Tag Archives: Lactobacillus

Human microbiome digest, September 29, 2014

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Smoking and the subgingival ecosystem, inflammatory bowel diseases, iron in the gut, and metabolism of acetaminophen.

Pregnancy and birth

External influence of early childhood establishment of gut microbiota and subsequent health implications – Peris M. Munyaka – Frontiers in Pediatrics

“Early exposures impacting the intestinal microbiota are associated with the development of childhood diseases that may persist to adulthood”

Human oral microbiome

* Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Human gut microbiome

Functional Impacts of the Intestinal Microbiome in the Pathogenesis of Inflammatory Bowel Disease – Jennifer Li – Inflammatory Bowel Diseases

“We highlight functional roles of specific bacterial groups in the development and management of IBD. “

Nutritional iron turned inside out: intestinal stress from a gut microbial perspective – Guus A.M. Kortman – FEMS Microbiology Reviews

“This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health.”

Animal models of microbiome research

The role of intestinal microbiota in murine models of acetaminophen-induced hepatotoxicity – Lucia A Possamai – Liver International

“A urinary metabolic profile was obtained using 1H-NMR. Baseline hepatic glutathione content and CYP2E1 expression were quantified.”

Dietary Xylo-oligosaccharide stimulates intestinal bifidobacteria and lactobacilli but has limited effect on intestinal integrity in rats – Ellen Gerd Christensen – BMC Research Notes

“Changes in faecal and caecal bacterial composition determined by 16S rRNA gene sequencing and quantitative PCR for selected bacterial groups revealed that the overall bacterial composition did not differ markedly“

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Human microbiome digest, August 19, 2014

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Lots of oral and gut microbiome papers today – Alzheimer’s, probiotics, chemotherapy and radiation.

Oral microbiome

Review: The Microbiome and Disease: Reviewing the Links between the Oral Microbiome, Aging, and Alzheimer’s Disease – Deborah K. Shoemark – Journal of Alzheimer’s Disease

“Evidence linking oral bacteria to Alzheimer’s disease (AD) is discussed in the context of aging, drawing together data from epidemiological, experimental, genetic, and environmental studies. “

* Human oral viruses are personal, persistent and gender-consistent – Shira R Abeles – ISME Journal

“To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. “

* Predictive modeling of gingivitis severity and susceptibility via oral microbiota – Shi Huang – ISME Journal

“In diseased plaque microbiota, 27 bacterial genera changed in relative abundance and functional genes including 33 flagellar biosynthesis-related groups were enriched.”

Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients – Yan Li – ISME Journal

“Here, we examined the phylogenetic and functional gene differences between periodontal and healthy individuals using MiSeq sequencing of 16S rRNA gene amplicons and a specific functional gene array”

Perspective: Fungal-bacterial interactions and their relevance to oral health: linking the clinic and the bench – Patricia I. Diaz – Frontiers in Cellular and Infection Microbiology

“We highlight the need to conduct longitudinal clinical studies to simultaneously characterize the bacterial and fungal components of the human oral microbiome in health and during disease progression.”

Effect of an oxygenating agent on oral bacteria in vitro and on dental plaque composition in healthy young adults – Mercedes Fernandez y Mostajo – Frontiers in Cellular and Infection Microbiology

“During the experiment individuals used AX mouthwash twice daily in absence of other oral hygiene measures. The microbiological composition of plaque was assessed by 16S rRNA gene amplicon sequencing.”

* Review: Advancements 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.”

Gut microbiome

* Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes – Meiling Zhang – PNAS USA

“Here we demonstrate that two human gut commensal Bacteroides are equipped with unique enzymes that allow degradation of xylan, a common hemicellulose in human diets.”

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol – Christian Milani – FEMS Microbiology Ecology

“Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hyper-variable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus.”

* Multi-omics analysis of Inflammatory Bowel Diseases – Hu Huang – Immunology Letters

“There is strong evidence of interactions between host genotype, environment, and gut microbiome profile in IBD.”

