June 15, 2017

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

March 4th, 2017

Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Bioinformatics

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist

 

Microbiome Digest, October 9, 2014

Human microbiome general

Advancing the Microbiome Research Community – Curtis Huttenhower – Cell

“We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. “

Human oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – K.J. Cross – Molecular Oral Microbiology

“The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins.”

Human skin microbiome

Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin – Elizabeth C. Murphy – Molecular Microbiology

“This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. “

Human gut microbiome

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders – N Tennoune – Translational Psychiatry

“Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH.”

Animal models of microbiome research

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs – Zhikai Zeng – Animal Science Journal

Soil microbiome

Poster presentation: Starting study of microbial genetics diversity in soils of mangrove preserved in sergipe – Karla Cristina Santos Freire – BMC Proceedings

“This paper proposes the characterization and evaluation of structures and diversity of microbial communities in the soil of mangroves in three conservation areas located in Sergipe.“

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession – Cheng Gao – New Phytologist

“We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing”

Metagenomics / Bioinformatics

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam – Juanjuan Chai – BMC Evolutionary Biology

“A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. “

More Microbiology

Halting harmful helminths – Karl F. Hoffmann, Paul J. Brindley, Matthew Berriman – Science

“More than 300 million people are infected each year with parasitic flatworms such as hydatid tapeworms and blood fluke schistosomes. “

Chromosome position effects on gene expression in Escherichia coli K-12 – Jack A. Bryant – Nucleic Acids Research

“Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. “

Microbes in the news

‘Good Poop’ Diet Is the Next Big Thing – Daniela Drake – The Daily Beast

“Now a new book, The Skinny Gut Diet, by nutritionist Brenda Watson, tracks the progress of people who follow a diet specifically designed to alter the gut microbiome. “

Another probiotic advantage: Bacteria protects against heavy metal poisoning – Jim Algar – Tech Times

“Probiotic bacteria found in yogurt can protect people from the effects of exposure to heavy metals, particularly in pregnant women and children, a Canadian study suggests.”

Science, publishing, career

The scientists who get credit for peer review – Richard Van Noorden – Nature

“Publons rewards researchers for putting their peer-review activity online. Nature spoke to the startup’s co-founder and two super-users.”

Meet the New Underclass: People With Ph.D.s in Science – Mark Strauss – iO9

“Once upon a time, newly-minted science Ph.D.s would get research jobs at a senior scientist’s laboratory, to train and hone the ideas they would explore at their own labs. But now the supply of post-doctoral students is outpacing demand, creating a new, hyper-educated underclass.”

Glut of postdoc researchers stirs quiet crisis in science –  Carolyn Y. Johnson – Boston Globe

Japan’s Missing Female Scientists – Jack Grove – Times Higher Education

“Too many female scientists are leaving Japan because they do not feel they can get ahead in its “male-dominated” society, a senior university leader has said.”

Bik’s Picks

Cave paintings change ideas about the origin of art – Pallab Ghosh – BBC

“Researchers tell the journal Nature that the Indonesian discovery transforms ideas about how humans first developed the ability to produce art.”

A timeline of a baby’s first hour – Laura Sanders – Science News

Fired science teacher did not have state license – 9 News

“The teacher fired after his science experiment injured four students, one seriously, did not have a valid Colorado teacher’s license.”

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Microbiome digest, October 8, 2014

Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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Human microbiome digest, October 7, 2014

Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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Human microbiome digest, October 6, 2014

Preterm birth, multiple sclerosis, aging, and Clostridium difficile infection in animal models.

Pregnancy and Birth

Necrotizing Enterocolitis: A Clinical Review on Diagnostic Biomarkers and the Role of the Intestinal Microbiota – Niemarkt, Hendrik J. – Inflammatory Bowel Diseases

“In this review, we discuss the pathogenesis, diagnosis, and treatment of NEC with a focus on the role of microbiota in the development of NEC.”

