Category Archives: Human oral

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 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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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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Human and bioreactor microbiome, July 18

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An upcoming radio show on the human microbiome that looks interesting, dental calculus from prehistoric skeletons (without bacterial analysis unfortunately), and animals models of microbiome research.

General microbiome

City Visions: Exploring the Human Microbiome – KALW public radio – Monday July 21 at 7 pm at 91.7 FM in San Francisco

“Join host David Onek as we explore these questions and more with Bay Area researchers who are leading the new field of microbiome exploration and discovery.”

Oral microbiome

Dental Calculus Reveals Unique Insights into Food Items, Cooking and Plant Processing in Prehistoric Central Sudan – Stephen Buckley – PLOS ONE

“Here we present a suite of results from the multi-period Central Sudanese site of Al Khiday. We demonstrate the ingestion in both pre-agricultural and agricultural periods of Cyperus rotundus tubers. “

Animal models of gut microbiota and disease

Gut Microbial Metabolism Drives Transformation of Msh2-Deficient Colon Epithelial Cells – Antoaneta Belcheva – Cell

“We report that altering the microbiota composition reduces CRC in APCMin/+MSH2−/− mice, and that a diet reduced in carbohydrates phenocopies this effect. “

Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota – Jeffrey D Galley – BMC Microbiology

“..we used high throughput pyrosequencing to assess the effects of a single 2-hour exposure to a social stressor, called social disruption (SDR), on colonic mucosa-associated microbial profiles of C57BL/6 mice.”

Bioreactor microbiome

Ethyl tert-Butyl Ether (ETBE)-degrading microbial communities in enrichments from polluted environments – Yoann Le Digabel – Journal of Hazardous Materials

“Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases.”

Microbial community structure of wastewater treatment subjected to high mortality rate due to ozonation of return activated sludge – S. Isazadeh – Journal of Applied Microbiology

“The bacterial community structures were investigated by 16S rRNA gene amplicon high-throughput pyrosequencing and fluorescence in situ hybridization (FISH). The structures remained highly similar throughout the experiment despite the ozone treatment.”

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Human microbiome, July 17

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Protozoa detection in fecal samples from children, airway microbiome, and Staphylococcus transmission between mother and child.

Oral microbiome

Oral Lihong GuoIntercellular communications in multispecies oral microbial communities – Lihong Guo – Frontiers in Microbiology

“This review will summarize the evidence that oral microbes participate in intercellular communications with co-inhabitants through cell contact-dependent physical interactions, metabolic interdependencies, as well as coordinative signaling systems to establish and maintain balanced microbial communities.”

Respiratory microbiome

Screen Shot 2014-07-17 at 4.58.37 PMAirway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease – Yvonne J. Huang – Journal of Clinical Microbiology

“In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD.”

Screen Shot 2014-07-17 at 4.59.26 PMTime between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions.”

Gut microbiome

Screen Shot 2014-07-17 at 4.58.09 PMThe devil lies in the details: How variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes – Eric C. Martens – Journal of Molecular Biology

“Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates”

Pregnancy and birth

Protozoa pediatricDetection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Staph transmTransmission of Staphylococcus aureus between mothers and infants in an African setting – F. Schaumburg – Clinical Microbiology and Infection

“We aimed to investigate the transmission of S. aureus between mothers and their newborns during the first year after delivery in an African setting. In a longitudinal cohort study, colonization of Gabonese mother–infant pairs was assessed at delivery and after 1, 9 and 12 months.”

Commentary: Travelling within the fetal gut: simple rules for an arduous journey
Qiling Xu – BMC Microbiology

“A recent paper in BMC Biology addresses this issue with live imaging of gut explants from mouse embryos.”

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Human (and fish) microbiome, July 16

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Oral microbiome in children with leukemia, and effects of antibiotics on fish microbiota.

Human oral microbiome

Oral Microbiota Distinguishes Acute Lymphoblastic Leukemia Pediatric Hosts from Healthy Populations – Yan Wang – PLOS ONE

“The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls.”

Human gut microbiome

Editorial: New bacteria associated with diarrhoea – Cláudio Nunes-Alves – Nature Reviews Microbiology

“Pop et al. used high throughput 16S rRNA sequencing to compare the faecal microbiota composition in 992 children from Gambia, Mali, Kenya and Bangladesh”

Pregnancy and birth

Yes, this one is not really microbiome-related, but it touched my heart:

Screen Shot 2014-07-16 at 11.49.15 PMStrangers help with photo in midst of tragedy – Dorrine Mendoza, CNN

“”My daughter recently passed away after a long battle in the children’s hospital. She was in the hospital her whole life and we were never able to get a photo without all her tubes. Can someone remove the tubes?””

Fish microbiome

Effects of antibiotic on the bacterial microflora in two commercially
important catfish species, Clarias batrachus and Heteropneustes fossilis in
Bangladesh – Md. Shahdat Hossain – Journal of Coastal Life Medicine

“During the experiment, bacterial loads were estimated as colony forming unit (CFU/g) by every alternate day in the aquarium water, gills, skin and intestine of fish.”

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Human microbiome, July 15

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Not-always-rare taxa in a wide range of ecosystems, microbiome in early life, focus on Lactobacillus and Bacteroides and microbiota and inflammation.

General microbiome

Science Webinar: The promise of the microbiome: Function and dysfunction in humans and beyond – David A. Relman, Jack A. Gilbert, Rob Knight

“Microbiomes–the distinct microbial populations that colonize an array of bodily and environmental niches–are rapidly gaining prominence in numerous fields of research. “

Gut microbiome

Screen shot 2014-07-15 at 05.18PM, Jul 15Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity – Ashley Shade – mBio

“Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure.”

Screen shot 2014-07-15 at 05.20PM, Jul 15Functional genomics of Lactobacillus casei establishment in the gut – Hélène Licandro-Seraut – PNAS

“By determining the relative quantity of each of the 1,110 mutants before and after the in vivo challenge, we identified a core of 47 L. casei genes necessary for its establishment in the gut. “

Screen shot 2014-07-15 at 05.21PM, Jul 15Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium – Varsha Raghavan – Molecular Microbiology

“We report that the regulator controlling utilization of chondroitin sulfate (CS) in the mammalian gut symbiont Bacteroides thetaiotaomicron is activated by an intermediate in CS breakdown rather than CS itself.”

Pregnancy and Birth

Screen shot 2014-07-15 at 06.38PM, Jul 15 1Review: The Microbiome in Early Life: Self-Completion and Microbiota Protection as Health Priorities – Rodney R. Dietert – Birth Defects Research Part B: Developmental and Reproductive Toxicology

“This minireview considers the benefits of refocusing attention away from treating the patient as a mammalian human to managing the complete patient: a majority microbial superorganism. “

Screen shot 2014-07-15 at 06.38PM, Jul 15Review: Anaerobes and Bacterial Vaginosis in Pregnancy: Virulence Factors Contributing to Vaginal Colonisation – Charlene W. J. Africa – Int. J. Environ. Res. Public Health

“This paper reviewed new available information regarding possible factors contributing to the establishment of the BV vaginal biofilm, examined the proposed role of anaerobic microbial species recently detected by new culture-independent methods and discusses developments related to the effects of BV on human pregnancy. “

Oral microbiome

Review: Acquisition and maturation of oral microbiome throughout childhood: An update – Benedita Sampaio-Maia – Dental Research Journal

“This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. “

 

Animal models of human microbiome and disease

Screen shot 2014-07-15 at 05.17PM, Jul 15Commensal microbes drive intestinal inflammation by IL-17–producing CD4+ T cells through ICOSL and OX40L costimulation in the absence of B7-1 and B7-2 – Lijun Xin – PNAS

“Here we show that B7 deprivation in mice overrides the necessity for Tregs in averting systemic autoimmunity and inflammation in extraintestinal tissues, whereas peripherally induced Tregs retained in the absence of B7 selectively mitigate intestinal inflammation caused by Th17 effector CD4+ T cells. “

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Human microbiome, July 14

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Ethnic variation in vaginal microbiomes, effect of chemotherapy on human milk, response of (murine) microbiota to infection.

Oral microbiome

Screen shot 2014-07-14 at 12.23PM, Jul 14Advancements toward a Systems Level Understanding of the Human Oral Microbiome – Jeffrey S. Mclean – Frontiers in Cellular and Infection Microbiology

“This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.”

Vaginal microbiome

Screen shot 2014-07-14 at 12.24PM, Jul 14Ethnic Variations in Cervical Cytokine Concentrations and Vaginal Flora During Pregnancy – Riana Dutt – American Journal of Reproductive Immunology

“Semi-quantitative vaginal cultures and concentrations of cervical cytokines were compared between Caucasian and non-Caucasian women.”

Gut microbiome

Screen shot 2014-07-14 at 12.25PM, Jul 14A 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.”

Pregnancy and birth

Screen shot 2014-07-14 at 12.26PM, Jul 14Effect of chemotherapy on the microbiota and metabolome of human milk, a case report – Camilla Urbaniak – Microbiome

“Mature milk was collected every two weeks over a four month period from a lactating woman undergoing chemotherapy for Hodgkin’s lymphoma. Mature milk was also collected from healthy lactating women for comparison. Microbial profiles were analyzed by 16S sequencing and the metabolome by gas chromatography-mass spectrometry.”

Animal models

Clara Belzer miceDynamics of the Microbiota in Response to Host Infection – Clara Belzer – PLOS ONE

“Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. “

Prune juice animal modelCarbohydrate-Free Peach (Prunus persica) and Plum (Prunus domestica) Juice Affects Fecal Microbial Ecology in an Obese Animal Model – Giuliana D. Noratto – PLOS ONE

“Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats.”

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