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei – Michael T. Leonard – Frontiers in Microbiology

“Here metagenomic sequencing using the Pacific Biosciences platform allowed for rapid identification of bacterial GATC methylation status of a bacterial species in human stool samples. “

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

“..we envision that multi-probiotic therapy and holistic personalized microbiome supplements may be scientifically justified and valued in individualized probiotic designs and even targeted therapy of life-threatening diseases such as cancers in the future. “

Editorial: gut microbiota and chemotherapy- or radiation-induced gastrointestinal mucositis – M. R. Ferreira and H. J. N. Andreyev – Alimentary Pharmacology & Therapeutics

“Studies in those undergoing cancer therapy will lead to a new era in the treatment and prevention of the currently dreadful GI toxicity suffered by so many patients, and what we learn will almost certainly bring important insights to many other GI disorders.”

Respiratory microbiome

Cell-associated bacteria in the human lung microbiome – Robert P Dickson – Microbiome

“We present a novel methodological and analytical approach to the localization of lung microbiota and show that the prominent members of the lung microbiome are cell-associated, potentially via biofilms, cell adhesion, or intracellularity.”

Vaginal microbiome

A Systems Biology Approach Investigating the Effect of Probiotics on the Vaginal Microbiome and Host Responses in a Double Blind, Placebo-Controlled Clinical Trial of Post-Menopausal Women – Jordan E. Bisanz – PLOS ONE

“Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. “

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women – Hanneke Borgdorff – ISME Journal

“In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. “

* also tweeted by @MicrobiomDigest (yup, that’s me).

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Human microbiome, August 12, 2014

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Oral microbiome in Aboriginals, gut microbiome and probiotics.

Human oral microbiome

Age-dependent changes in Porphyromonas gingivalis and Prevotella species/phylotypes in healthy gingiva and inflamed/diseased sub-gingival sites – Mangala A. Nadkarni – Clinical Oral Investigations

“The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators.”

The effect of propidium monoazide treatment on the measured bacterial composition of clinical samples after the use of a mouthwash – R. A. M. Exterkate – Clinical Oral Investigations

“Propidium monoazide (PMA) has been used to overcome this problem, by preventing the amplification of DNA from membrane-damaged cells. The aim of this study was to evaluate the use of PMA when measuring compositional shifts in clinical samples after mouthwash use.”

Human gut microbiome

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms – Joe Alcock – BioEssays

“We review several potential mechanisms for microbial control over eating behavior including microbial influence on reward and satiety pathways, production of toxins that alter mood, changes to receptors including taste receptors, and hijacking of the vagus nerve, the neural axis between the gut and the brain”

Influence of the microbiota on vaccine effectiveness – Yanet Valdez – Trends in Immunology

“Recent findings suggest novel complex mechanisms by which the microbiome impacts immune cell development and differentiation.”

Current Status and Prospects of Intestinal Microbiome Studies – Dong Soo Han – Intest Res

“Evidences have implicated gut microbes in the development of IBD, but no causative microorganisms have been identified.”

Synbiotic Lactobacillus acidophilus NCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids: a randomized, double-blinded cross-over trial – Gabriella C. van Zanten – FEMS Microbiology Ecology

“Furthermore, 454 tag encoded amplicon pyrosequencing was used to monitor the effect of synbiotic on the composition of the microbiota. “

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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 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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Non-human microbiome, June 30

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Primate vaginal microbiome, birds painting eggs with bacteria, MHC and microbiota in fish, onions and tomato, bacteria on the beach, and (#BacteriaHysteria alert) “fecal veneer on climbing walls”.

Primate microbiome (also see Human digest)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Bird microbiome

Screen Shot 2014-06-30 at 11.43.49 PMSpecial structures of hoopoe eggshells enhance the adhesion of symbiont-carrying uropygial secretion that increase hatching success – Manuel Martín-Vivaldi – Journal of Animal Ecology

“The findings of specialized crypts on the eggshells of hoopoes, and of video-recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. “

and:  The Bird That Paints Its Eggs With Bacteria – Ed Yong – National Geographic

“Now, they’ve found evidence that these birds use the same bacteria to protect their young before they’re even born. By filming nesting females, they confirmed that the birds actively paint their eggs with their uropygial secretions.”

