Author Archives: eliesbik

Non-human microbiome

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Microbiome of sheep, Drosophila on cherries, wild and sugar beets, sauerkraut, sake, and cheese. Sounds like a good meal.
Sheep microbiome

Pros and Cons of Ion-Torrent Next Generation Sequencing versus Terminal Restriction Fragment Length Polymorphism T-RFLP for Studying the Rumen Bacterial Community – Gabriel de la Fuente – PLOS ONE

“We analysed the bacterial diversity in the rumen of defaunated sheep following the introduction of different protozoal populations, using both next generation sequencing (NGS: Ion Torrent PGM) and terminal restriction fragment length polymorphism (T-RFLP).”

Insect microbiome

The bacterial communities of Drosophila suzukii collected from undamaged cherries
James Angus Chandler – PeerJ

“Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adult D. suzukii collected from undamaged, attached cherries in California, USA. “

Evaluating Insect-Microbiomes at the Plant-Insect Interface – Clare L. Casteel, Allison K. Hansen – Journal of Chemical Ecology

“In this review, we critically evaluate the requirements for insect-associated microbes to develop synergistic relationships with their hosts, and we mechanistically discuss how some of these insect-associated microbes can target or modify host plant defenses.”

Saccharide breakdown and fermentation by the honey bee gut microbiome
Authors – Fredrick J. Lee – Environmental microbiology

“In order to better understand the contribution of the microbial community to food processing in the honey bee, we generated a metatranscriptome of the honey bee gut microbiome.”

Plant microbiome

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima – ancestor of all beet crops – and modern sugar beets – Christin Zachow – Frontiers in Microbiology

“Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions.”

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process – Daniela Bulgari – BMC Microbiology

“Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. “

Water microbiology

Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover – Christopher Staley – Frontiers in Microbiology

“In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt) approaches.”

Potential drivers of microbial community structure and function in Arctic snow – Lorrie Maccario – Frontiers in Microbiology

“We applied a metagenomic approach to nine snow samples taken over two months during the spring season. Fungi, Bacteroidetes and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season.”

Soil microbiology

Nutrient addition dramatically accelerates microbial community succession – Knelman JE – PLOS ONE

“We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization.”

Food microbiology

Sauerkraut: bacteria making food – S.E. Gould – Lab Rat – Scientific American

“As the bacteria required for sauerkraut fermentation are found on the cabbage leaves, it’s a very easy and healthy dish to produce. All you need is cabbage! “

Indigenous bacteria and fungi drive traditional kimoto sake fermentations
Nicholas A. Bokulich – Applied and Environmental Microbiology

“Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus subsp. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. “

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis – V. Delcenserie – Journal of Dairy Science

“The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. “

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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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General microbiology and science, July 22

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Amplifying long PCR products, primer design, metagenomic analysis and ecology, network analysis and the Picks.

Techniques

Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer – Haiying Jia – Nature Scientific Reports

“We evaluated six long-range DNA polymerases to amplify three amplicons, with sizes of 12.9 kb, 9.7 kb, and 5.8 kb, respectively. “

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies – Luisa W. Hugerth – Applied and Environmental Microbiology

“Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions.”

Metagenomic analysis and ecology

Implications of streamlining theory for microbial ecology – Stephen J Giovannoni – ISME Journal

“The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth.”

Parallel Evolution of Streptococcus pneumoniae and Streptococcus mitis to Pathogenic and Mutualistic Lifestyles – Mogens Kilian – mBio

“In a comparative analysis of 35 genomes, including phylogenetic analyses of all predicted genes, we have shown that the pathogenic pneumococcus has evolved into a master of genomic flexibility while lineages that evolved into the nonpathogenic S. mitis secured harmonious coexistence with their host by stabilizing an approximately 15%-reduced genome devoid of many virulence genes.”

Proteomics

Elevated temperature alters proteomic responses of individual organisms within a biofilm community – Annika C Mosier – ISME Journal

“The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. “

Bioinformatics

Detecting Communities Based on Network Topology – Wei Liu – Nature Scientific Reports

“We analyzed 16 different types of networks, and compared our partitions with Infomap, LPA, Fastgreedy and Walktrap, which are popular algorithms for community detection. Most of the partitions generated using our approach compare favorably to those generated by these other algorithms. “

Dr. Bik’s Picks

FGF5 is a crucial regulator of hair length in humans – Claire A. Higgins – PNAS

“In this study, we obtained DNA from families segregating excessively long eyelashes consistent with an autosomal recessive trait.”