* Intestinal microbiota of preterm infants differ over time and between hospitals – Diana H Taft – Microbiome Journal

“DNA extracted from stool was used to sequence the 16S rRNA gene by Illumina MiSeq using universal primers. “

Babies’ Gut Bacteria Are Mostly Fixed By Time Spent In The Womb – Nicholas Ellaby – Science 2.0

“Now, a new study published in the journal Proceedings of the National Academy of Sciences has added a critical piece to the puzzle. “

Human Gut Microbiome

Gut microbiome and the risk factors in central nervous system autoimmunity – Javier Ochoa-Repárazemail, Lloyd H. Kasper – FEBS Letters

“Of interest to this review is the consistency between this range of MS risk factors and the gut microbiome. We postulate that the gut microbiome serves as the niche where different MS risk factors merge, thereby influencing the disease process.”

Compositional dynamics of the human intestinal microbiota with aging: Implications for health – B. Lakshminarayanan – The Journal of Nutrition, Health & Aging

“This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. “

Animal models of microbiome research

A Beneficial Effect of Oral Tigecycline Treatment on Clostridium difficile Infection in Gnotobiotic Piglets – Hyeun Bum Kim – Antimicrobial Agents and Chemotherapy

“The efficacy of oral tigecycline treatment (2mg/kg for 7 days) on Clostridium difficile infection (CDI) was evaluated in the gnotobiotic pig model, and its effect on human gut microflora transplanted into the gnotobiotic pig was determined. “

A novel multi-strain probiotic and synbiotic supplement for prevention of Clostridium difficile infection in a murine model – Kanthi Kiran Kondepudi – Microbiology and Immunology

“Feces and cecal contents were collected for microbial cell viability, quantitative PCR (qPCR), toxin analyses and histopathology.“

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Human microbiome digest, September 29, 2014

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Smoking and the subgingival ecosystem, inflammatory bowel diseases, iron in the gut, and metabolism of acetaminophen.

Pregnancy and birth

External influence of early childhood establishment of gut microbiota and subsequent health implications – Peris M. Munyaka – Frontiers in Pediatrics

“Early exposures impacting the intestinal microbiota are associated with the development of childhood diseases that may persist to adulthood”

Human oral microbiome

* Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Human gut microbiome

Functional Impacts of the Intestinal Microbiome in the Pathogenesis of Inflammatory Bowel Disease – Jennifer Li – Inflammatory Bowel Diseases

“We highlight functional roles of specific bacterial groups in the development and management of IBD. “

Nutritional iron turned inside out: intestinal stress from a gut microbial perspective – Guus A.M. Kortman – FEMS Microbiology Reviews

“This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health.”

Animal models of microbiome research

The role of intestinal microbiota in murine models of acetaminophen-induced hepatotoxicity – Lucia A Possamai – Liver International

“A urinary metabolic profile was obtained using 1H-NMR. Baseline hepatic glutathione content and CYP2E1 expression were quantified.”

Dietary Xylo-oligosaccharide stimulates intestinal bifidobacteria and lactobacilli but has limited effect on intestinal integrity in rats – Ellen Gerd Christensen – BMC Research Notes

“Changes in faecal and caecal bacterial composition determined by 16S rRNA gene sequencing and quantitative PCR for selected bacterial groups revealed that the overall bacterial composition did not differ markedly“

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Microbiome digest, September 23, 2014

I don’t have much time tonight, so I’ll keep it short.