Fish microbiology

Screen Shot 2014-06-30 at 11.45.12 PMMajor Histocompatibility Complex class II polymorphism influences gut microbiota composition and diversity – Daniel I. Bolnick – Molecular Ecology

“Here, we show that MHC II polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. “

Insect microbiome

WolbachiaThe Coevolutionary Period of Wolbachia pipientis Infecting Drosophila ananassae and its Impact on the Evolution of the Host Germline Stem Cell Regulating Genes – Jae Young Choi and Charles F. Aquadro – Molecular Biology and Evolution

“Phylogenetic analysis of D. ananassae mitochondrial DNA and W. pipientis DNA sequence diversity revealed the current W. pipientis infection is not recent. In addition, we examined the population genetics and molecular evolution of several Germline Stem Cell (GSC) regulating genes of D. ananassae”

Plant microbiome

Screen Shot 2014-06-30 at 11.43.01 PMIdentification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene – Jean M. Bonasera – Journal of Microbiological Methods

“We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.”

Occurrence and distribution of tomato seed-borne mycoflora in Saudi Arabia and its correlation with the climatic variables – Abdulaziz A. Al-Askar – Microbial Biotechnology

“One hundred samples of tomato seeds were collected in 2011 and 2012 from tomato-cultivated fields in Saudi Arabia and screened for their seed-borne mycoflora. A total of 30 genera and 57 species of fungi were recovered from the collected seed samples using agar plate and deep-freezing blotter methods. “

WasabiManagement of Meloidogyne incognita on tomato with endophytic bacteria and fresh residue of Wasabia japonica – Guang-Ju Li – Journal of Applied Microbiology

“By in vitro bioassay, 53 NEB strains showing nematicidal efficacies of >50% against J2 of M. incognita were isolated from wasabi. Basing on 16S rRNA gene sequences, these NEB were identified into 18 species of 11 genera.”

Lichen and fungi

Screen Shot 2014-06-30 at 11.46.20 PMA single macrolichen constitutes hundreds of unrecognized species – Robert Lücking – PNAS

“This lichen was long believed to represent a single species, but after revising this number to 16 in two genera (Cora and Corella), here we show that at least 126 phylogenetically and morphologically distinct species are contained within this group, with statistical analysis predicting more than 400. “

Soil, sand, and slurry microbiome

The Ecological Controls on the Prevalence of Candidate Division TM7 in Polar Regions – Tristrom Winsley – Frontiers in Microbiology

“We correlated chemical, physical and biological parameters of each soil with the relative abundance of the two major classes of the phylum to deduce factors that influence the groups’ seemingly ubiquitous nature. “

Review: Present status of effect of microorganisms from sand beach on public
health – Emmanuel Velonakis – Journal of Coastal Life Medicine

“Relatively, recent epidemiological studies in the USA revealed positive correlation between time spent at the beach and gastroenteritis. New parameters such as wind blowing and beach users’ density are also introduced for discussion in association with the sand microbial load”

Crusts slurryMethanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts – Yun-Feng Duan – Journal of Applied Microbiology

“Microbial communities in four crusts from cattle and swine slurries were investigated using DGGE and tag-encoded amplicon pyrosequencing. All crusts had distinct compositions of bacteria and archaea.”

Water microbiology

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria
Vinayak Agarwal – Nature Chemical Biology

“Herein we report the discovery of a conserved biosynthetic gene cluster in marine bacteria responsible for the synthesis of widespread polybrominated aromatic compounds”

Environmental bacteriophages : viruses of microbes in aquatic ecosystems – Télesphore Sime – Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.”

Built Environment

I really dislike this title …
Screen Shot 2014-06-30 at 11.47.38 PMMicrobial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds – S. L. Bräuer – Current Microbiology

“In contrast to many other studies of built environments, the majority of microorganisms on holds were most closely related to microbes annotated as being recovered from environmental sources, such as soil, with human skin also representing an important source.”

