Category Archives: Human gut

Human microbiome, August 14, 2014

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Culturing TM7, antibiotics early in life and obesity, preterm labor, breast milk, two articles by Carl Zimmer and one by Jop de Vrieze.

Pregnancy and Birth

Science has a special this week on Parenting, with a couple of relevant papers:

Preterm labor: One syndrome, many causes – Roberto Romero, Sudhansu K. Dey, Susan J. Fisher – Science

“We summarize the current understanding of the mechanisms of disease implicated in this condition and review advances relevant to intra-amniotic infection, decidual senescence, and breakdown of maternal-fetal tolerance.”

Nature’s first functional food – Trisha Gura – Science

“Building upon a century-old study that first indicated that milk nourished certain bacteria in infants, the new work has characterized the complexity of breast milk carbohydrates called oligosaccharides, or HMOs, that particularly nourish one species of beneficial bacteria.”

The taste of things to come – Emily Underwood – Science

“Indeed, studies in human infants and animals suggest that we may start to learn and love different flavors as early as in the womb.”

Human oral microbiome

Axenic Culture of a Candidate Division TM7 Bacterium from the Human Oral Cavity and Biofilm Interactions with Other Oral Bacteria – Valeria Soro – Applied and Environmental Microbiology

“Successive rounds of enrichment in laboratory media led to the isolation of a pure culture of one of these candidate division TM7 phylotypes.”

Human gut microbiome

Review: Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics – Rachel N. Carmody and Peter J. Turnbaugh – Journal of Clinical Investigation

“Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. “

Taking the Yuck Out of Microbiome Medicine – Carl Zimmer – National Geographic

“I can still remember the shock I felt when I heard about fecal microbiota transplants for the first time. It is not the sort of thing you forget.”

Our Microbiome May Be Looking Out for Itself – Carl Zimmer – New York Times

“But in the journal Bioessays, a team of scientists has raised a creepier possibility. Perhaps our menagerie of germs is also influencing our behavior in order to advance its own evolutionary success — giving us cravings for certain foods, for example.”

Animal models of microbiome research

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences – Laura M. Cox – Cell

Press coverage: Taking antibiotics early in life leaves mice prone to obesity – Jop de Vrieze

“A new study of mice shows that interrupting the development of gut microbial populations with low doses of antibiotics early in life disturbs their metabolism and boosts the risk of obesity later on.”

The Gut Microbiota and Developmental Programming of the Testis in Mice – Maha Al-Asmakh – PLOS ONE

“Interestingly, exposure of GF mice to Clostridium Tyrobutyricum (CBUT), which secrete high levels of butyrate, restored the integrity of the BTB and normalized the levels of cell adhesion proteins. “

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Microbiome digest, August 13, 2014

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Nose, glycan, butyrate, microbes on plastics, seawater microbial mats, and plants with microbes.

Respiratory microbiome

The nasal cavity microbiota of healthy adults – Christine M Bassis, Alice L Tang, Vincent B Young and Melissa A Pynnonen – Microbiome

“In our initial analysis, we compared the bacterial communities of the nasal cavity and the oral cavity from ten of these subjects.”

Gut microbiome

Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations – Omer Eilam – mBio

“Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics.”

Microbial-Derived Butyrate: An Oncometabolite or Tumor-Suppressive Metabolite? -Scott J. Bultman, Christian Jobin – Cell Host & Microbe

“Dietary factors, microbial composition, and metabolism are intimately intertwined into a complex network whose activities influence important intestinal functions”

Review: Collateral Damage: Microbiota-Derived Metabolites and Immune Function in the Antibiotic Era – Christopher A. Lopez – Cell Host & Microbe

“A disruption of gut-associated microbial communities by antibiotic treatment can result in a depletion of microbiota-derived metabolites, thereby enhancing pathogen susceptibility, impairing immune homeostasis, and contributing to the rise of certain chronic inflammatory diseases”

Animal model of microbiome

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids
Sabina Lukovac – mBio

“The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids.”

Plant microbiome

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors – Thomas R. Williams, Maria L. Marco – mBio

“We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce.”

