Monthly Archives: July 2014

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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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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General microbiology and science, July 18

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Talking to bacteria to make them feel more comfortable (Bacteria whisperers!), probiotics, viruses vs. helminths, and women in Science.

Phages, viruses, helminths

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

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

Probiotics

Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells – Prapaporn Boonma – BMC Microbiology

“We screened Lactobacillus conditioned media from 34 infant fecal isolates for the ability to suppress C. difficile-induced IL-8 production from HT-29 cells. Factors produced by two vancomycin-resistant lactobacilli, L. rhamnosus L34 (LR-L34) and L.casei L39 (LC-L39), suppressed the secretion and transcription of IL-8 without inhibiting C. difficile viability or toxin production. “

Cross-talk between probiotic lactobacilli and host immune system – T.S. Kemgang – Journal of Applied Microbiology

“This review summarizes the interplay existing between the host immune system and probiotic lactobacilli, that is, with emphasis on lactobacilli as a prototype probiotic genus.”

General microbiology

Talking to bacteria? Towards light-mediated sensing of bacterial comfort – G. Zafrilla – Letters in Applied Microbiology

“The framework is to convert the human voice into electric pulses, these into light pulses exciting bacterial fluorescent proteins, and convert light-emission back into electric pulses, which will be finally transformed into synthetic voice messages.”

Bacteria in the news

More Forgotten Virus, Bacteria Vials Found at Federal Lab – Newsplex.com

“Food and Drug Administration officials said Wednesday the undocumented collection contained 327 carefully packaged vials, listing pathogens like dengue, influenza and rickettsia.”

1 weird tip to not die of smallpox – Beth Skwarecki – PLOS Blogs

“Jenner then attempted to infect the child with smallpox twenty more times in his life. Fortunately for the kid, the vaccine had worked.”

Women in Science

Science Has a Gender Problem. Science Just Made It Worse – Katy Waldman – Slate

“Transgender sex workers should not be expected to thank Science for “raising awareness” of them as erotic objects, jokes, or disease vectors. “

Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault – Kathryn B. H. Clancy – PLOS ONE

“Little is known about the climate of the scientific fieldwork setting as it relates to gendered experiences, sexual harassment, and sexual assault. We conducted an internet-based survey of field scientists (N = 666) to characterize these experiences. “

Dr. Bik’s Picks

Long read: One of a kind: What do you do if your child has a condition that is new to science? – Seth Mnookin – The New Yorker

“At first, they said, he seemed to represent a challenging problem for each new specialist to solve. But, as one conjecture after another was proved wrong, the specialists lost interest; many then insisted that the cause of Bertrand’s illness lay in someone else’s area of expertise. “

Introduction to special issue: Slicing the wheat genome – Kellye Eversole – Science

“Together, these Research Articles explore multiple dimensions of the 17-gigabase wheat genome and pave the way toward achieving a full reference sequence to underpin wheat research and breeding”

 

Earth-like soils on Mars? Ancient fossilized soils potentially found deep inside impact crater suggest microbial life – Science Daily

“Soil deep in a crater dating to some 3.7 billion years ago contains evidence that Mars was once much warmer and wetter, says a geologist based on images and data captured by the rover Curiosity.”

How Colors Smell – Julie Beck – The Atlantic

“But what color is the smell of, say, soap? A new study published in PLOS One finds that some people say white, some say yellow, some say blue. “

Suspects in science museum’s dinosaur heist turn themselves in – Andrew Kenney – Charlotte Observer

“A man and woman, both 21, turned themselves over to N.C. State Capitol Police on Thursday in the case of the missing model dinosaur.”

 

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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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Playing with post frequency and format

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UPDATE:

OK, this is embarrassing – the instructions below are not enough to stop the immediate notifications of new posts. You will also need to unsubscribe from the direct email. But this is getting very complicated. Apparently, it not currently possible for me in WordPress to set up a daily digest for my subscribers. I apologize to all my readers and I will switch back to 1-3 updates a day.

Still, I would appreciate any suggestions on improvements for this blog. Thanks!

Elisabeth Bik

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Dear readers,

If you have subscribed to receive MicrobiomeDigest updates per email, you will have noticed that I have been playing with the post format. One of my readers suggested to post each interesting paper separately, which might allow for an easier way to search and find older posts. The search function in WordPress, and also some other plug-ins that I played with do a good job finding posts, but it does not really show you where the search terms show up in the posts.

So, for today, I will post each paper that I find separately. This would work best in combination with a “daily digest” that will send out an email once a day that will lists all the recent posts.  Unfortunately, I have not found a way to send out daily compilations – any suggestions would be appreciated. I am currently working with the Jetpack plugin of WordPress, and it does not have that option.

But there is a work-around: You can set up to receive a daily (or weekly) digest by creating (or updating) a WordPress account. You can do that here.

Fill out the email adress on which you want to have the updates, create username/password. An email will be sent to your email address, and you will need to activate the account by clicking a button in the email.

Then, you will need to go back to the WordPress account page, and on the right, click the Edit button next to “Blogs I Follow”. Here is a direct link to that page. The name of my blog is “Microbiomedigest.com”. Click “delivery settings” to change the email frequency to “daily” or “weekly”.

We will see if this works better. If you absolutely hate this, or have any suggestions to make this blog format work, please let me know. My email is eliesbik [at] stanford [dot] edu   without spaces and brackets. I’d be happy to switch to any format, but with only one suggestion so far, I am not sure what the majority of my readers would like.

Also, I would love to have a bigger audience! So please spread the word about this blog.

Thanks you all, and have a great weekend,

Elisabeth Bik

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