Science and Culture: Hunting fractals in the music of J. S. Bach – Stephen Ornes – PNAS

“Bach has similarly attracted the attention of other fractal hunters, including Harlan Brothers, a jazz guitarist, composer, and mathematician in Branford, Connecticut. For more than a decade, Brothers has been mapping fractals in music.”

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Non-human microbiome, July 22

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Symbionts of tortoises, bees, diatoms, amoebae, and seaweed.

Reptile microbiome

Thesis: Population genetics and microbial communities of the gopher tortoise (Gopherus polyphemus) – Gaillard, Daniel Lyle – University of Sourthern Missisippi]

“Microbial communities did not show a correlation between community dissimilarity and geographic distance nor did they change in response to changes in plant communities at each site.”

Insect microbiome

Genomics and host specialization of honey bee and bumble bee gut symbionts – Waldan K. Kwong – PNAS

“We show that the simple microbiota of eusocial bees exhibits host specificity and that coresident species in the bee gut possess complementary capabilities for energy metabolism, implying their occupancy in distinct ecological niches.”

Diatom microbiome

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle – Takuro Nakayama – PNAS

“Here we present what is, to our knowledge, the first completely sequenced spheroid body genome from a rhopalodiacean diatom. Comparative analyses revealed that the endosymbiont is metabolically reduced, confirming its status as an obligate endosymbiont. “

Amoeba microbiome

Life in an unusual intracellular niche: a bacterial symbiont infecting the nucleus of amoebae – Frederik Schulz – ISME Journal

“This symbiont, tentatively named ‘Candidatus Nucleicultrix amoebiphila’, is only moderately related to known bacteria (~90% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. “

Seaweed microbiota

Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota
Marjolaine Martin – Applied and Environmental Microbiology

“A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci.”

Aquatic microbiology

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes – Alyse K. Hawley – PNAS

“Here we use metagenomic and metaproteomic methods to chart in situ metabolic networks linking key microbial players driving carbon and nutrient cycling in a seasonally stratified fjord, Saanich Inlet, a model ecosystem for studying microbial responses to changing levels of water column oxygen deficiency.”

EVENT: An Evening with the World’s Leading Marine Microbiologists – A Creative Collisions Initiative – Wednesday July 30, 2014 – Tech Museum San Jose, CA

“Mingle with the 16 Investigators of the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative”

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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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General microbiology and science, July 21

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Pyrosequencing reproducibility, Microbes in the News, plague, tatoos, and Dr. Bik’s Picks.

Techniques

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities – Aibin Zhan – Methods in Ecology and Evolution

“Here we evaluated reproducibility by analyzing 454 pyrosequenced biological replicates of two complex plankton communities collected from one freshwater port and one marine port. We also tested whether reproducibility potentially influences biodiversity estimates, notably α- and β-diversity.”

Microbial Ecology / Bioinformatics

Synthetic microbial consortia: from systematic analysis to construction and applications –
Hao Song – Chem Soc Rev

“Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell–cell interactions in synthetic microbial consortia. “

Microbes in the News

Be nice to your germs, they keep you alive – Nicky Phillips – Sydney Morning Herald

“Without a well-balanced community of these microscopic critters we would not survive, says Holmes. ‘‘We shouldn’t view them as a separate thing, we should view them as a part of us,’’ he says.”

Desert Rat Relies on Microbes To Detoxify Its Deadly Meals – Ed Yong – National Geographic

“When Kevin Kohl learned about the woodrat, he wondered if bacteria in the rodent’s gut might help it to tolerate its otherwise lethal diet… The idea made sense. Kohl just needed to test it.”

Four Cases of Life-Threatening Plague Found in Colorado –  Sonali Basak and Jennifer Oldham – Bloomberg.com

“Three more plague cases were found in Colorado, a week after the first infection of the deadliest form of the disease was reported in the state in a decade.”

Tattoo Inks, Needles Recalled Due To Bacterial Contamination
Kristen McConnaughey – SiouxLandMatters.com

“”Extreme risks. I mean we’re talking death. There’s things out there that can kill you,” says Scott Alphawolf Davis, a tattoo artist.”

Science and career

Happy Thoughts May Help Postdocs Handle Stress – Rachel Bernstein – Science Careers

“It could be something as simple as watching a funny TV show or going out for a walk or jog. These little things really add up.”

Women in Science

Why is STEM Still a 4-Letter Word for Women? 7 Leaders Weigh In – Ravishly

“Women receive fewer invitations to professional meetings, and research paper acceptance, pay scales and promotion to tenure favor males over females.“

Dr. Bik’s Picks

Sixth-Grader’s Science Fair Finding Shocks Ecologists – NPR All Things Considered

“When 12-year-old Lauren Arrington heard about her sixth-grade science project, she knew she wanted to study lionfish. Growing up in Jupiter, Fla., she saw them in the ocean while snorkeling and fishing with her dad.”

Editorial: Science speaking up – Pensacola News Journal

“The letter read: “We note you have been asked several times about how, as Governor, you will handle the issue of climate change. You responded that you are ‘not a scientist.’ We are scientists and we would like the opportunity to explain what is at stake for our state.””

Book Review: Raising a Glass to Chemistry: ‘Proof’ Drinks in the Science of Alcohol – Alessandra Montalto – The New York Times

“How important is yeast? In 1996, it became the first living organism to have its DNA sequenced. As one modern alehouse puts it in a dubious ad: “Yeast — not just for infections anymore.””

New Allele Hopeful of Making The Big Time – The Allium – Science News You Won’t Read Nowhere Else

“Right now, I am at a low frequency and nobody really knows about me. Tomorrow I could be gone. It is that tough!”

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Non-human microbiome, July 21

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Microbiomes of water fleas, marine zooplankton, soil, rumen, and how a microbiome can help woodrats eat toxic plants.

Rumen microbiome

Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities – M. Kim – Journal of Applied Microbiology

“A total of 1,666 OTU-specific probes were designed and synthesized on microarray slides (referred to as RumenBactArray) in a 6×5k format with each probe being represented in triplicate.”

Rodent microbiome

Gut microbes of mammalian herbivores facilitate intake of plant toxins – Kevin D. Kohl – Ecology Letters

“We investigated the gut microbiota of desert woodrats (Neotoma lepida), some populations of which specialise on highly toxic creosote bush (Larrea tridentata). Here, we demonstrate that gut microbes are crucial in allowing herbivores to consume toxic plants. “

Crustacean microbiome

Water fleas require microbiota for survival, growth and reproduction – Marilou P Sison-Mangus – ISME Journal

“We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts.”

Soil microbiome

Soil Properties and Spatial Processes Influence Bacterial Metacommunities within a Grassland Restoration Experiment – Cheryl A. Murphy – Restoration Ecology

“We found that soil bacterial communities were not influenced by plant restoration, but rather, by the local heterogeneity of soil environmental properties (16.9% of bacterial community variation) and pure spatial effects (11.1%).”

Environmental drivers of soil microbial community distribution at the Koiliaris Critical Zone Observatory – Myrto Tsiknia – FEMS Microbiology Ecology

“This study investigates the distribution of archaea, bacteria and fungi as well as the dominant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes), and classes of Proteobacteria (α- and β-Proteobacteria) across the Koiliaris watershed by qPCR and associate them with environmental variables. “

Soil microbial community structure and activity along a montane elevational gradient on the Tibetan Plateau – Meng Xu – European Journal of Soil Biology

“We investigated the microbial community composition and functional patterns along an elevational gradient (3100–4600 m above sea level) on Mount Segrila using phospholipid fatty acids (PLFAs) and community level physiological profiles (CLPP). “

Oil pipeline microbiome

Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces – Tiffany R. Lenhart – The Journal of Bioadhesion and Biofilm Research

“Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed ‘cookies,’ revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. “

Plankton microbiome

Zooplankton diversity across three Red Sea reefs using pyrosequencing – John K. Pearman – Frontiers in Marine Science

“The diversity of metazoan plankton was investigated by targeting the 18S rRNA gene and clustering OTUs at 97% sequence similarity. A total of 754 and 854 metazoan OTUs were observed in the data set for the 1380F and 1389F primer sets respectively. “

Food microbiology

Cheese Rind Communities Provide Tractable Systems for In Situ and In Vitro Studies of Microbial Diversity – Benjamin E. Wolfe – Cell

“Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. “

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