Fundamental Plant Chemicals Rooted in Bacteria – Jenna Iacurci – Nature World News

“A fundamental chemical pathway that all plants use to create the essential amino acid phenylalanine has now been traced to two groups of ancient bacteria, a new study reports.”

Water microbiome

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters – Sonja Oberbeckmann – FEMS Microbial Ecology

“Denaturing Gradient Gel Electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location, and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. “

Molecular Ecology of Microbial Mats – Henk Bolhuis – FEMS Microbial Ecology

“Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring and hypersaline).”

Microbes in the news

Wearable structure of bacteria references antique animal bone corsets

“in terms of the material, it is grown from acetobacter xylinum, a strain of bacteria that produces a microbial cellulose textile as it consumes glucose.”

Bik’s Picks

Google Maps Dives Underwater – Scientific American

“Google has taken its ‘street view’ maps to a whole new level—namely, the ocean’s depths. “

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Human microbiome, August 12, 2014

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Oral microbiome in Aboriginals, gut microbiome and probiotics.

Human oral microbiome

Age-dependent changes in Porphyromonas gingivalis and Prevotella species/phylotypes in healthy gingiva and inflamed/diseased sub-gingival sites – Mangala A. Nadkarni – Clinical Oral Investigations

“The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators.”

The effect of propidium monoazide treatment on the measured bacterial composition of clinical samples after the use of a mouthwash – R. A. M. Exterkate – Clinical Oral Investigations

“Propidium monoazide (PMA) has been used to overcome this problem, by preventing the amplification of DNA from membrane-damaged cells. The aim of this study was to evaluate the use of PMA when measuring compositional shifts in clinical samples after mouthwash use.”

Human gut microbiome

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms – Joe Alcock – BioEssays

“We review several potential mechanisms for microbial control over eating behavior including microbial influence on reward and satiety pathways, production of toxins that alter mood, changes to receptors including taste receptors, and hijacking of the vagus nerve, the neural axis between the gut and the brain”

Influence of the microbiota on vaccine effectiveness – Yanet Valdez – Trends in Immunology

“Recent findings suggest novel complex mechanisms by which the microbiome impacts immune cell development and differentiation.”

Current Status and Prospects of Intestinal Microbiome Studies – Dong Soo Han – Intest Res

“Evidences have implicated gut microbes in the development of IBD, but no causative microorganisms have been identified.”

Synbiotic Lactobacillus acidophilus NCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids: a randomized, double-blinded cross-over trial – Gabriella C. van Zanten – FEMS Microbiology Ecology

“Furthermore, 454 tag encoded amplicon pyrosequencing was used to monitor the effect of synbiotic on the composition of the microbiota. “

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Human microbiome, August 11, 2014

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Microbiome of Hadza Hunter, the premature infant gut, neonatal sepsis, skin and respiratory microbiome.

Microbiome general

BacterioFiles 178 – Hadza Hunters Have Heterogeneous Helpers (14 min) – Jesse Noar – BacterioFiles

“This episode: Modern hunter-gatherers have very different gut microbes from people from agricultural societies! “

“What is the FDA Going to Think?” – Negotiating Values through Reflective and Strategic Category Work in Microbiome Science – Katherine W. Darling – Science, Technology & Human Values

“Here, we describe how values are conceptualized and negotiated within microbiome research.”

Pregnancy and Birth microbiome

Patterned progression of bacterial populations in the premature infant gut – Patricio S. La Rosa – PNAS USA

“We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes“

Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis – Marre van den Brand – Journal of Microbiological Methods

“we developed a real-time multiplex PCR assay tailored to LOS diagnosis which is easy-to-use, is applicable on small blood volumes and provides species-specific results within 4 h.”

Respiratory microbiome

Uncovering the hidden villain within the human respiratory microbiome – Chun Kiat Lee, Stephen James Bent – Diagnosis

“The review herein presents the current status of human airway microbiome research and highlights potential gaps which can be translated into research possibilities for future work on respiratory tract infection diagnosis”

Skin microbiome

The skin microbiome: potential for novel diagnostic and therapeutic approaches to cutaneous disease – Elizabeth A. Grice – Skin and Allergy News

“It is increasingly apparent that this collective set of microorganisms and their genetic material, the “microbiome”, contributes genetic diversity, modulates disease, influences metabolic processes, and is essential for immunity.”

