Category Archives: Pregnancy and birth

November 21, 2017

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A review discussing metabolic-flux dependent regulation in microbes, diversity of coral-associated viral communities, what an Antarctic fungus can tell us about astrobiology.

General microbiome

Pre-print: Extending species-area relationships (SAR) to diversity-area relationships (DAR)© – Zhanshan Ma – aRxiv

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health – Ajar Nath Yadav – Journal of Applied Biology and Biotechnology

Pregnancy and early life

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants – Anuradha Ravi – FEMS Microbiology Ecology

Human respiratory microbiome

Pre-print: Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children – Shu Mei Teo – bioRxiv

Human gut microbiome

Pre-print: A perturbation model of the gut microbiome’s response to antibiotics – Liam P Shaw – bioRxiv

Animal experiments

Pre-print: Within host selection for faster replicating bacterial symbionts – Ewa Chrostek – bioRxiv

Plant, root, and soil microbiome

Molecular characterization of Associative N2 fixing bacterium isolated from the roots of Finger millet (Eleusine coracana L.) and its interaction effects with microbial consortia on growth and yield – G B Santosha Gowda – Research Journal of Biotechnology

Significance of temperature and water availability for soil phosphorus transformation and microbial community composition as affected by fertilizer sources – Dasheng Sun – Biology and Fertility of Soils

Water and extremophile microbiome

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile – Maria Eugenia Farias – PLOS ONE

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring – Takafumi Kataoka – Archives of Microbiology

Microbes in space

Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance – Laura Selbmann – Fungal Biology

Phages and viruses

Pre-print: Coral-associated viral communities show high levels of diversity and host auxiliary functions – Karen D Weynberg – PeerJ

Biological Control of Pectobacterium carotovorum Via Specific Lytic Bacteriophage – Eman Marei – Journal of Basic and Applied Scientific Research

Bioinformatics

Book chapter: Chapter 1 – Metagenomics: A Paradigm Shift in Microbiology – Andrey V Mardanov – Metagenomics

More microbes

Review: Metabolic-flux dependent regulation of microbial physiology – Athanosios Litsios – Current Opinion in Microbiology

Microbes in the news

High-salt diet throws microbiome out of whack – Katharine Sanderson – Chemical & Engineering News

Rare Bacterial Taxa May Play Outsize Role in Soil Microbiome Structure, Study Suggests – Genome Web

Forsyth Institute researcher Floyd Dewhirst named as AAAS Fellow – EurekAlert

What makes soil, soil? Researchers find hidden clues in DNA – Phys.Org

Microbes on the market

PathoQuest Announces Formation of Scientific Advisory Board – Business Wire

November 15, 2017

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Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

November 10, 2017

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Events and jobs
Postdoctoral Fellow – Institute of Genome Sciences (IGS) with Hotopp Lab – Baltimore, Maryland

Pregnancy and early life
Influence of vitamin D on key bacterial taxa in infant microbiota in the KOALA Birth Cohort Study – Chris E. Talsness – PLoS One

Review: Role of the Human Breast Milk-Associated Microbiota on the Newborns’ Immune System: A Mini Review – Marco Toscano – Frontiers in Microbiology

Review: The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota – Christian Milani – Microbiology and Molecular Biology Reviews

Multi-site human microbiome
Segmented Filamentous Bacteria Provoke Lung Autoimmunity by Inducing Gut-Lung Axis Th17 Cells Expressing Dual TCRs – C. Pierce Bradley – Cell Host and Microbe

Human vaginal microbiome
Genitourinary Syndrome of the Menopause: Vaginal Health and Microbiota – Maria Jesús Cancelo-Hidalgo – Menopause

Human gut microbiome
Review: Microbial biotransformations in the human distal gut – Elisabeth M Bik – British Journal of Pharmacology

Review: The Human Microbiome and Obesity: Moving beyond Associations – Padma Maruvada – Cell Host and Microbe

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation – Hassan Brim – Genes

Multiple articles from Frontiers in Immunology:
LC3-Associated Phagocytosis Is Required for Dendritic Cell Inflammatory Cytokine Response to Gut Commensal Yeast Saccharomyces cerevisiae – Dimitra Lamprinaki – Frontiers in Immunology