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Human microbiome, June 30

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Hypotheses about oral microbiota and disease, effect of rhinovirus infection on nasal microbiome,  the gut microbiome in children with diarrhea in low-income countries, primate vaginal microbiomes, and much more.

Oral microbiome (also see Probiotics and Biofilms in today’s General digest)

Screen Shot 2014-06-30 at 11.18.32 PMHistorical and contemporary hypotheses on the development of oral diseases: are we there yet? – Bob T. Rosier – Frontiers in Cellular and Infection Microbiology

“In this comprehensive review, we describe how these different hypotheses, and the ideas around them, arose and test their current applicability to the understanding of the development of oral disease. Finally, we conclude that an all-encompassing ecological hypothesis explaining the shifts from health to disease is still lacking.”

PeriodontitisThe inflammophilic character of the periodontitis-associated microbiota – George Hajishengallis – Molecular Oral Microbiology

“This Review discusses evidence that periodontitis-associated communities are ‘inflammo-philic’ (= loving or attracted to inflammation) in that they have evolved to not only endure inflammation but also to take advantage of it. “

Respiratory microbiome

Screen Shot 2014-06-30 at 11.19.43 PMCharacterization of the nasopharyngeal microbiota in health and during rhinovirus challenge – Allen EK – Microbiome

“Rhinovirus illnesses were induced by self-inoculation using the finger to nose or eye natural transmission route in ten otherwise healthy young adults.”

Gut microbiome

Screen Shot 2014-06-30 at 11.20.28 PMDiarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition – Mihai Pop – Genome Biology

“We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. “

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden – Baxter NT – Microbiome

“We transplanted fecal microbiota from three CRC patients and three healthy individuals into germ-free mice, resulting in six structurally distinct microbial communities. Subjecting these mice to a chemically induced model of CRC resulted in different levels of tumorigenesis between mice. “

Commensal bacteria directly suppress in vitro degranulation of mast cells in a MyD88-independent manner – Kazumi Kasakura – Bioscience, Biotechnology, and Biochemistry

“Here, we show that heat-killed commensal bacteria suppressed degranulation of mast cells in vitro in a MyD88-independent manner.”

Screen Shot 2014-06-30 at 11.21.29 PMCo-occurrence of driver and passenger bacteria in human colorectal cancer
Jiawei Geng – Gut Pathogens

“Building on the driver-passenger model, we used 454 pyrosequencing of bacterial 16S rRNA genes associated with 10 normal, 10 adenoma, and 8 tumor biopsy samples, and found 7 potential driver bacterial genera and 12 potential passenger bacterial genera (7 being pro-inflammatory and 5 anti-inflammatory). “

Review: Intestinal Microbiota and the Efficacy of Fecal Microbiota Transplantation in Gastrointestinal Disease – Olga Aroniadis – Gastroenterology & Hepatology

“The published revelations about the human microbiome are bringing the strength of science to clinical observation and enhancing the understanding of not only disease but also how much of a person’s daily function and health depends on the microorganisms living in intimate relationship with each cell in the body.”

Screen Shot 2014-06-30 at 11.22.43 PMDietary Intervention with Yoghurt, Synbiotic Yogurt or Traditional Fermented Sobya: Bio-Potency among Male Adolescents Using Five Bio-Markers of Relevance to Colonic Metabolic Activities – Laila Hussein – Food and Nutrition Sciences

“The mean fecal total lactobacilli counts increased (P < 0.05) three weeks after daily consumption of the three fermented supplements (P < 0.05), when compared to the pre-intervention levels. Similar trends were observed for genus bifidobacterium. On the contrary, enterobacteraceae counts were reduced in all the three groups consuming fermented supplements.”

Vaginal microbiome (also see pregnancy)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Skin microbiome

New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers
Jean-Philippe Lavigne – Advances in Wound Care

“Molecular tools have better documented the composition and organization of the skin flora. Further advances are required to elucidate which among the many bacteria in the DFU flora are likely to be pathogens, rather than colonizers.”

