Category Archives: Human gut

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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Human microbiome, July 29

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Papillomaviruses in human skin, gastric mucosa in cancer patients, breast milk metabolome, microbiome of a human family, and more.

Skin microbiome

Deep sequencing extends the diversity of human papillomaviruses in human skin –
Davit Bzhalava – Nature Scientific Reports

“This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses.”

Gastric microbiome

Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods – Chang Soo Eun – Helicobacter

“Gastric mucosal biopsy samples were collected from 31 patients during endoscopy. After the extraction of genomic DNA, variable region V5 of the 16S rRNA gene was amplified. PCR products were sequenced using 454 high-throughput sequencer. “

Pregnancy and Birth

Breast milk metabolome characterization in a single phase extraction, multiplatform analytical approach – Alma Villaseñor – Analytical Chemistry

“We conducted this single-phase extraction procedure on a representative pool of BM, and characterized the metabolic composition using LC-QTOF-MS and GC-Q-MS for polar and lipidic metabolites. “

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the
Prevention of Allergy Development in Infants and on Fecal Microbiota [PDF]- Tadao Enomoto – Allergology International

“Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota”

Gut microbiome
The dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.”

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression – Charles K. Fisher – PLOS ONE

“Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. “

Antivirulence Activity of the Human Gut Metabolome – L. Caetano M. Antunes – mBio

“We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion.”

 Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase – Eamonn P. Culligan – PLOS ONE

“Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. “

Review: Archaea and the human gut: New beginning of an old story [DOC]- Gaci N – World Journal of Gastroenterology

“Here we provide an updated census of the archaeal diversity associated to human GIT and their possible role in the gut physiology and health.”

 

Animal models of human microbiome and disease

Maternal high protein or prebiotic fiber diets affect maternal milk composition and gut microbiota in rat dams and their offspring – Megan C. Hallam – Obesity

“Fecal microbiota was analyzed in dams at parturition and 2 weeks post-partum and in offspring at 5 and 22 weeks along with cecal digesta at termination.”

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Human microbiome, July 28

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Oral microbes balancing their budgets, bacteria see blue, why Obama likes to fist bump, Gardnerella, and oxygen gradients in the gut.

Oral microbiome

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

“For Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Streptococcus sanguinis, the outer membrane/extracellular proteins are made up of a much larger percentage of lower average mass amino acids whereas cytoplasmic proteins are made up of a larger proportion of higher average mass amino acid residues.”

Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity – Ashley M. Richards – Molecular Oral Microbiology

“A. baumannii can sense blue light through a blue-light sensing using flavin (BLUF) domain protein, BlsA. The resulting conformational change in BlsA leads to changes in gene expression, including virulence genes.”

Skin microbiome

Study: Fist bumps are less germy than handshakes – Kim Painter – USA Today

“Whitworth and a colleague systematically tested the three greetings for a study published Monday in the American Journal of Infection Control.” (article not available yet – MD).

Vaginal microbiome

Gardnerella vaginalis Outcompetes 29 Other Bacterial Species Isolated From Patients With Bacterial Vaginosis, Using in an In Vitro Biofilm Formation Model – Patrícia Alvesa – Journal of Infectious Diseases

“Here, we isolated 30 BV-associated species and characterized their virulence, using an in vitro biofilm formation model. “

Long-term Effect of Depot Medroxyprogesterone Acetate on Vaginal Microbiota, Epithelial Thickness and HIV Target Cells – Caroline M. Mitchell – Journal of Infectious Diseases

“Vaginal microbiota of women using DMPA for up to 2 years were cultured. Mucosal immune cell populations were measured by immunohistological staining.”

Gut microbiome

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota in Humans and Mice – L. Albenberg – Gastroenterology

“In humans, 16S rRNA gene analyses revealed an increased proportion of oxygen-tolerant organisms of the Proteobacteria and Actinobacteria phyla associated with the rectal mucosa, compared with the feces, indicating an effect of oxygenation on the microbiota. “

Patients with cystic fibrosis have a high carriage rate of non-toxigenic Clostridium difficile – M. P. Bauer – Clinical Microbiology and Infection

“In this case-control study, we found more carriers among CF patients than controls (47% versus 11%), but most strains carried by CF patients were non-toxigenic (77% versus 17%). “

Animal models of human microbiome and disease

Obese-type Gut Microbiota Induce Neurobehavioral Changes in the Absence of Obesity
Annadora J. Bruce-Keller – Biological Phychiatry

“Sequencing-based phylogenetic analysis confirmed the presence of distinct core microbiota between groups, with alterations in α- and β-diversity, modulation in taxonomic distribution, and statistically significant alterations to metabolically active taxa. “

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Microbiome Digest, July 25

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A year worth of oral/stool samples shows relative stability, antibiotics and preterm infants, reagent contamination, and 42. Have a great weekend!

 

Oral and gut microbiome

Screen Shot 2014-07-25 at 9.45.01 PMHost lifestyle affects human microbiota on daily timescales – Lawrence A David – Genome Biology

“Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. “

Pregnancy and Birth

Screen Shot 2014-07-25 at 9.44.20 PMThe impact of postnatal antibiotics on the preterm intestinal microbiome – Majd Dardas – Pediatric Research

“Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics.”

Techniques

Screen Shot 2014-07-25 at 9.45.50 PMReagent contamination can critically impact sequence-based microbiome analyses – Susannah Salter – BioRxiv (preprint)

“In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. “

Dengue

Speaking about “matter of timing”, seems like this paper came out a bit too late.
Screen Shot 2014-07-25 at 9.46.14 PMDengue and the World Football Cup: A Matter of Timing – Christovam Barcellos, Rachel Lowe – PLOS Neglected Tropical Diseases

“We provide a nationwide risk map, averaging June dengue incidence rates for 2001–2012. The areas along the Amazonian rivers and in the inner portions of southernmost states are actually low-risk areas, while elevated dengue risk is found in the central Brazilian plateau.”

Infection and host response

Don’t forget your towel! Even the issue number, 1004201, contains the “The Answer to the Ultimate Question of Life, the Universe, and Everything”. Perfection.
Screen Shot 2014-07-25 at 9.46.22 PMMicrobial Egress: A Hitchhiker’s Guide to Freedom – Ana Traven, Thomas Naderer – PLOS Pathogens

“The Restaurant at the End of the Infection — Macrophages as Host Cells”
“So Long and Thanks for All the Inflammatory Cell Death”

Dr. Bik’s Picks

crowSmarter than a first-grader? Crows can perform as well as 7- to 10-year-olds on cause-and-effect water displacement tasks

“New research conducted by UC Santa Barbara’s Corina Logan, with her collaborators at the University of Auckland in New Zealand, demonstrates the birds’ intellectual prowess may be more fact than fiction.”

JBC Journal of Biological ChemistryFour billion-year-old chemistry in cells today – Phys.org

“Parts of the primordial soup in which life arose have been maintained in our cells today according to scientists at the University of East Anglia.”

Screen Shot 2014-07-25 at 9.47.50 PMDustup Over Lionfish Science Fair Project – Bob Grant – The Scientist

A former graduate student says he feels slighted by a failure to attribute his contributions to a line of research regarding the salinity tolerances of an invasive species. “I’m not sure what happened, but my main issue is that the national media has presented a story that is sensationalized, and has left me out of the picture.”

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Microbiome digest, July 24

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Introducing the crAssphage, an 84 bp BLAST from the past, archaea in the Savannah, metabolomics of racehorse microbiome, and X-raying headphones.

Human oral microbiome

Proceedings RoyalMolecular analysis of ancient caries – Marc Simón – Proceedings of the Royal Society, Biological Sciences

“An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. “

Human gut microbiome

Nature CommunicationsA highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes – Bas E. Dutilh – Nature Communications

“Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage.”

Gut family SchlossThe dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Using 16S rRNA gene and metagenomic shotgun sequence data, it was possible to distinguish the family from a cohort of normal individuals living in the same geographic region and to differentiate each family member”

Pregnancy and Birth

Screen Shot 2014-07-24 at 05.53PM, Jul 24An unnecessary cut? – Sky Dylan-Robbins – The New Yorker

“The most common operating-room procedure in the United States is the Cesarean section. “

Animal microbiome

Equine Vet JournalCharacterisation of the faecal metabolome and microbiome of Thoroughbred racehorses – C. J. Proudman – Equine Veterinary Journal

“Faecal metabolome was characterised using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS), with spectral analysis performed using AMDIS and compared against the NIST database. Taxonomic description of the faecal microbiota was achieved using error-corrected 454 pyrosequencing data from 16S rRNA gene amplicons”

Journal of MicrobiologyPyrosequencing-based analysis of fecal microbial communities in three purebred pig lines – Edward Alain B. Pajarillo – Journal of Microbiology

“Taxon-dependent and -independent analyses were performed to evaluate differences in the fecal bacterial communities and to identify bacterial genera that can be used to discriminate breeds, following high-throughput pyrosequencing of 16S rRNA genes. “

Environmental microbiome

Screen Shot 2014-07-24 at 05.55PM, Jul 24Seasonal Effects in a Lake Sediment Archaeal Community of the Brazilian Savanna – Thiago Rodrigues – Archaea

“Here we describe for the first time the diversity of archaeal communities from freshwater lake sediments of the Cerrado in the dry season and in the transition period between the dry and rainy seasons, when the first rains occur. Gene libraries were constructed, using Archaea-specific primers for the 16S rRNA and amoA genes.”

Screen Shot 2014-07-24 at 05.56PM, Jul 24Spatial patterns and links between microbial community composition and function in cyanobacterial mats – Mohammad A. Al-Najjar – Frontiers in Microbiology

“Similar clustering was found when the community composition of the mats’ cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis, indicating a significant link between the microbial community composition and function. “

MicrobeNetNew Joint Initiative from the Knight and Sogin Labs as a Follow-up to the MoBEDAC Initiative – Embriette Hyde

“By the end of the funded period, standard 16S rRNA and ITS (fungal) analysis pipelines will be developed and made available to the MoBe community, 16S rRNA and ITS databases will be markedly improved, QIIME and VAMPS will be tightly integrated into a new database engine called QiiTA to facilitate analysis by all MoBe researchers, and two major training workshops will be offered. “

Dr. Bik’s PicksDNA

DNA mostly ‘junk?’ Only 8.2 percent of human DNA is ‘functional’, study finds – Science Daily

“This figure is very different from one given in 2012, when some scientists involved in the ENCODE (Encyclopedia of DNA Elements) project stated that 80% of our genome has some biochemical function.”

Screen Shot 2014-07-24 at 05.58PM, Jul 24Sex differences in medicine – BeWell – Stanford University

“A man can be diagnosed with the same disease as a woman, and yet the course the disease takes in each could prove very different. And a treatment which works for one gender may prove ineffective for the other. “

corksIs Climate Change Ruining Wine Corks? – Kelly Dickerson – LiveScience

“Many people may only worry about corks when it’s time to pop the Champagne, but some experts are worried about wine cork quality, which has been mysteriously in decline for almost 20 years.“

Headphone x rayDoc X-Rays His Broken Headphones to Fix Them – Bahar Gholipour – LiveScience

“”Closed fracture of a speaker wire within its rubber/plastic sleeve is a rare headphone injury, usually due to a traction trauma,” Skalski wrote in his report of the case.”

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Microbiome digest, July 23

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Just one post today. Invading oral bacteria found in liver cirrhosis patients guts, obesity, biofilms and dispersal, motile and electric bacteria, dengue, and Weird Al Yankovic.

General microbiome

Screen Shot 2014-07-23 at 7.12.37 PMRadio show: City Visions: Exploring the Human Microbiome

“City Visions host David Onek explores these questions and more with Bay Area leading researchers Katie Pollard of the Gladstone Institutes, Susan Lynch of UCSF, and Peter diLaura of Second Genome.”

Human gut microbiome

Nan Qin Nature GutAlterations of the human gut microbiome in liver cirrhosis – Nan Qin – Nature

“Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals… Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. “

Lancet DiabetesObesity, inflammation, and the gut microbiota – Amanda J Cox – The Lancet Diabetes & Endocrinology

“In this Review, we provide evidence supporting perturbation of the intestinal microbiota and changes in intestinal permeability as potential triggers of inflammation in obesity.”

ParasitesOpinion: (Self-) infections with parasites: re-interpretations for the present
Julius Lukeš – Trends in Parasitology

“Here, we critically review cases in which humans were deliberately infected with parasites. Moreover, we summarize the contribution of (self-) infections and propose protist and helminth candidates, chosen on the basis of several criteria, to test as possible therapy for selected human diseases.”

General Microbiology

Screen Shot 2014-07-23 at 7.14.29 PMDispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles – Song Lin Chua – Nature Communications

“Here we use single-nucleotide resolution transcriptomic analysis to show that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells. “

Screen Shot 2014-07-23 at 7.15.00 PMBrownian motion? – Bacteria swim with bodies and flagella – Kevin Stacey – Brown University

“Using a new technique to track the swimming motion of a single bacterium, researchers have discovered that the movement of the bacterium’s body — not just thrust from the flagellum — allow movement through fluids.”

NewScientistBacteria that don’t need to eat: Meet the electric life forms that live on pure energy – Catherine Brahic – New Scientist

“Unlike any other living thing on Earth, electric bacteria use energy in its purest form – naked electricity in the shape of electrons harvested from rocks and metals. “

NatureCell communication: Stop the microbial chatter – Vivien Marx – Nature

“Bacteria can coat everything from thermal springs to teeth. Researchers are looking for antibiotics that can subvert the signalling that the microbes use to carve their niche.”

Dengue

Screen Shot 2014-07-23 at 7.19.32 PMSafety, immunogenicity and efficacy of a recombinant tetravalent dengue vaccine: A meta-analysis of randomized trials – Vivaldo G. da Costa – Vaccine

“..we conducted a meta-analysis to determine a more precise estimate of the overall parameters of safety, immunogenicity and efficacy of CYD-TDV. A data search was conducted in the PubMed, Medline, Cochrane Central Register of Controlled Trials and SciELO databases with defined selection criteria.”

Screen Shot 2014-07-23 at 7.19.57 PMKinome siRNA screen identifies novel cell-type specific dengue host target genes – Yong-Jun Kwon – Antiviral Research

“To identify novel human host cell targets important for dengue virus infection and replication, an image-based high-throughput siRNA assay screening of a human kinome siRNA library was conducted using human hepatocyte cell line Huh7 infected with a recent dengue serotype 2 virus isolate BR DEN2 01-01.”

Dr. Bik’s Picks

Bat polarizationA functional role of the sky’s polarization pattern for orientation in the greater mouse-eared bat – Stefan Greif – Nature Communications

“Here we demonstrate that the female greater mouse-eared bat (Myotis myotis) uses polarization cues at sunset to calibrate a magnetic compass, which is subsequently used for orientation during a homing experiment. “

Screen Shot 2014-07-23 at 7.20.54 PMScience and politics: Hello, Governor – Virginia Gewin – Nature

“When California’s governor enlisted the aid of two palaeoecologists, their careers took an unusual turn.”

Screen Shot 2014-07-23 at 7.21.49 PMYouTube distraction: Foil – Weird Al Yankovic music video

“fungal rot, bacterial formation, microbes, enzymes, mould and oxidation”

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Human microbiome, July 22

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Transcriptome in periodontitis, metabolomic analysis of breath in IBD patients, cystic fibrosis microbiome, and Clostridium difficile.

Human microbiome general

Review: Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana and Dennis L. Kasper – Journal of Clinical Investigation

“In this Review, we discuss the current state of knowledge regarding the role of the intestinal microbiota in immunologic development, highlighting mechanistic principles that can guide future work.”

Meeting report: Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 – Jacques Ravel and many others – Microbiome

“This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.”

Metabolomics

Metabolomic analysis of breath volatile organic compounds reveals unique breathprints in children with inflammatory bowel disease: a pilot study – N. Patel – Alimentary Pharmacology & Therapeutics

“Exhaled breath was collected and analysed using a selective ion flow tube mass spectroscopy (SIFT-MS) to identify new markers or patterns of IBD.”

Metabolites related to gut bacterial metabolism, peroxisome proliferator-activated receptor-alpha activation, and insulin sensitivity are associated with physical function in functionally-limited older adults – Michael S. Lustgarten – Aging Cell

“Collectively, these data suggest that gut microbial metabolism, PPAR-α activation, and insulin sensitivity may be involved in mechanisms that underlie physical function in functionally-limited older adults.”

Oral microbiome

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis – Ana E Duran-Pinedo – ISME J

“We report here the in situ genome-wide transcriptome of the subgingival microbiome in six periodontally healthy individuals and seven individuals with periodontitis.”

Respiratory microbiome

Predominant pathogen competition and core microbiota divergence in chronic airway infection – Geraint B Rogers – ISME Journal

“..we analysed 16S rRNA gene pyrosequencing data generated previously from 60 adult bronchiectasis patients, whose airway microbiota was dominated by either P. aeruginosa or H. influenzae.”

Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics – Daniel J. Smith – European Respiratory Journal

“Microbial community profiles were derived through analysis of bacterial-derived 16S ribosomal RNA by pyrosequencing and changes over time were compared.”

Review: Respiratory microbiota: addressing clinical questions, informing clinical practice – Geraint B Rogers – Thorax

“In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. “

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation – Michael S. Wollenberg – mBio

“We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. “

Gut microbiome

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection – Susana Fuentes – ISME Journal

“Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. “

Review: Clostridium difficile and the microbiota – Anna M. Seekatz and Vincent B. Young – Journal of Clinical Investigation

“Both human and animal models have demonstrated the importance of the gut microbiota’s capability of providing colonization resistance against C. difficile.”

Vaginal microbiome

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME Journal

“We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. … humans were distinct from other primates in both microbiome composition and diversity.“

Semen microbiome

The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection – Cindy M. Liu – PLOS Pathogens

“HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART.”

Antibiotic perturbation and microbiome

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations – Torey Looft – ISME Journal

“In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. “

Impact of Antibiotics on the Intestinal Microbiota and on the Treatment of Shiga-toxin-Producing Escherichia coli and Salmonella Infections – Szych, Jolanta – Current Pharmaceutical Design

“This review evaluates the current literature based on the impact of antibiotics on the intestinal microbiota and the critical role of intestinal bacteria in controlling infection and subsequent clinical disease caused by STEC and Salmonella, and the transmissibility of these important pathogens”

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Human microbiome digest, July 21

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Today we have articles on two microbiome pioneers: Rob Knight and Jeffrey Gordon, as well as papers on periodontitis, eczema, Crohn’s disease, and Helicobacter.

General microbiome

The effects of the microbiota on the host immune system – Jacek Karczewski – Autoimmunity

“This review is focused on host–microbiota interactions, specifically on influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory and autoimmune diseases.”

Imposition of encapsulated non-indigenous probiotics into intestine may disturbs human core microbiome – Abolfazl Barzegari – Frontiers in Microbiology

“We envision that the lack of survivability of some of the probiotic candidates within such hostile milieu of GIT may negatively affect the coevolving process of bacteria in human host and hence impact the endpoint health promotion goals.”

40 under 40: Rob Knight – Cell

“Some dead scientists who I would have loved to have had the opportunity to work with include Carl Woese, Richard Feynman, Francis Crick, Erwin Chargaff, Sewall Wright, Benjamin Franklin, Antonie van Leeuwenhoek, Robert Boyle, Eratosthenes, and Lucretius. These lists are intended to be illustrative rather than exhaustive; according to my NSF Conflict of Interest form I have written grants or papers with about 750 people, all of whom I admire.”

Jeffrey I. Gordon, M.D., Will Receive Pitt’s Dickson Prize at Science 2014—Sustain It! – University of Pittsburgh

“A scientist who has explored how the tens of trillions of microbes that live in the gastrointestinal tract and their genes influence human physiology, metabolism and nutritional status will receive the University of Pittsburgh’s 2014 Dickson Prize in Medicine.”

Oral microbiome

Quantitative analysis of classical and new putative periodontal pathogens in subgingival biofilm: a case–control study – N. N. Al-hebshi – Journal of Periodontal Research

“Pooled subgingival biofilm samples were obtained from 40 patients with chronic periodontitis and 40 healthy controls. Taqman q-PCR assays were used to determine the absolute and relative counts of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Parvimonas micra, Filifactor alocis, oral Synergistetes and oral TM7s. “

Skin microbiome

Review: Microbiota in Healthy Skin and in Atopic Eczema – Giuseppe Baviera – BioMed Research International

“This review also highlights recent observations on the importance of innate immune systems and the relationship with normal skin microflora for the maintenance of healthy skin.”

Gastric microbiome

Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient – Incheol Seo – Journal of Bacteriology and Virology

“In this study, we identified differences in the microbial communities between gastric cancer and normal gastric mucosa by comparing the microbiomes of tissues from the same patients. The clustering analysis results showed different bacterial communities between normal gastric mucosa and gastric cancer.”

Motility and Chemotaxis Mediate the Preferential Colonization of Gastric Injury Sites by Helicobacter pylori – Eitaro Aihara – PLOS Pathogens

“Using anesthetized mice in which we have induced microscopic damage to the stomach surface, we find that H. pylori is able to rapidly detect and navigate towards this damage site. Within minutes, bacterial accumulation slows repair of the damage.”

Gut microbiome

Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome
Yue-Dong Gao – BioMed Research International

“we investigated the E. coli strains in human gut microbiome using deep sequencing data and reconstructed genome-wide metabolic networks for the three most common E. coli strains, including E. coli HS, UTI89, and CFT073. “

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease [PDF] – Sumathi Sankaran Walters – Symbiosis

“Fecal samples were obtained from patients with Crohn’s disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms. The gut microbiota composition was assessed using a high-density DNA microarray PhyloChip “

Review: Managing the manager: Gut microbes, stem cells and metabolism –
M. Serino – Diabetes & Metabolism

“The LPS-sensitive cell types can be seen within bone marrow-derived cells (BMC), which are involved in the development of inflammation in the adipose tissue of obese and type 2 diabetic mice. “

 

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