Immunological and Clinical Effect of Diet Modulation of the Gut Microbiome in Multiple Sclerosis Patients: A Pilot Study – Marina Saresella – Frontiers in Immunology

Review: TH17 Cell and Epithelial Cell Crosstalk during Inflammatory Bowel Disease and Carcinogenesis – Jan Kempski – Frontiers in Immunology

Animal experiments
Difference in the gut microbiome between ovariectomy-induced obesity and diet-induced obesity – S. Choi – Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

The effects of starter microbiota and the early life feeding of medium chain triglycerides on the gastric transcriptome profile of 2- or 3-week-old cesarean delivered piglets – Paolo Trevisi – Journal of Animal Science and Biotechnology

Animal microbiome
Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens – Douglas C. Woodhams – Microbial Ecology

Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota – Alina S. Grigorescu – Microbial Ecology

Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis – Na Zhang – PLoS One

Diets Alter the Gut Microbiome of Crocodile Lizards – Hai-Ying Jiang – Frontiers in Microbiology

Plant, root, and soil microbiome
Opinion: Nitrogen limitation of decomposition and decay: how can it occur? – Colin Averill – Global Change Biology

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth – Dalia Molina-Romero – PLoS One

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil – Da-Wei Jing – PLoS One

Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil – Junhui Chen – Biology and Fertility of Soils

Book of interest: Endophytes: Biology and Biotechnology – Dinesh K. Maheshwari

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea – I. G. Shirokikh – Eurasian Soil Science

Water and extremophile microbiome
Editorial: Deep Carbon in Earth: Early Career Scientist Contributions to the Deep Carbon Observatory – Donato Giovannelli – Frontiers in Earth Science

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum – Mireia Mestre – Molecular Ecology

Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities – Marc W. Van Goethem – Frontiers in Microbiology

Influences of anthropogenic land use on microbial community structure and functional potentials of stream benthic biofilms – Xiaodong Qu – Scientific Reports

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea – Bernd Wemheuer – Microorganisms

Biohydrogen production at pH below 3.0: Is it possible? – V.T. Mota – Water Research

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China – Y Sheng – Ground Water
No link available yet, linked to PubMed.

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity – Bruno L. Mello – Biotechnology for Biofuels

Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China – Wenting Guo – Applied Microbiology and Biotechnology

Built environment
The Nosocomial Risk of Bacterial Contamination of Surgical Wards at Saint Francis Hospital in Katete District of Zambia – Frank Mtonga – ARC Journal of Clinical Case Reports

Food microbiology
Preventive effects of a probiotic mixture in an ovalbumin-induced food allergy model – HS Shin -Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro by human intestinal microbiota of polysaccharides from Fuzhuan brick tea – Guijie Chen – Food Chemistry

Phages and viruses
Several book chapters from Bacteriophage Therapy:
Book Section: Methods for Bacteriophage Preservation – Małgorzata B. Łobocka
Interaction of Bacteriophages with Mammalian Cells – Zuzanna Kaźmierczak

Perspective: The Intra-Dependence of Viruses and the Holobiont – Juris A. Grasis – Frontiers in Immunology

Bioinformatics
Metagenome sequence clustering with hash-based canopies – Mohammad Arifur Rahman – Journal of Bioinformatics and Computational Biology

Book: UNIT 1E.14 Computational Methods for Human Microbiome Analysis – Matthieu J. Miossec – Current Protocols in Microbiology

Microbes in the news
Enhanced understanding of the microbiome is helping medicine – The Economist

Microbes on the market
Seres Therapeutics to Participate in Three Upcoming November Conferences – Business Wire

Global Microbiome Sequencing Services Market Outlook 2017 Growth, Trends, Forecasts 2022 – Samuel – Talk Daily News

Space travel changes gut bacteria in mice – Science Nordic

New model reveals possibility of pumping antibiotics into bacteria – Phys Org
Paper: New free-exchange model of EmrE transport – Anne E. Robinson – PNAS

EPA approves bacteria-infected insects to kill mosquitoes – Bonnie Burton – CNET

Bacteria Hysteria
Deadly bacterial infections could be coming from your kitchen sink PLUGHOLE – Matt Atherton – Express

Science, publishing, and career
The GOP tax bill could be a disaster for PhD students – Jen Kirby – Vox

November 3, 2017

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Events and jobs

Assistant Professor in Food Microbiology/Safety – The University of Texas Rio Grande Valley – Close Date: 12/3/2017

Assistant Professor Microbiology – University of New Haven, Connecticut

Microbiology Technician On-Call – Battle Creek, MI – Michigan

 

General microbiome

Closely related methicillin-resistant Staphylococcus aureus isolates from retail meat, cows with mastitis, and humans in Japan – T Sato – PLoS One

Letter:A global resource allocation strategy governs growth transition kinetics of Escherichia coli – DW Erickson – Nature

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – RM Cooper – eLife

 

Pregnancy and early life

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – C Dahl – PLoS One

 

 

Human vaginal microbiome

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. – JM Wessels – PLoS One

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

Opinion: Committee Opinion No. 725: Vaginal Seeding – KR Wharton – Obstetrics and Gynecology

 

Human gut microbiome

“Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”. – V Marzano – PLoS Neglected Tropical Diseases

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use – BN Parsons – PLoS Pathogens

Modeling the temporal dynamics of the gut microbial community in adults and infants – L Shenhav – bioRxiv

The ethnic distribution of sessile serrated polyps in the United States is inversely associated with Helicobacter pylori prevalence – A Sonnenberg – Colorectal Disease

Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum. – S Hasan – Acta obstetricia et gynecologica Scandinavica

Protective Roles of Intestinal Microbiota derived Short Chain Fatty Acids in Alzheimer’s Disease-type Beta-Amyloid Neuropathological Mechanisms. – L Ho – Expert Review of Neurotherapeutics

 

Animal experiments 

Microbiota control immune regulation in humanized mice – E Gülden – Journal of Clinical Investigation Insight

Effects of essential oils from Liquidambar orientalis Mill. leaves on growth performance, carcass and some organ traits, some blood metabolites and intestinal microbiota in broilers. –  A Altop – British Poultry Science

PD-1 deficiency protects experimental colitis via alteration of gut microbiota. – SJ Park – Journal of biochemistry and molecular biology.

The Mouse Model of Infection with Citrobacter rodentium – N Bouladoux – Current Protocols in Immunology

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels. – LN Nielsen – Environmental Pollution

 

Animal microbiome 

Strong responses of Drosophila melanogaster microbiota to developmental temperature – NN Moghadam – Fly (Austin)

Amphibian skin defences show variation in ability to inhibit growth of Batrachochytrium dendrobatidis isolates from the Global Panzootic Lineage. – RE Antwis – Microbiology (Reading, England)

Midgut Bacterial Diversity of Wild Populations of Phlebotomus (P.) papatasi, the Vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Turkey. – M Karakuş – Scientific Reports

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – KF Beckers – PLoS One

 

Plant, root and soil microbiome

Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower). – G Moya – International Journal of Systematic and Evolutionary Microbiology

Priority effects can persist across floral generations in nectar microbial meta-communities – T Hirokazu – Oikos

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Y Zhao – PLoS One

Microbial community-level regulation explains soil carbon responses to long-term litter manipulations – K Georgiou – Nature Communications

 

Water microbiome and extremophiles

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – MW Hinson – bioRxiv

Lessons from simple marine models on the bacterial regulation of eukaryotic development – A Woznica – bioRxiv

Chapter: Sponge Disease and Climate Change – HM Luter – Climate Change, Ocean Acidification and Sponges

 

Probiotics / prebiotics

Lactobacillus plantarum HNU082-derived improvements in the intestinal microbiome prevent the development of hyperlipidaemia – Y Shao – Food & Function

Can Probiotic Supplements Improve Outcomes in Rheumatoid Arthritis? – A Schorpion – Current Rheumatology Reports

 

 

Techniques

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – B Ghodsalavi – PLoS One

Bacterium-triggered remodeling of chromatin identifies BasR, a novel regulator of fungal natural product biosynthesis – J Fischer – bioRxiv

Transcriptome analysis of sheep oral mucosa response to Orf virus infection – H Jia – PLoS One

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

Microbes in the news

How caries-causing bacteria can survive in dental plaque – EurekAlert

Nicotine’s hold: What the gut and gender have to do with it – Phys.org

‘Big Chicken’ Connects Poultry Farming To Antibiotic-Resistant Bacteria – npr

Microbiology: Crowdsourcing Earth’s microbes – Nature

Fresh off the petri dish: Spend your Thursdays creating art with bacteria – FSU Torch

 

Non-microbiology picks

Nigritoxin is a bacterial toxin for crustaceans and insects – Y Labreuche – Nature Communications

The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity – A Santanach – Nature Communications

 

October 26, 2017

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In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

* Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

October 17, 2017

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The effects of antimicrobials in household products on the maternal and infant microbiome, water quality of an urban stream network, and using adaptive evolution to improve lager yeast hybrids.

Pregnancy and early life

Household triclosan and triclocarban effects on the infant and maternal microbiome – Jessica V Ribado – EMBO Molecular Medicine

Water and extremophile microbiome

Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations – L M Ward – Geobiology

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole – T L Hamilton – Geobiology

Built environment

Urban infrastructure influences dissolved organic matter quality and bacterial metabolism in an urban stream network – Clay P Arango – Freshwater Biology

Food microbiology

Pre-print: Enhanced wort fermentation with de novo lager hybrids adapted to high ethanol environments – Kristoffer Krogerus – bioRxiv

More microbes

Pre-print: Phosphate starvation induces replacement of phospholipids with the betaine lipid diacylglycerol-N,N,N-trimethylhomoserine in the human fungal pathogen Candida albicans – Surabhi Naik – bioRxiv

Microbes in the news

Infections by C.diff bacteria are on the rise and can cause serious problems – Consumer Reports – The Washington Post

Engineered bacteria build microstructures on their own – Michael Torrice – Chemical & Engineering News

Gut fungi might be linked to obesity and inflammatory bowel disorders – Tina Hesman Saey – Science News

Rare bacteria in dead elephant sparks alarm – Siba Mohanty – The New Indian Express

Woman Contracts Rare Bacterial Infection on 12-Hour Flight – Rachael Rettner – Live Science

Microbial Drug Resistant Mutations Found via Novel Genome Screen – Genetic Engineering and Biotechnology News

One More Small Piece of the Puzzle on the Role of Gut Micro-organisms in MS – Ana Belo Van Wijk – Multiple Sclerosis News Today

Microbes on the market

New Clinical Data and Microbiome Research from Rebiotix’s Phase 2 Program for RBX2660 Highlighted at the World Congress of Gastroenterology at ACG2017 – PR Newswire

October 14, 2017

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The marine sponge microbiome, bacterial communication mediated by hydrogen sulfide, a gnotobiotic pig model to study interactions between a defined gut community and antibiotics, probiotics, and rotavirus.

General microbiome

Evolutionary contribution to coexistence of competitors in microbial food webs – Teppo Hiltunen – Proceedings of the Royal Society Biological Sciences

Pregnancy and early life

Effects of Therapeutic Hypothermia on the Gut Microbiota and Metabolome of Infants suffering Hypoxic-Ischemic Encephalopathy at birth – C Watkins – The International Journal of Biochemistry and Cell Biology

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? – O Sakwinska – Beneficial Microbes

Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy – J S Y Low – Beneficial Microbes

Human oral microbiome

Exopolysaccharides regulate calcium flow in cariogenic biofilms – Monika Astasov-Frauenhoffer – PLOS ONE

Human gut microbiome

The Gut Microbiome Feelings of the Brain: A Perspective for Non-Microbiologists – Aaron Lerner – Microorganisms

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study – K Adamberg – Beneficial Microbes

Review: Our gut microbiota: a long walk to homeostasis – L M T Dicks – Beneficial Microbes

Animal experiments

Flavanol-Rich Cocoa Powder Interacts with Lactobacillus rhamnossus LGG to Alter the Antibody Response to Infection with the Parasitic Nematode Ascaris suum – Saebyeol Jang – Nutrients

Effect of antibiotic, probiotic, and human rotavirus infection on colonisation dynamics of defined commensal microbiota in a gnotobiotic pig model – H C Huang – Beneficial Microbes

Animal microbiome

Pre-print: An RNA Virome associated to the Golden Orb-weaver Spider Nephila clavipes – Humberto J Debat – bioRxiv

The sponge microbiome project – Lucas Moutinho-Silva – Gigascience

Water and extremophile microbiome

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline – Luis Linares-Otoya – Marine Drugs

Bioinformatics

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data – Fanny Berglund – Microbiome

More microbes

Pre-print: Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria – Xiaowei Jiang – bioRxiv

Pre-print: H2S mediates interbacterial communication through the air reverting intrinsic antibiotic resistance – Daniel Thomas-Lopez – bioRxiv

Pre-print: Interplay between antibiotic efficacy and drug-induced lysis underlies enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

Microbes in the news

How switches work in bacteria – EurekAlert

Opinion: Microbiology Needs More Math – Mikhail Tikhonov – The Scientist

Fluctuating environments can help cooperating bacteria – Science Daily

How to study the inside of a humpback whale’s blowhole? Drones, of course – Teresa Welsh – The Sacramento Bee

Scientists Generate 3D Map of Gut Microbiome – Genetic Engineering and Biotechnology News

Microbes on the market

Research Foundation Calls for Canadian Proposals to Study Dietary Interactions with Microbiota – PR Newswire

October 11, 2017

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Events and jobs

Microbiology Laboratory Analyst – Cork (Ringaskiddy Road, Monkstown, Co. Cork)

 

Pregnancy and early life

Effect of probiotics on perinatal outcome in patients at high risk of preterm birth. – N Kirihara – The Journal of Obstetrics and Gynaecology Research

 

 

Human oral microbiome

Quantification of carious pathogens in the interdental microbiota of young caries-free adults. – D Bourgeois – PLoS One

 

Human gut microbiome

The gut microbiome in atherosclerotic cardiovascular disease – Z Jie – Nature Communications

Review: The microbiome as a novel paradigm in studying stress and mental health. – RT Liu – The American Psychologist

Review: The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – CL Hager – Digestive and Liver Disease

Review: Selected aspects of the human gut microbiota – M Ventura – Cellular and Molecular Life Sciences

 

Animal experiments 

Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. – C Ciu – PLoS One

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – X Qu – PLoS One

 

Animal microbiome 

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites – C Richards – PLoS One

 

Plant, root, and soil microbiome

The impact of the omics era on the knowledge and use of Lysobacter spp. to control phytopathogenic microorganisms. – G Puopolo – Journal of Applied Microbiology

The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores. – M Walter – Plant and Soil

Pathogenic potential of environmental resident fungi from ornithogenic soils of Antarctica – JRP Sousa – Fungal Biology

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh – DR Chaudhary – Microbial Ecology

 

Built environment 

Unravelling the core microbiome of biofilms in cooling tower systems. – L Di Gregorio – Biofouling

 

 

Phages and viruses

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics – S Roux – Nature Communications

Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – A Harms – bioRxiv

 

Techniques

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. – YW Yan – PLoS One

A GLM-based latent variable ordination method for microbiome samples. – MB Sohn – Biometrics

Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial – JM Pernica – PLoS One

A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast –  K Ishibashi – Scientific Reports

Analyses Approaches for Bacteria – E Ribeiro – Exposure to Microbiological Agents in Indoor and Occupational Environments

 

Microbes in the news

Bacteria self-organize to build working sensors – EurekAlert

Effects of nutritional factors on the intestinal microbiota – Freie Universität

October 10, 2017

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Effects of amino acid supplements on metabolic health, a discussion of the broader risks and benefits of microbiome research, a book chapter evaluating microbiome statistical analysis tools.