Animal models of human microbiome

Citrobacter rodentium: infection, inflammation and the microbiota – James W. Collins – Nature Reviews Microbiology

“In this Review, we discuss recent studies in which C. rodentium has been used to study mucosal immunology, including the deregulation of intestinal inflammatory responses during bacteria-induced colitis and the role of the intestinal microbiota in mediating resistance to colonization by enteric pathogens. “

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Microbiome digest, August 7, 2014

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Microbiome and caries, colorectal cancer, and inflammatory bowel diseases. Microbiomes of fish, dogs, and mosses, microscopic life in an asphalt lake, and the Picks.

Human mouth microbiome

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing – Junko Obata – PLOS ONE

“In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the 16S rRNA gene.”

Human gut microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer – Joseph P. Zackular, Mary A.M. Rogers, Mack T. Ruffin IV, and Patrick D. Schloss – Cancer Prevention Research

“Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas.”

Manipulation of Microbiome, a Promising Therapy for Inflammatory Bowel Diseases – Dapeng Jin, Hongyu Zhang, and Jun Sun – Clinical & Cellular Immunology

“In this review, we summarize the current knowledge of how changes in microbiota may affect the pathogenesis of IBD. “

A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota – Bruce R. Hamaker, Yunus E. Tuncil – Journal of Molecular Biology

“the article encourages the building of a framework of information to manipulate the colon microbiota in a predicted way for improved health”

 

Human microbiome after death

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans – Ismail Can – Journal of Microbiological Methods

“We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers”

Animal models of human microbiome

Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats
S.M. O’Mahony – Neuroscience

“Neonatal antibiotic treatment leads to an increase in visceral sensitivity in adulthood in rats.”

Dog microbiome

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque – Ian J Davis, Christopher Bull, Alexander Horsfall, Ian Morley and Stephen Harris – BMC Microbiology

“Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. ‘

Fish microbiome

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish – Lenka Gerzova – PLOS ONE

“In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents.”

Insect microbiome

The mosquito microbiota influences vector competence for human pathogens – Nathan J Dennison, Natapong Jupatanakul, George Dimopoulos – Current Opinion in Insect Science

“Understanding the interaction between the vector, its microbiota and transmitted pathogens will provide novel opportunities to limit disease transmission.”

Plant microbiome

Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Faisal Hammad Mekky Koua – Saudi Journal of Biological Sciences

“..we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan.”

Soil and water microbiome

Two Neumann U students discover new types of viruses – CatholicPhilly.com

“They collected arthrobacter (a bacteria present in soil) from under trees and near lakes, found and filtered out the phages that were present, and then studied phage anatomy and life cycles.”

Water droplets in oil are microhabitats for microbial life – Rainer U. Meckenstock – Science

“In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. “

Microbiome of the built environment

Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings – Jörg D. Ettenauer – PLOS ONE

“In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques.”

Metagenomics

High-resolution metagenomics – Eran Mick & Rotem Sorek – Nature Biotechnology

In this issue, Nielsen et al. present a powerful method for interpreting metagenomic data at the level of individual genomes without relying on reference sequences of cultured isolates, which can be generated for only a small fraction of microbial life.

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

“But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.”

Science and Career

Ph.D.’s, come out of the closet! – Lina Nilsson – Science

“If you promise not to tell Fisher’s Ph.D. adviser (or mine), I’ll let you in on this well-hidden truth: Fisher isn’t planning to pursue an academic career.”

Bik’s Picks

Stress during pregnancy can be passed down through generations, rat study shows – Science Daily

“Scientists investigating pregnancies in four generations of rats show that inherited epigenetic effects of stress could affect pregnancies for generations.”

This Is Your Brain on Fish – James Hamblin – The Atlantic

“Thicker, stronger, and more resilient. Once a week is all it takes, new research says.”

10 Great Novels That Will Make You More Passionate About Science – Charlie Jane Anders – io9

“A lot of the best science fiction features scientists who solve problems and make breakthroughs.”

Scientist looking forward to weekend of binge-experimenting – The Allium

“Imperial college Scientist Dr. Lou Pole announced earlier today that he was going to spend the entirety of this weekend binge-experimenting.”

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Human microbiome digest, August 5, 2014

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Lots of microbiome papers today, so I will split it up into three posts. Here you will find papers on human gut, respiratory, oral, and vaginal microbiomes, as well as animal models.

Pregnancy and Birth

Prevalence and Clinical Significance of Sterile Intra-amniotic Inflammation in Patients with Preterm Labor and Intact Membranes – Roberto Romero – American Journal of Reproductive Immunology

“The purpose of this study was to (i) determine the prevalence and clinical significance of sterile intra-amniotic inflammation and (ii) examine the relationship between amniotic fluid (AF) concentrations of high mobility group box-1 (HMGB1) and the interval from amniocentesis to delivery in patients with sterile intra-amniotic inflammation.”

A Holobiont Birth Narrative: The Epigenetic Transmission of the Human Microbiome –
Scott F. Gilbert – Frontiers in Genetics

“Birth is nothing less than the passage from one set of symbiotic relationships to another.”

Fecal Short Chain Fatty Acids of Very Low Birth Weight Preterm Infants Fed Expressed Breast Milk or Formula – Pourcyrous, M.; Nolan, V.G.; Goodwin, A.; Davis, S.L.; Buddington, R.K. – Journal of Pediatric Gastroenterology & Nutrition

“ Ion chromatography was used to measure fecal SCFAs (acetate, formate, propionate, butyrate, and isobutyrate), lactate, and chloride in fresh stool samples collected from 32 preterm infants”

Human mouth microbiome

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis – M. N. Zakaria – International Endodontic Journal

“DNA was directly extracted from each sample and the microbial composition was comprehensively analyzed using clone library analysis of the 16S rRNA gene”

 Respiratory microbiome

A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx – Maria Chiara E. Catenazzi, Helen Jones, Iain Wallace, Jacqueline Clifton, James P. J. Chong, Matthew A. Jackson, Sandy Macdonald, James Edwards andJames W. B. Moir – Molecular Microbiology

“Data from classical microbiological and sequence-based microbiome studies provide several lines of supporting evidence that N. meningitidis colonization is correlated with propionic acid generating bacteria, with a strong correlation between prp-containing Neisseria and propionic acid generating bacteria from the genus Porphyromonas, and that this may explain adolescent/adult colonization by N. meningitidis.”

Analysis of Culture-Dependent vs. Culture-Independent Techniques for the Identification of Bacteria in Clinically-Obtained Bronchoalveolar Lavage Fluid – Robert P. Dickson – Journal of Clinical Microbiology

“We analyzed forty six clinically-obtained bronchoalveolar lavage (BAL) specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. “

Vaginal microbiome

Differences in vaginal microbiome in African American women versus women of European ancestry – Jennifer M. Fettweis – Microbiology

“we performed 16S rRNA gene survey to compare the microbiomes of vaginal samples from 1,268 African American women and 416 women of European ancestry. Our results confirmed significant differences in the vaginal microbiomes of the two groups and identified several taxa relevant to these differences.”

Human gut microbiome

Unraveling the mechanisms underlying associations between the microbiome and gastrointestinal malignancies – Tiffany L. Weir – Translational Gastrointestinal Cancer

“While many reviews have focused on research identifying microbial signatures associated with malignancies, including changes in diversity or evenness of GI microbial communities and depletion or overrepresentation of particular bacterial groups; this comprehensive review emphasizes research that explores the cause rather than effects of microbe-malignancy relationships.”

Animal models of human microbiome

Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice – Merete Ellekilde, Ellika Selfjord, Christian S. Larsen, Maja Jakesevic, Ida Rune, Britt Tranberg, Finn K. Vogensen, Dennis S. Nielsen, Martin I. Bahl, Tine R. Licht, Axel K. Hansen & Camilla H. F. Hansen – Nature Scientific Reports

“To date, most studies of gut microbiota transfer are performed in germ-free mice. In the studies presented, it was tested whether an antibiotic treatment approach could be used instead. “

Postnatal Prebiotic Fiber Intake in Offspring Exposed to Gestational Protein Restriction Has Sex-Specific Effects on Insulin Resistance and Intestinal Permeability in Rats – Megan C. Hallam and Raylene A. Reimer – Journal of Nutrition

“At 24 wk of age, glucose tolerance, body composition, satiety hormones, gut microbiota, and markers of intestinal permeability were measured in the offspring. “

A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice – Fernando F Anhê – Gut

“CE exerts beneficial metabolic effects through improving HFHS diet-induced features of the metabolic syndrome, which is associated with a proportional increase in Akkermansia spp. population.”