Pregnancy and birth

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women – Yi-E Huang- Microbial Ecology

Impact of Feeding and Medical Practices on the Development of Necrotizing Enterocolitis – Brian L. Montenegro, Camilia R. Martin – Current Pediatrics Reports

Human respiratory microbiome

Expanding Our Understanding of Respiratory Microbiota in Cystic Fibrosis – John J. LiPuma – Annals of the American Thoracic Society

Microbiota in the throat and risk factors of laryngeal carcinoma – Hongli Gong – Applied and Environmental Microbiology

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

The Overarching Influence of the Gut Microbiome on End-Organ Function: The Role of Live Probiotic Cultures – Luis Vitetta – Pharmaceuticals

Excretion of host DNA in feces is associated with risk of Clostridium difficile infection –  Caroline Vincent – Journal of Immunology Research

Animal and in vitro studies of human microbiome

Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs – Hirotaka Igarashi – PLOS ONE

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Hannah Lees – PLOS ONE

A comparative evaluation of prebiotic oligosaccharides using in vitro cultures of infant fecal microbiome – J Stiverson – Applied and Environmental Microbiology

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs – Crystal L. Levesque – PLOS ONE

Mammal microbiome

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas), and binturongs (Arctictis binturong) – Erin A. McKenney – Integrative Zoology

Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey – Ibrahim Hamad – Scientific Reports

Insect microbiome

Routes of acquisition of the gut microbiota of Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

Sponge microbiome

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12427/abstract

Plant microbiome

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars – Márton Szoboszlay – Soil Biology and Biochemistry

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria – Pilar Martínez-Hidalgo – Scientific Reports

Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian – Ningfei Lei – PLOS ONE

Soil type dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

Soil microbiome

Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils – Keisuke Obase – FEMS Microbiology Ecology

Food microbiology

Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese – Bei Zhang – Dairy Science & Technology

Metabolomics / Functional metagenomics

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library – Fiona Fouhy – PLOS ONE

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

Aleksandr Milshteyn, Jessica S. Schneider, Sean F. Brady – Chemistry & Biology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of dietary polydextrose fiber on the human gut metabolome – Santosh Lamichhane – Journal of Agricultural and Food Chemistry

Preserving the earth’s microbes for drug discovery in the future – Ranjith N. Kumavath and Satyanarayana S.V – Journal of Microbiology and Microbial Research

Microbial Ecology

PNAS has a special issue this week on Biogeography (with the Panama forest trees paper by Jessica Green): The emergence and promise of functional biogeography – Cyrille Violle – PNAS

Active invasion of bacteria into living fungal cells – Nadine Moebius – eLife

Microbes in the news

Microbiome: You are never alone – John A Goldman – Atlanta Medicine

Seeking the Sweet Spot, from Mouth to Microbiome – David Katz – Huffington Post

New evidence suggests long-term relationships with bacteria begins before we’re born – Norbert Berzog and David Niesel – Galveston County Daily News

MIT Developing Ship-Repairing Bacteria – World Maritime News

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science

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Microbiome digest, September 19, 2014

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An update from the Cochrane Review Journal on probiotics to prevent necrotizing enterocolitis, oral microbiome in apical periodontitis or polycystic ovary syndrome, vaginal and gut microbiome, and bacteria in shrimp, soil, and water.
Pregnancy and birth

Probiotics for prevention of necrotizing enterocolitis in preterm infants – Khalid AlFaleh, and Jasim Anabrees – Evidence-Based Child Health: A Cochrane Review Journal

“For this update, searches were made of MEDLINE (1966 to October 2013), EMBASE (1980 to October 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (2013, Issue 10), and abstracts of annual meetings of the Society for Pediatric Research (1995 to 2013).”

Anne Geddes Unveils New Image Of A Baby Born Too Soon – March of Dimes

“Mrs. Geddes donated the image of Alfred, who was born 8 weeks too soon, weighing just two pounds, six ounces, to the March of Dimes, which made the photo the center of its 2014 World Prematurity Day campaign.”

Human oral microbiome

Highly Diverse Microbiota in Dental Root Canals in Cases of Apical Periodontitis (Data of Illumina Sequencing) – Veiko Vengerfeldt – Journal of Endodontics

“Samples were collected under strict aseptic conditions from 12 teeth … and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.”

Association between Polycystic Ovary Syndrome, Oral Microbiota and Systemic Antibody Responses – Aliye Akcalı – PLOS ONE

“Salivary levels of seven putative periodontal pathogens were analyzed by quantitative real-time polymerase chain reaction and serum antibody levels were analyzed by ELISA. “

Human genital microbiome

The Changing Landscape of the Vaginal Microbiome – Bernice Huang – Clinics in Laboratory Medicine

“The vaginal microbiome is a dynamic ecosystem in which the microbiota play a major role in regulating parameters such as pH and in limiting the growth of potentially harmful organisms”

Human gut microbiome

Review: Diet, gut microbes, and genetics in immune function: can we leverage our current knowledge to achieve better outcomes in inflammatory bowel diseases? – Vanessa A Leone – Current Opinion in Immunology

“This review summarizes our current understanding of dietary-induced changes in gut microbiota on autoimmunity in the context of IBD.”

The evolving role of the gut microbiome in human disease – Lloyd H. Kasper – FEBS Letters

“We are delighted to introduce this Special Issue, which summarizes the current understanding of the complex relationship between the gut microbiome and the host.”

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B Burns – bioRxiv Preprints

“We characterized the microbiome in 44 primary tumor and 44 patient-matched normal colon tissues. We find that tumors harbor distinct microbial communities compared to nearby healthy tissue.”

Gut Microbiota: A Natural Adjuvant for Vaccination – Oliver Pabst, Mathias Hornef – Immunity

“In this issue of Immunity, Oh et al. (2014) reveal an unappreciated facet of how the microbiota influences immune responses. Immunity to nonadjuvanted vaccines depends on Toll-like-receptor-5-mediated sensing of the microbiota.”

Animal and bioreactor models

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“Vaccination of Trl5−/− mice resulted in reduced antibody titers and lower frequencies of plasma cells, demonstrating a role for TLR5 in immunity to TIV. This was due to a failure to sense host microbiota. “

In vivo degradation of alginate in the presence and in the absence of resistant starch – Melliana Jonathan – Food Chemistry

“This study evaluated the intestinal degradability of alginate during 74 days intake in pigs as models for humans. “

Effect of prebiotics on the fecal microbiota of elderly volunteers after dietary supplementation of Bacillus coagulans GBI-30, 6086 – Edna P. Nyangale – Anaerobe

“Single stage batch culture anaerobic fermenters were used and inoculated with fecal microbiota obtained from volunteers after taking a 28 day treatment of Bacillus coagulans GBI-30, 6086 (GanedenBC30 (BC30)) or a placebo.”

Intestinal anastomotic injury alters spatially defined microbiome composition and function – Benjamin D Shogan – Microbiome journal

“Using 16S rRNA amplicon sequencing of samples collected on the day of surgery … and the 6th day following surgery …, we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats.”

General human microbiome

Microbiome in Human Immunodeficiency Virus Infection – January T. Salas, Theresa L. Chang – Clinics in Laboratory Medicine

“Individuals infected with the human immunodeficiency virus (HIV) have altered microbiome associated with immune activation that impacts the consquence of disease progression”

Shrimp microbiome

Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources – Meiling Zhang – Aquaculture

“an Illumina-based sequencing method was used to examine the intestinal bacterial composition of L. vannamei following six diets with different lipid sources.”

Soil microbiome

Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil –
S. Lladó – Journal of Hazardous Materials

“Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided”

Water microbiome

High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters – Joe D. Taylor and Michael Cunliffe – Journal of Phycology

“Here, we use high-throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time-series station and compare with underlying plankton assemblages. “

Microbes in the news

Sex in the Sink: Gene-Swapping Bacteria Are Making New Superbugs – Maggie Fox – NBC News

“Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria, a trend that poses a serious threat to the U.S. medical system,” Segre and colleagues wrote in their report.

Science, publishing, and career

To Get More Out of Science, Show the Rejected Research – Brendan Nyhan – New York Times

“In a new white paper, I propose that the American Political Science Association offer options for articles in a Registered Reports-style format. “

Pushing Women and People of Color Out of Science Before We Go In – Jennifer Selvidge – Huffington Post

“The misogyny and racism I experienced and saw at MIT became more and more concerning, between professors making “get back in the kitchen jokes” and hearing about what seemed to be legions of male PhD student sexually harassing woman undergraduates.”

Bik’s Picks

I want one! These adorable giant African rats detect land mines and TB for a living – Bec Crew – Scientific American

“So yesterday, I adopted an unborn land-mine-detecting African giant pouched rat (Cricetomys gambianus) from Tanzania. “

No sedative necessary: Scientists discover new ‘sleep node’ in the brain – Science Daily

“A sleep-promoting circuit located deep in the primitive brainstem has revealed how we fall into deep sleep. “

Experts: Science Class Can Dazzle With Less Danger – Dan Elliott – ABC News

“On Sept. 3, 13 people, mostly children, were burned by a methanol-fueled flash fire during a science demonstration at the Terry Lee Wells Nevada Discovery Museum in Reno.”

(Satire) Bono Showcases New Genome Sequencers, The i-LUMINA 6 and i-LUMINA 6 plus – the Allium

“Lead singer with the rock band U2, Bono, revealed the latest in genome sequencing technology at a gala event in the Moscone Center in San Francisco, yesterday.”

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Microbiome digest, September 17, 2014

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Human gut microbiome and artificial sweeteners, cholera recovery, or ancient coprolites, protbiotics and the brain, coastal soil, diversity and science, metabolomics, and Bik’s Picks.
Human gut microbiome

Artificial sweeteners induce glucose intolerance by altering the gut microbiota – Jotham Suez – Nature

“We identify NAS-altered microbial metabolic pathways that are linked to host susceptibility to metabolic disease, and demonstrate similar NAS-induced dysbiosis and glucose intolerance in healthy human subjects.”

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection – Ansel Hsiao – Nature

“We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children”

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures – Raul J. Cano – PLOS ONE

“We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico.”

Animal models of microbiome research

Modulation of Intestinal Microbiota by the Probiotic VSL#3 Resets Brain Gene Expression and Ameliorates the Age-Related Deficit in LTP – Eleonora Distrutti – PLOS ONE

“Here, we report that treatment of aged rats with VSL#3 induced a robust change in the composition of intestinal microbiota with an increase in the abundance of Actinobacteria and Bacterioidetes, which was reduced in control-treated aged rats.”

Soil microbiome

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities – Basit Yousuf – PLOS ONE

“Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling”

Techniques

Partition Enrichment of Nucleotide Sequences (PINS) – A Generally Applicable, Sequence Based Method for Enrichment of Complex DNA Samples – Thomas Kvist, Line Sondt-Marcussen, Marie Just Mikkelsen – PLOS ONE

“The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. “

Metabolomics

Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species – Edoardo Saccenti – PLOS ONE

“we show that despite the standardization of diet as the most relevant extrinsic factor, a clear individual and discriminative metabolic fingerprint also exists for monkeys.”

Science and Career

Diversity: Pride in science – M Mitchell Waldrop – Nature

“The sciences can be a sanctuary for gay, lesbian, bisexual and transgender individuals, but biases may still discourage many from coming out.”

Bik’s Picks

Only 4 of them are women…. – The top 50 science stars of Twitter – Jia You – Science

“Though Hall says he meant his K-index lightheartedly, his article in Genome Biology sparked a Twitter storm of criticism. So just who are the Kardashians of science, and is Hall’s criticism justified?”

Breast milk reveals a correlation between dietary fats and academic success – Science Daily

“You are what you eat, the saying goes, and now a study conducted by researchers at UC Santa Barbara and the University of Pittsburgh suggests that the oft-repeated adage applies not just to physical health but to brain power as well.”

Forensic science solves mystery of Richard III’s death (the parking-lot king) –  Agata Blaszczak-Boxe – CBS News

“More than 500 years after Richard III became the last king of England to die in battle, researchers using modern forensic science have figured out which injuries likely caused his death.”

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