Events and jobs

Assistant Professor in Microbiology, Tenure Track – Department of Microbiology & Immunology, University of British Columbia

General microbiome

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research – Daria Shamarina – Microbiome

Pregnancy and early life

Review: Early microbiota, antibiotics and health – Alicja M Nogacka – Cellular and Molecular Life Sciences

Human gut microbiome

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control – Francesco Bifari – Genes & Nutrition

Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? – Dario Sorrentino – World Journal of Gastroenterology

Phages and viruses

Pre-print: Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – Alexander Harms – bioRxiv

Bioinformatics

Book Chapter: Processing and Analyzing Human Microbiome Data – Xuan Zhu – Statistical Human Genetics

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions – A Eck – BMC Bioinformatics

Techniques

Pre-print: Umbilical cord blood diagnostics for early onset sepsis in premature infants: detection of bacterial DNA and systemic inflammatory response – Leena B Mithal – bioRxiv

Pre-print: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs – Robert C Edgar – PeerJ

Microbes in the news

Bacteria with synthetic gene circuit self-assemble to build working device with gold nanoparticles – Phys Org

New test identifies antibiotic-resistant bacteria in 30 minutes – The Statesman

Microbes on the market

Summit Highlights Microbiome Preservation During Ridinilazole Treatment in Exploratory Phase 2 Clinical Trial at ID Week 2017 – Globe Newswire

October 7, 2017

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Events and jobs

Director of the Microbiome Research Laboratory – UT Southwestern

DOCTORAL STUDENT OR POSTDOCTORAL RESEARCHER –  Faculty of Veterinary Medicine, University of Helsinki – Application deadline: Nov 5, 2017

 

General microbiome

Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production – Y Boltyanskaya – Antonie van Leeuwenhoek

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. – MA Engevik – Microbiology Spectrum

 

Pregnancy and early life

Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father – LC Kenny – bioRxiv

 

Human respiratory microbiome

Long-term effects of inhaled corticosteroids on sputum bacterial and viral loads in COPD. – M Contoli – The European Respiratory Journal

 

 

Human gut microbiome

Bifidobacteria and the infant gut: an example of co-evolution and natural selection. – F Turroni – Cellular and Molecular Life Sciences

Inflammatory bactericidal lectin RegIIIβ: Friend or Foe for the host? – T Miki – Gut Microbes

Review: Host-microbiota interplay in mediating immune disorders. – KM Felix – Annals of the New York Academy of Sciences

Review: Probiotics for the prevention of Hirschsprung-associated enterocolitis: a systematic review and meta-analysis. – H Nakamura – Pediatric Surgery International

 

Animal experiments 

Can intestinal microbiota be associated with non-intestinal cancers? – C Jacqueline – Scientific Reports

Gnotobiotics: getting a grip on the microbiome boom – S Mallapaty – Lab Animal

Nanoparticle curcumin ameliorates experimental colitis via modulation of gut microbiota and induction of regulatory T cells. – M Ohno – PLoS One

 

Animal microbiome 

Comparative analysis of microbial communities associated with bacteriomes, reproductive organs and eggs of the cicada Subpsaltria yangi. – D Wang – Archives of Microbiology

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. – H Shen – Microbiology Open

Elucidating the microbial community associated with the protein preference of sludge degrading worms – S de Valk – Environmental Technology

 

Plant, root and soil microbiome

Mycorrhizal fungi show regular community compositions in natural ecosystems. – E Verbruggen – The ISME Journal

Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays – J Vacheron – Molecular Plant-Microbe Interactions

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development. – SC Castle – Oecologica

 

Water microbiome and extremophile 

Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. – D Kalenitchenko – The ISME Journal

Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages – BS  Park – Marine and Freshwater Research

Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. – R Rathour – Genome Announcements

 

Built environment 

Managing the excessive proliferation of glycogen accumulating organisms in industrial activated sludge by nitrogen supplementation: A FISH-NanoSIMS approach – CA Onetto – Systematic and Applied Microbiology

 

 

Phages and viruses

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. – G Freer – Current Medicinal Chemistry

 

Techniques

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing – P Schwendner – Microbiome

 

Microbes in the news

Puppies Linked To Bacterial Infection Outbreak Across 12 States – Forbes

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

Episode Review: VICE’s ‘Post-Truth News and Microbiome’ – The Hoya

Second grade handwashing experiment leads to big decrease in bacteria, illness – EurekAlert

Validating microbiome claims:Including the latest DNA techniques-Formulation Summit – Cosmetics Design Europe

Macromolecules: Weapons in the Fight Against Antibiotic Resistance  – American Veterinarian

Scientists are trying to figure out how to keep bacteria from running rampant on space missions – Popular Science

Bacteria can spread antibiotic resistance through soil – Phys.org