiota: a randomized, crossover study – María Carmen Collado – The FASEB Journal

Human vaginal microbiome

Influence of Orally Administered Probiotic Lactobacillus Strains on Vaginal Microbiota in Women with Breast Cancer during Chemotherapy: A Randomized Placebo-Controlled Double-Blinded Pilot Study – J Marschalek – Breast Care

Human gut microbiome

A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics – Pamela Vernocchi – Nutrients

Entamoeba Species in South Africa: Correlations With the Host Microbiome, Parasite Burdens, and First Description of Entamoeba bangladeshi Outside of Asia – Renay Ngobeni – Journal of Infectious Diseases

Mutual interaction of phenolic compounds and microbiota: Metabolism of complex phenolic apigenin C- and kaempferol O-derivatives by human fecal samples – Maren Vollmer – Journal of Agricultural and Food Chemistry

Estimation of the bioaccessibility and bioavailability of Fe, Mn, Cu, and Zn in Chinese vegetables using the in vitro digestion/Caco-2 cell model: the influence of gut microbiota – Xiaolin Cai – Food and Function

Food-Associated Lactobacillus plantarum and Yeasts Inhibit the Genotoxic Effect of 4-Nitroquinoline-1-Oxide – Roberta Prete – Frontiers in Microbiology

Butyrate suppresses motility of colorectal cancer cells via deactivating Akt/ERK signaling in histone deacetylase dependent manner – Qingran Li – Journal of Pharmacological Sciences

Review: Exercise has the guts: How physical activity may positively modulate gut microbiota in chronic and immune-based diseases – Roberto Codella – Digestive and Liver Disease

Review: Alzheimer’s disease and gut microbiota modifications: The long way between preclinical studies and clinical evidence – Cesare Mancuso – Pharmacological Research

Adjuvant Probiotics and the Intestinal Microbiome: Enhancing Vaccines and Immunotherapy Outcomes – Luis Vitetta – Vaccines

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Animal experiments

Fecal short-chain fatty acids at different time points after ceftriaxone administration in rats – Yu. V. Holota – The Ukrainian Biochemical Journal

1H NMR-Based Metabonomic Study of Functional Dyspepsia in Stressed Rats Treated with Chinese Medicine Weikangning – Yu Guo – Evidence-Based Complementary and Alternative Medicine

A Novel Prebiotic Blend Product Prevents Irritable Bowel Syndrome in Mice by Improving Gut Microbiota and Modulating Immune Response – Qian Chen – Nutrients

Animal microbiome

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes – Margaret I. Steele – mBio

Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens? – Luis A. Ramírez-Camejo – International Journal of Microbiology

Archaeal community structure and underlying ecological processes in swine manure slurry – Priyanka Kumari – bioRxiv

Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment – Qifan Zeng – Scientific Reports

Altered Gut Microbiota Profiles in Sows and Neonatal Piglets Associated with Porcine Epidemic Diarrhea Virus Infection – Deping Song – Scientific Reports

Plant, root, and soil microbiome

*Tales from the tomb: the microbial ecology of exposed rock surfaces
Authors – Tess E Brewer – Environmental Microbiology

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse – Chi Liu – Scientific Reports

Impact of Glyphosate on the Rhizosphere Microbial Communities of An EPSPS-Transgenic Soybean Line ZUTS31 by Metagenome Sequencing – Gui-Hua Lu – Current Genomics

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber – Mélanie Salomez – Journal of Applied Microbiology

Manure and mineral fertilization change enzyme activity and bacterial community in millet rhizosphere soils – Lixia Xu – World Journal of Microbiology and Biotechnology

Resistome

Drivers of dissolved organic carbon export in a subarctic catchment: Importance of microbial decomposition, sorption-desorption, peatland and lateral flow – Itziar Lekunberri – Environmental Pollution

Food microbiology

Conference Proceedings: The microbial community and free amino acid composition in salted and fermented squid products – Daisuke Ouchi- The JSFS 85th Anniversary-Commemorative International Symposium

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Waste and Pollution

Anaerobic Baffled Reactor in Treatment of Natural Rubber Processing Wastewater: Reactor Performance and Analysis of Microbial Community – Phuong Thao Tran – Journal of Water and Environment Technology

Microbial Community Structure and Enumeration of Bacillus species in Activated Sludge – Masashi Hatamoto – Journal of Water and Environment Technology

Techniques

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities – Pedro J. Torres – In: Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press

*Sequencing of Genomes from Environmental Single Cells – Robert Bowers – In: Methods in Molecular Biology, vol 1712. Humana Press

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Microbes in the news

Why Probiotic Skin Care Is (Actually) Worth It, According to Experts – Lauren Valenti – – Vogue

Celebrating a decade of interdisciplinary microbiology – Raleigh McElvery – MIT News

Plant pathologists discover unusual evolutionary transition in common bacteria – Chris Branam – Phys.org

Efforts of bacteria to defend against predators is so great that few resources left for offspring – Science Daily

Specially designed protein fights several species of bacteria – EurekaAlert

Reprogramming bacteria instead of killing them could be the answer to antibiotic resistance – Yu-Hsuan Tsai – Phys.org

Bacteria and Art

Shout Out: Hunter Cole, biology lecturer and artist – Genevieve Bookwalter- Chicago Tribune

Kathy High with Sadie R. Starnes, Gut Love: You are my future – Esther Klein – The Brooklyn Rail

 

 

December 13, 2017

Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of Tcongolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider