Category Archives: Pregnancy and birth

Microbiome digest, August 15, 2014

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Today we got donkey, goat, and camel milk, deodorants, kitten microbiomes, and coffee as a new mouth rinse.

Pregnancy and birth

Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study – Mohamed Ben Said – Early Human Development

“Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. “

Human oral microbiome

Antibacterial effect of coffee: calcium concentration in a culture containing teeth/biofilm exposed to Coffea Canephora aqueous extract – N. Meckelburg – Letters in Applied Microbiology

“This study revealed an inhibitory action of Coffea canephora against dental biofilm. This coffee species caused bacterial lysis and consequent release of calcium into the medium.”

Human gut microbiome

Review: Exploring gut microbes in Human health and disease: pushing the envelope
Jun Sun, Eugene B. Chang – Genes & Diseases

“In this review and commentary, we highlight recent progress in our understanding of the intestinal microbiome in the context of health and diseases, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.”

Review: Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology – Alexander Khoruts, Alexa R. Weingarden – Immunology Letters

“Mechanistic understanding will be required in development of next generation microbiota therapeutics, which may include FMT or defined microbial consortia.”

Gut Bacteria May Play a Role in Autism – Melinda Wenner Moyer – Scientific American

“One open question is whether these microbial differences drive the development of the condition or are instead a consequence of it. “

Skin microbiome

Deodorants and antiperspirants affect the axillary bacterial community – Chris Callewaert — Archives of Dermatological Research

“The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics.”

Goat and Ass Milk microbiome

Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity – Elizabeth A. McInnis – Food Microbiology

“Milk from transgenic goats containing lysozyme had a similar microbiota over time.”

Fasscinating stuff: Cleopatra took daily baths in assmilk to keep her skin wrinklefree. Maybe lactic acid bacteria were her secret?  Biotyping of cultivable lactic acid bacteria isolated from donkey milk – D. Carminati – Letters in Applied Microbiology

“The large amounts of antimicrobial components and defence factors present in donkey’s milk provide protection from microbial infections and distinguish donkey’s milk from the milks of other mammals”

The Kitten Microbiome Project

“Keeping track of the cutest, fluffiest microbiome project around”

Insect microbiome

Microbial impacts on insect evolutionary diversification: From patterns to mechanisms
Fabrice Vavre, Natacha Kremer – Current Opinion in Insect Science

“Symbiosis can favor rapid shifts in host phenotypic traits, particularly through the contribution of symbionts to the host’s physiology.”

How resident microbes modulate ecologically-important traits of insects
Kerry M. Oliver, Adam J. Martinez – Current Opinion in Insect Science

“In addition to their better-known roles in nutrient provisioning and degrading plant polymers, there is emerging evidence that microorganisms also aid herbivores in countering plant defenses. “

Metabolomics

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking – Kalai Vanii Jayaseelan and Christoph Steinbeck – BMC Bioinformatics

“In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process.”

Phages and viruses

Bacteriophage as effective decolonising agent for elimination of MRSA from anterior nares of BALB/c mice – Sanjay Chhibber – BMC Microbiology

“Phage MR-10, given along with mupirocin showed an additive effect and the combination was able to effectively eradicate the colonising MRSA population from the nares of mice by day 5.”

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target – Sabin Mulepati, Annie Héroux, Scott Bailey – Science

“The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. “

Bik’s Picks – weekend edition

15 Real-Life Scientists Share Their Favorite Science Fiction Books, Movies – Jacqueline Howard – Huffington Post

“There’s a big difference between science and science fiction, but there’s abundant evidence to suggest that sci-fi books and movies can spark a lifelong interest in science.”

After donkey and goat milk, this one was only appropriate: A Nice Tall Glass of Camel’s Milk – Olga Khazan – The Atlantic

“An oasis in the dromedary-dairy desert?”

Male Mathematicians Agree That Fields Medal Gender Balance Is Now OK – The Allium

“Now that a woman has won the fields medal, there is true and genuine equality and there is no need to worry any more about it.”

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General microbiology and science, August 14

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A metabolic map of Faecalibacterium prausnitzii, bacteria injections to cure cancer, a researcher smuggling live bacteria in a lunchbox,  and a scientist in trouble for posting a PhD thesis.

Metabolomics

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe – Almut Heinken – Journal of Bacteriology

“In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms.”

Transcriptomics

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes – Joseph T. Wade & David C. Grainger – Nature Reviews Microbiology

“In this Opinion article, we discuss our current understanding of pervasive transcription, its genetic origin and its regulation. “

More microbiology

Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses
Nicholas J. Roberts – Science Translational Medicine

“On the basis of these encouraging results, we treated a human patient who had an advanced leiomyosarcoma with an intratumoral injection of C. novyi-NT spores. This treatment reduced the tumor within and surrounding the bone. “

Canadian ex-researcher pleads guilty in attempted bacteria-smuggling case – Lee-Anne Goodman

“With his wife in the passenger seat, they discovered in his suitcase 17 vials of live Brucella — contained in a block of ice and swathed in bubble wrap in a children’s lunch bag — and a substantial quantity of goat’s blood.”

Techniques

Preprint: Swabs to Genomes: A Comprehensive Workflow – David A Coil – PeerJ

“The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome”

Accuracy of Next Generation Sequencing Platforms – Edward J Fox – Next Generation: Sequencing & Applications

“The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates”

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences — Pablo Yarza – Nature Reviews Microbiology

“Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.”

Science, Publishing, Career

Financial costs and personal consequences of research misconduct resulting in retracted publications – Andrew M Stern, Arturo Casadevall, R Grant Steen, Ferric C Fang – eLife

“We found that papers retracted due to misconduct accounted for approximately $58 million in direct funding by the NIH between 1992 and 2012, less than 1% of the NIH budget over this period. ”

Student may be jailed for posting scientist’s thesis on web – David Reay – Nature News Blog

“Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network. Diego Gómez Hoyos posted the 2006 work, about amphibian taxonomy, on Scribd in 2011.

Study: Uncivil work environment pushing women out of the engineering field – Brigid Schulte – Washington Post

“a new National Science Foundation report released on Saturday about why so few women go into engineering, or stay in the field, highlights a key reason: a workplace culture of incivility toward women.”

Science of inclusion – Holly McDede – SFBG.com

“As Big Tech struggles with diversity, women find support and fellowship in the biotech industry.”

Bik’s Picks

Pour on the Salt? New Research Suggests More Is OK – Judy Silverman and Lisa Tolin – NBC News

“New research suggests that healthy people can eat about twice the amount of salt that’s currently recommended — or about as much as most people consume anyway. “

At Harvard, tiny robots ‘swarm’ into shape – Carolyn Y. Johnson – Boston Globe

“When Harvard scientist Michael Rubenstein walks into the laboratory in the morning, he is greeted with a scene somewhere between a disco and the opening of a science fiction movie about a robot apocalypse. A constellation of LED lights blinks in the darkness — the electronic heartbeat of his 1,024-robot horde. They are ready to do his bidding.”

Newborns’ genetic code sends infection distress signal – Science Daily

“Babies suffering from life-threatening bacterial infections such as sepsis could benefit from improved treatment, thanks to a ground-breaking study. “

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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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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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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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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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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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Bifidobacterium longum and Bifidobacterium breve isolates from preterm and full term neonates: Comparison of cell surface properties

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Screen Shot 2014-07-18 at 2.31.12 PMBifidobacterium longum and Bifidobacterium breve isolates from preterm and full term neonates: Comparison of cell surface properties
Valérie Andriantsoanirina – Anaerobe

“Our results suggest the existence of variations in bifidobacteria membrane structure and/or composition that may reflect adaptation of these bacteria to the intestinal environment of either preterm or full term neonates. “