Category Archives: Metagenomics & Bioinformatics

November 1, 2017

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Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

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

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone

 

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 25, 2017

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A short Digest for today. The evolution of E. coli in the lab for over 60,000 generations, the necessity of including a mock community for every sequencing run, and plenty of news pieces.

Events and jobs

Free Webinar: Not Just for Neurons – Electrical Signaling in Bacterial Biofilm Communities – Select Science

Laboratory Assistant-Microbiology – Raritan New Jersey

General microbiology

*The dynamics of molecular evolution over 60,000 generations – Benjamin H. Good et al. – Nature

Press: The evolution experiment that has been watching bacteria mutate for 30 years – Rich Haridy – New Atlas

Bacterial pathogenesis: Activating Helicobacter effector delivery – Irene Vacca – Nature Reviews Microbiology

Human gut microbiome

Discovery of α-L-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42 – Alexander Holm Viborg et al. – Journal of Biological Chemistry

Letter: Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC – Nádia Conceição-Neto et al. – Gut

Bioinformatics

*Preprint: Taxon disappearance from microbiome analysis indicates need for mock communities as a standard in every sequencing run – Yi-Chun Yeh et al. – bioRxiv

Microbes in the news

Strength in numbers: How biofilms outfox antibiotics – Yella Hewings-Martin – Medical News Today

Lung microbiome plays major role in asthma severity and response to treatment – News Medical

New way to prevent unfavorable intestinal microbiota – Hokkaido University – EurekAlert

VIDEO: Gut microbiome research sped by technology, informatics, but diet a major confounder – Eamonn M.M. Quigley – Healio

New Study Shows Link Between Gut Bacteria And Breast Cancer – CBS New York

Harvey-linked flesh-eating bacteria claims Galveston man – Todd Ackerman – Chron

Major changes in balance of gut bacteria occur soon after serious injury/trauma – Medical Xpress

‘Achilles heel’ found in antibiotic-resistant bacteria – John von Radowitz – Irish Independent

 

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

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 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 4, 2017

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Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

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

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass

 

October 3, 2017

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Review on bioinformatics software for virus sequence analysis, the wild baboon microbiome, potential health risks of spontaneous food fermentation.

Human oral microbiome

Pre-print: Novel genes required for the fitness of Streptococcus pyogenes in human saliva – Luchang Zhu – bioRxiv

Human gut microbiome

Antibiotic use and new-onset inflammatory bowel disease in Olmsted County, Minnesota: a population-based case-control study – Satimai Aniwan – Journal of Crohn’s and Colitis

The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young – Gaorui Bian – mSphere

Animal experiments

Young Pigs Consuming Lysozyme Transgenic Goat Milk Are Protected from Clinical Symptoms of Enterotoxigenic Escherichia coli Infection – Lydia C Garas – The Journal of Nutrition

Whole-Grain Starch and Fiber Composition Modifies Ileal Flow of Nutrients and Nutrient Availability in the Hindgut, Shifting Fecal Microbial Profiles in Pigs – Janelle M Fouhse – The Journal of Nutrition

Lotus Seed Resistant Starch Regulates Gut Microbiota and Increases SCFAs Production and Mineral Absorption in Mice – Hongliang Zeng – Journal of Agricultural and Food Chemistry

Animal microbiome

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species – Emmanuel Guivier – Microbial Ecology

Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons – Laura E Grieneisen – Integrative and Comparative Biology

Plant, root, and soil microbiome

Pre-print: Rice paddy Nitrospirae encode and express genes related to sulfate respiration: proposal of the new genus Candidatus Sulfobium – Sarah Zecchin – bioRxiv

Effects of Grazing and Fire Frequency on Floristic Quality and its Relationship to Indicators of Soil Quality in Tallgrass Prairie – George C Manning – Environmental Management

Pre-print: Hunters or gardeners? Linking community structure and function of trap-associated microbes to the nutrient acquisition strategy of a carnivorous plant – Dagmara Sirová – bioRxiv

Multitrophic interactions in the rhizosphere of a temperate forest tree affect plant carbon flow into the belowground food web – H R Maboreke – Soil Biology and Biochemistry

Water and extremophile microbiome

Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring – Lan Liu – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: Spontaneous Food Fermentations and Potential Risks for Human Health – Vittorio Capozzi – Fermentation

Phages and viruses

Review: Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” – Martin Hölzer – Advances in Virus Research

Bioinformatics

Nephele: A cloud platform for simplified, standardized, and reproducible microbiome data analysis – Nick Weber – Bioinformatics

More microbes

Pre-print: A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus – Abigail L Lind – bioRxiv

Pre-print: Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark of Plasmodium exoerythrocytic infection – Gregory M LaMonte – bioRxiv

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

September 29, 2017

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General microbiome

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria – I. Martínez, Journal of Biotechnology

Biofilms: Survival and defense strategy for pathogens – Ashutosh Kumar, International Journal of Medical Microbiology

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities – Zhao Yang-Guo, Environmental Engineering Science

Comparison of the impacts of zinc ions and zinc nanoparticles on nitrifying microbial community – Qiang Wu, Journal of Hazardous Materials

Models of microbiome evolution incorporating host and microbial selection – Qinglong Zeng, Microbiome

Pregnancy and early life

Impact of delivery mode on the colostrum microbiota composition – Marco Toscano, BMC Microbiology

Multi-site human microbiome

Human Microbiome in Brazil – Luciana Campos Paulino, The Brazilian Microbiome

Forensic genetics and genomics: Much more than just a human affair – Miguel Arenas, PLoS Genetics

South Asian Health: Inflammation, Infection, Exposure, and the Human Microbiome – Jennifer Leng, Journal of Immigrant and Minority Health

Natural Products as Platforms To Overcome Antibiotic Resistance – Sean E. Rossiter, Chemical Reviews

Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis – Gabriel Horta-Baas, Journal of Immunology Research

Human respiratory microbiome

Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period – Juan de Dios Caballero, mBio

Sputum microbiota in severe asthma patients: Relationship to eosinophilic inflammation – Naijian Li, Respiratory Medicine

Human skin microbiome

Culture characterization of the skin microbiome in type 2 diabetes mellitus: a focus on the role of innate immunity – Akshay Thimmappaiah Jagadeesh, Diabetes Research and Clinical Practice

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt, Epidemiology

Human gut microbiome

Bacterial chat: intestinal metabolites and signals in host -microbiota -pathogen interactions – Bruna C. Lustri, Infection and Immunity

Gut inflammation and dysbiosis in human motor neuron disease – Julie Rowin, Physiological Reports

Molecular basis of gut microbiome-associated colorectal cancer: A synthetic perspective – Alan R. Healy, Journal of American Chemical Society

Metagenomic Paleomicrobiology Characterizes Fecal Microbiomes and Viromes of Pre-Columbian Cultures from Vieques, Puerto Rico – Jessica I. Rivera-Perez, ProQuest

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota – Henry Watson, BMJ Journals

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer – Scott G. Daniel, mSystems

The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species – Aaron W. Miller, mSystems

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – Zachary A. Costliow, mSystems

Human oral microbiome

Host Genetic and Environemental Associations and the Human Salivary Microbiome – Brittany Ann Demmitt, ProQuest

Animal microbiome

Pathogenesis of oral FIV infection – Craig Miller, PLoS ONE

Photosynthetic epibionts and endobionts of Pacific oyster shells from oyster reefs in rocky versus mudflat shores – Laurent Barillé, PLoS ONE

Free-living and captive turtles and tortoises as carriers of new Chlamydia spp. – Agata Mitura, PLoS ONE

Microbiomes Associated with Animals: Implications for Livestock and Animal Production – Hilario Cuquetto Mantovani, The Brazilian Microbiome

Maintenance of distal intestinal structure in the face of prolonged fasting: A comparative examination of species from five vertebrate classes – Marshall D. McCue, The Anatomical Record

Plant, root, and soil microbiome

Assessment of derelict soil quality: Abiotic, biotic and functional approaches – Quentin Vincent, Science of The Total Environment

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza, PLoS ONE

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira, PLoS ONE

Temporal dynamics in microbial soil communities at anthrax carcass sites – Karoline Valseth, BMC Microbiology

Pyrosequencing reveals soil enzyme activities and bacterial communities impacted by graphene and its oxides – Yan Rong, Journal of Agriculture and Food Chemistry

Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome – Chao Xue, Biology and Fertility of Soils

The Brazilian Soil Microbiome – Fernando Dini Andreote, The Brazilian Microbiome

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria – Junwei Zhao, International Journal of Systematic and Evolutionary Microbiology

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem – Yi Hao, Environmental Pollution

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime, ISME

Jaminaea pallidilutea sp. nov. (Microstromatales), a basidiomycetous yeast isolated from plant material of mangrove forests in Iran – Shaghayegh Nasr, International Journal of Systematic and Evolutionary Microbiology

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa) – Swapnil Sapre, Microbiological Research

Bacterial traits and quality contribute to the diet choice and survival of bacterial-feeding nematodes – Ting Liu, Soil Biology and Biochemistry

A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth – Ester Simonetti, Microbiological Research

Impact of herbicide application on Beneficial soil microbial community, Nodulation and Yield parameters of chickpea (Cicer arietinum L.) – Raghavendra, K. S, Bulletin of Environment, Pharmacology and Life Sciences

Isolation And Characterization of Phosphate Solubilizing Microorganisms From Maize Rhizosperic Soils – S. Vinod Babu, Bulletin of Environment, Pharmacology and Life Sciences

Aerobic deterioration of corn stalk silage and its effect on methane production and microbial community dynamics in anaerobic digestion – Huan Zhang, Bioresource Technology

Plant Microbiome: Composition and Functions in Plant Compartments – Maike Rossmann, The Brazilian Microbiome

Changing soil legacies to direct restoration of plant communities – E Pernilla Brinkman, AoB Plants

Water and extremophile microbiome

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment – Andrea Highfield, Viruses

Shifts in diversity and function of lake bacterial communities upon glacier retreat – Hannes Peter, ISME

Expression and characterization of a new heat-stable endo-type alginate lyase from deep-sea bacterium Flammeovirga sp. NJ-04 – Benwei Zhu, Extremophiles

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams – Jacob R. Price, Science of The Total Environment

Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers – Bing Tang, Bioresource Technology

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics – Hailin Tian, Bioresource Technology

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage – Yaneth Vasquez, Bioresource Technology

Microbial megacities fueled by methane oxidation in a mineral spring cave – Clemens Karwautz, ISME

Built environment

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces – Rachel I. Adams, Microbiome

Food microbiology

Traditional Norwegian Kveik Yeasts: Underexplored Domesticated Saccharomyces cerevisiae Yeasts – Richard Preiss, bioRxiv

Probiotics / prebiotics

Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides, Its Biosynthesis and Bioactivity – Sudhir P. Singh, Applied Biochemistry and Biotechnology

Single-strain vs multi-strain probiotic supplementation strategy against rheumatoid arthritis – Giancarlo Ceccarelli, Arthritis and Rheumatology

The Genomic Basis of Lactobacilli as Health-Promoting Organisms –  Elisa Salvetti, Microbiology Spectrum

Phages and viruses

Phage mobility is a core determinant of phage-bacteria coexistence in biofilms – Matthew Simmons, bioRxiv

Bioinformatics

Bioinformatics for Microbiome Research: Concepts, Strategies, and Advances – Leandro Nascimento Lemos, The Brazilian Microbiome

Techniques

A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes – Michelle Spoto, bioRxiv

Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes – Elin Videvall, bioRxiv

Microbes in the news

Artwork brings ‘echoes of DNA’ to UB’s new medical school building – ELLEN GOLDBAUM, UBNow

JooMo launches new body wash with skin bacteria tech – Lucy Whitehouse, Cosmetics Design Europe