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Microbiome digest, August 4, 2014

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Relief in a pressing problem, microbes at high altitude, and microbiome in cystic fibrosis.

Human gut microbiome

So glad this one finally came out!  Structural changes in the gut microbiome of constipated patients – Lixin Zhu – Physiological Genomics

“A cross-sectional pilot study was performed to compare stool microbial composition of 8 constipated patients and 14 non-constipated controls using 16S rRNA gene pyrosequencing.”

Microbiota and diabetes: an evolving relationship – Herbert Tilg, Alexander R Moschen – Gut

“A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism.”

Harnessing the Intestinal Microbiome for Optimal Therapeutic Immunomodulation – S. Viaud – Cancer Research

“gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively.”

Specific genetic and microbial signature associated with paediatric ileal Crohn’s disease -Isobel Leake – Nature Reviews Gastroenterology & Hepatology

“An increase in DUOX2 expression was associated with an expansion of Proteobacteria across all forms of IBD, whereas downregulation of APOA1 expression in association with depletion of certain Firmicutes and Bacteroidetes taxa was found to be specific for Crohn’s disease.”

Skin and wounds microbiome

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research – Brendan Hodkinson and Elizabeth Grice – Advances in Wound Care

“The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing.”

Human respiratory microbiome

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota – Perry S Brown – Annals ATS

“After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial rRNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.”

Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj – Samir Benkouiten – Emerging Infectious Diseases

“One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.”

Fish microbiome

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae – Christos Giatsis – PLOS ONE

“Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. “

Soil microbiome

FEMS Microbiology Ecology has a special issue on Polar and Alpine Microbiology with many papers on microbiomes of ice and soil. Here is the Editorial:
Polar and alpine microbiology in a changing world – John C. Priscu – FEMS Microbiology Ecology

“By virtue of their relatively rapid growth rates and metabolic diversity, we can expect microorganisms to be the first responders to fluctuating climatic conditions.”

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau – Jun-Tao Wang – Microbial Ecology

“Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation.”

Water microbiome

Satellite remote sensing data can be used to model marine microbial metabolite turnover – Peter E Larsen – ISME Journal

“We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters”

Microbial Ecology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function – Joseph E. Knelman and Diana R. Nemergut – Frontiers Microbiology

“Can differences in community assembly alter the relationship between biodiversity and ecosystem function?”

Probiotics

Lactobacillus rhamnosus GG suspected infection in a newborn with intrauterine growth restriction – I. Sadowska-Krawczenko – Beneficial Microbes

“Genotyping with the rep-PCR and AFLP methods confirmed the 100% genetic similarity for both the strain isolated from patient blood and the probiotic product.”

Can Eating Probiotic Yogurt Help Lower Your High Blood Pressure? – Susmita Baral – Wall St Cheat Sheet

“Now, a new study (published Monday in the journal Hypertension) has found another added benefit of probiotics — it may reduce high blood pressure.”

Microbes in the News

Your garden hose: a potential health risk due to Legionella spp. growth facilitated by free-living amoebae – Jacqueline Marie Thomas – Environmental Science & Technology

“Here we present data on FLA and Legionella spp. detected in water and biofilm of two garden hose types over 18 months. “

Truth about your toothbrush – Anne Agbaje – Bussiness Day Online

“You don’t store your plates and glasses by the toilet, so why would you want to place your toothbrush there?” McCombs says. “It’s just common sense to store your toothbrush as far away from the toilet as possible.”

Metabolomics

Fecal volatile organic compounds: a novel, cheaper method of diagnosing inflammatory bowel disease? – Chris SJ Probert – Expert Review of Clinical Immunology

“…this article will focus specifically on the fecal VOC metabolome and its potential role in identifying a novel diagnostic method for IBD.”

Review: Emerging mass spectrometry techniques for the direct analysis of microbial colonies – Jinshu Fang, Pieter C Dorrestein – Current Opinion in Microbiology

“In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies.”

Techniques

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing – Jennifer J. Mosher – Journal of Microbiological Methods

“With accurate read lengths of > 1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples.”

 

Bik’s Picks

The Secret to a Tattoo’s Permanence: The Immune System – Olga Khazan – The Atlantic

“We rarely stop and think about the science of tattoos. In fact, some people don’t even stop and think before getting tattooed.”

 

Mathematical equation to predict happiness: Doesn’t depend on how well things go, but on whether things are better than expected – Science Daily

“The happiness of over 18,000 people worldwide has been predicted by a mathematical equation, with results showing that moment-to-moment happiness reflects not just how well things are going, but whether things are going better than expected.”

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Microbiome Digest, August 1, 2014

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Microbiome composition and vaccine response or chemotherapy, cassava beer, two nice articles about metagenomics tools and contamination, and the weekend picks.

Human gut microbiome

Stool Microbiota and Vaccine Responses of Infants – M. Nazmul Huda – Pediatrics

“Actinobacteria abundance was positively associated with T-cell responses to BCG, OPV, and TT; with the delayed-type hypersensitivity response; with immunoglobulin G responses; and with TI. B longum subspecies infantis correlated positively with TI and several vaccine responses. “

Systematic review: the role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis – current evidence and potential clinical applications – Y. Touchefeu – Alimentary Pharmacology & Therapeutics

“Search of the literature published in English using Medline, Scopus and the Cochrane Library, with main search terms ‘intestinal microbiota’, ‘bacteremia’, ‘mucositis’, ‘chemotherapy-induced diarrhoea’, ‘chemotherapy-induced mucositis’, ‘radiotherapy-induced mucositis’.”

Food microbiology

Local domestication of lactic acid bacteria via cassava beer fermentation – Alese M. Colehour – PeerJ

“Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. “

Microbes in the News

It’s a bit – eh – graphic, but a nice overview of science and the people working in this field. I wish it would have contained a couple of pictures of non-pregnant women though. It feels as if we are only a vessel:  The Body’s Ecosystem – The Scientist

“Research on the human microbiome is booming, and scientists have moved from simply taking stock of gut flora to understanding the influence of microbes throughout the body.”

‘I’m not fat, it’s viral’ – Phage found in gut bacteria may aid obesity – Dan Stanton 0 Biopharma Reporter

“A newly discovered virus which infects intestinal bacteria might be a cause of obesity, but could increasing interest in bacteriophages drive new personalised medicines and alternatives to antibiotics?”

Diet Must be Different for Men and Women: Study – Soumo Ghosh – International Business Times

“The researchers found that the microscopic bacteria, or other such organism housed inside the human stomach are different in the case of men and women. Hence, they believe that the same diet for both may not have the same effect in them.”

Metabolomics

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems.”

Metagenomics

Metagenomics Mash-Up – Kelly Rae Chi – The Scientist

“The Scientist spoke with developers of tools for parsing genomic data from diverse communities of microorganisms. Here are some of the newest strategies and programs for taxonomic, functional, and comparative analyses.”

Microbial detection

Who are the contaminants in your sequencing project? – Jonathan Eisen – MicrobeNet

“Such amplification is alas pretty common – due to contamination occurring in some other material added to the PCR reaction. “

Science and publishing

The Self-Edited Woman – Paige Brown – SciLogs International

“Un-prompted, several young female science bloggers I’ve interviewed mention having blogged anonymously in the past, being self-conscious about expressing their expertise on a topic, or avoiding certain topics because of the nasty comments they might receive. “

Bik’s Picks

We have the science to build an Ebola vaccine. So why hasn’t it happened? – Sarah Kliff – Vox

“This isn’t how an Ebola outbreak has to work. Researchers have devoted lots of time to building a vaccine that could stop the disease altogether — and according to Daniel Bausch, a Tulane professor who researches Ebola and other infectious diseases, they’re making really significant progress.”

Littering and Following the Crowd – Vivian Wagner – The Atlantic

“Why it’s so tempting to throw trash on the ground, and how environmentalists are using psychology to change that”

F.D.A. Acts on Lab Tests Developed In-House – Andrew Pollack – The New York Times

“The Food and Drug Administration announced on Thursday that it would start regulating medical laboratory testing, saying that tests used to make important treatment decisions must be vetted and validated before they go into use.”

Grad Student Freed By Police After Three Years Trapped In The Same Experiment – The Allium

“He is thought to have survived by eating printouts of PloS One papers and drinking his own tears.”

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Microbiome digest, July 31

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A snapshot of the human microbiome, a robot helping the Knight lab process samples (I want one!), and finally something that does NOT involve the microbiome.

Human microbiome general

SnapShot: The Human Microbiome – Antonio González – Cell

“This SnapShot presents several aspects of the human microbiome, including the characterization of the microbial species populating different body sites, the distribution of microbes across different geographic locations, and how the microbiome can be altered by a physiological process, exemplified by pregnancy.”

 

Animal models of microbiome

Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4 – Madhukumar Venkatesh – Immunity

“Here we showed that microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR).”

Bacterial Sensor Nod2 Prevents Inflammation of the Small Intestine by Restricting the Expansion of the Commensal Bacteroides vulgatus – Deepshika Ramanan – Immunity

“Here, we identified several abnormalities in the small-intestinal epithelium of Nod2−/− mice including inflammatory gene expression and goblet cell dysfunction, which were associated with excess interferon-γ production by intraepithelial lymphocytes and Myd88 activity.”

Effect of virgin and refined olive oil consumption on gut microbiota. Comparison to butter – M. Hidalgo – Food Research International

“Evolution of symbiont population in feces was studied using culture-dependent and culture-independent methods. In the latter, the V3 region of 16S rDNA was amplified and separated by Denaturing Gradient Gel Electrophoresis; followed by sequencing of the most representative bands. “

Animal gut microbiome

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture – D.W. Pitta – Anaerobe

“Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. “

Metabolomics

The cross talk between microbiota and the immune system: metabolites take center stage – Hagit Shapiro – Current Opinion in Immunology

“While most attention has focused on the innate recognition of immune-stimulatory bacterial molecules, such as cell wall components and nucleic acids, we emphasize here the impact of diet-dependent microbial metabolites on the development and function of the immune system.”

Bioinformatics tools

eSNaPD: A Versatile, Web-Based Bioinformatics Platform for Surveying and Mining Natural Product Biosynthetic Diversity from Metagenomes – Boojala Vijay B. Reddy – Chemistry & Biology

“Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. “

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA – Imogen A. Wright and Simon A. Travers

“To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA”

Computational integration of genomic traits into 16S rDNA microbiota sequencing studies – Alexander Keller – Gene

“Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes.”

Viruses and helminths

How helminths go viral – Rick M Maizels1, William C Gause

“On pages 573 and 578 of this issue, Reese et al. (3) and Osborne et al. (4), respectively, provide fine detail on how helminth worms can substantially enhance and reactivate viral infection, with major health implications for tropical medicine.”

Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter – T. A. Reese – Science

“We found that helminth infection, characterized by the induction of the cytokine interleukin-4 (IL-4) and the activation of the transcription factor Stat6, reactivated murine γ-herpesvirus infection in vivo.”

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation – Lisa C. Osborne – Science

“Helminth coinfection resulted in impaired antiviral immunity and was associated with changes in the microbiota and STAT6-dependent helminth-induced alternative activation of macrophages. “

More Microbiology

Larger Mammalian Body Size Leads to Lower Retroviral Activity – Aris Katzourakis – PLOS Pathogens

“Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. “

Microbes in the news

Researcher: Bacteria Ate Some Gulf Spill Toxins, but Worst Remain – Sandy Smith – EHS Today

“In two new studies conducted in a deep sea plume, Assistant Professor Olivia Mason found a species of bacteria called Colwellia likely consumed gaseous hydrocarbons and perhaps benzene, toluene, ethylbenzene and xylene compounds that were released as part of the oil spill. “

Baxter breaks out – Hal Hodson – New Scientist
http://www.sciencedirect.com/science/article/pii/S0262407914614342

“Baxter is even turning its grippers to lab work. Correll is working with UCB’s Rob Knight to teach Baxter the job of preparing faeces samples for research.”

Science and Career

The stressed-out postdoc – Carrie Arnold – Science

“After he defended his dissertation and moved to a new lab for his postdoc, Ian Street hoped his battles with anxiety and depression were over.”

Bik’s Picks

Africa Needs Science, Not Aid – Nkem Khumbah and Melvin P. Foote –  The New York Times

“Scientific and technological advancement will help eradicate poverty and promote homegrown economic development by providing Africa with the tools to address its own challenges and expand its industrial productivity. “

DDT Linked To Obesity In Female Mice Long After Exposure – Hank Campbell – Science 2.0

“A new epidemiology paper in PLOS One doesn’t try to prove that, the authors instead correlate DDT use from generations ago with increased waistlines of today.  DDT exposure may have made you fat, they conclude.”

 

A Lick Of The Tongue Changes This Ice Cream’s Color – Loren Grush – Popular Science

“The result was Xamaleón, which is Spanish for “chameleon.” With a patent pending, Linares is staying tight-lipped on the recipe, but apparently there’s a special ingredient dubbed the “love elixir,” which must be spritzed on the ice cream before it’s eaten. “

 

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Scientists explain mystery of our ‘lemon Moon’ – James Vincent – The Independent

“A new accurate map of the Moon has shown that it bulges slightly at one side and is flattened at the top and bottom – but how did it get this way?”

 

 

 

Microbiome digest, July 30

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Host diet, sex, and the microbiome, smoking cessation, eukaryotic microbes, CRISPRs and my picks.

Gut microbiome

Individual diet has sex-dependent effects on vertebrate gut microbiota – Daniel I. Bolnick – Nature Communications

“Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. “

Smoking Cessation Alters Intestinal Microbiota: Insights from Quantitative Investigations on Human Fecal Samples Using FISH – Biedermann L – Inflammatory Bowel Diseases

“As determined by fluorescence in situ hybridization, an independent direct quantitative microbial approach, we could confirm that intestinal microbiota composition in humans is influenced by smoking.”

More microbiology

Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria – Jean-David Grattepanche – Trends in Microbiology

“High-throughput sequencing tools underestimate the diversity of eukaryotes by removing morphospecies.”

Microbes in the news

A Trip Overseas Could Change The Bugs Living In Your Gut – Bahar Gholipour – Huntington Post

“I was amazed to see how profoundly a single food poisoning event impacted the gut bacteria,” David, who was a researcher at Harvard University at the time of the study, said in a statement.

Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens – Joe Montgomery – Kansas State University News Office – Labmanager.com

“Benjamin Hause, an assistant research professor at the Kansas State Veterinary Diagnostic Laboratory at Kansas State University, recently published an article about one of his discoveries, porcine enterovirus G, which is an important find in the United States.”

Antibiotics and resistance

Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance – Orsolya Méhi – Molecular Biology and Evolution

“To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated that the set of genes regulated by Fur change substantially in response to antibiotic treatment. “

Phages, viruses, and CRISPRs

Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages – Alexander P. Hynes – Nature Communications

“Here we demonstrate that cells can acquire spacers from defective phages at a rate directly proportional to the quantity of replication-deficient phages to which the cells are exposed.”

Dr. Bik’s Picks

Contamination hits cell work: Mycoplasma infestations are widespread and costing laboratories millions of dollars in lost research – Ewen Callaway – Nature

“A total of 11% of the samples were found to contain Mycoplasma DNA at levels indicative of contamination.”

Five daily portions of fruit and vegetables may be enough to lower risk of early death – Science Daily

“Eating five daily portions of fruit and vegetables is associated with a lower risk of death from any cause, particularly from cardiovascular disease, but beyond five portions appears to have no further effect, finds a new study.”

Lands’ End Announces Science-Themed Tees For Girls After Mom’s Letter Goes Viral – Jessica Samakow – The Huffington Post

“My daughter was very confused. Lots of her friends that are girls love science, too. Why were there no cool science shirts for girls?”

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