General human microbiome 

Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks – Abolfazl Barzegari – Future Microbiology

“This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.”

Review: Blowing on Embers: Commensal Microbiota and our Immune System
Darina S. Spasova and Charles D. Surh – Frontiers in Immunology

“This review discusses the recent advances in this field, focusing on the close relationship between the adaptive immune system and commensal microbiota, a constant and abundant source of foreign antigens.”

Microbiome: Second Genome Is Finding Disease Mechanisms, Biomarkers, And Therapeutics – Wayne Koberstein – Life Science Leader

“We now understand that biological processes such as inflammation, barrier function, metabolism, and energy homeostasis are directly linked to our microbiome,” says Peter DiLaura, president and CEO of Second Genome.

Mayo Clinic and Whole Biome Announce Collaboration to Research the Role of the Human Microbiome in Women’s Diseases Using Unique Medical Laboratory Tests – DarkDaily

“This joint research effort will initiate a new field of clinical laboratory diagnostic tests that target the human microbiome”

Prokaryotes versus Eukaryotes: Who is hosting whom? – Guillermo Tellez – Frontiers in Veterinary Science

“Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is hosting whom?”

Animal models of microbiome and disease

Combination of Metagenomics and Culture Based Methods to Study the Interaction Between Ochratoxin A and Gut Microbiota – Mingzhang Guo

“Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system and mismatch repair were observed.”

Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice – G. B. Rogers – Scientific Reports

“We report significant divergence in both the composition and metabolism of gut microbiota in genetically-identical adult C57BL/6 mice housed in separate controlled units within a single commercial production facility.”

Alteration of Gut Bacteria and Metabolomes After Glucaro-1,4-Lactone Treatment Contributes to the Prevention of Hypercholesterolemia – Baogang Xie – J. Agric. Food Chem

“Colonic flora test results reveal that the quantity of Bifidobacterium and Lactobacillus in the intestines respectively increase by about 1.7- and 4.2-fold in rats treated with 1,4-GL compared with those in the control group. “

Pregnancy and birth

Oral presentation: The evolution of the vaginal microbiome throughout uncomplicated pregnancy in a UK population – M Chandiramani – Arch Dis Child Fetal Neonatal Ed

“Vaginal swabs were collected at time points across gestation (8–12, 20–22, 28–30 and 34–36 weeks) and the postpartum period (6 weeks) from 43 women delivered at term. Resident bacterial communities were determined using the Illumina MiSeq platform generated from bar-coded amplicons of 16S rRNA gene fragments.”

Screen Shot 2014-06-30 at 11.26.14 PMGroup B Streptococcus β-hemolysin/Cytolysin Breaches Maternal-Fetal Barriers to Cause Preterm Birth and Intrauterine Fetal Demise in Vivo – Tara M. Randis – Journal of Infectious Diseases

“We used a new murine model to evaluate the contribution of the pore-forming GBS β-hemolysin/cytolysin (βH/C) to vaginal colonization, ascension, and fetal infection.”

Zinc and copper levels in low birth weight deliveries in Medani Hospital, Sudan –
Abass RM – BMC Research Notes

“Maternal zinc and copper levels, as well as cord copper levels, are lower in LBW newborns than in those with normal weight.”

Effective Biomarkers for Diagnosis of Neonatal Sepsis – Vineet Bhandari – Journal of Pediatric Infectious Diseases

“The diagnostic utility of the following biomarkers seems to be most practical in the early (interleukin [IL]-6, IL-8, tumor necrosis factor-alpha, neutrophil CD64), mid (procalcitonin) and late (C-reactive protein) phases of neonatal sepsis.”

Review: Association of Periodontal Disease and Pre-term Low Birth Weight Infants
Manjusha Varadan, Jaiganesh Ramamurthy – The Journal of Obstetrics and Gynecology of India

“The association of periodontitis as risk factor for pre-term birth has been in extensive research in the past two decades when a number of studies investigated this relationship.”

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Human microbiome, June 23

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Lactobacillus feeding on human milk, Mycoplasma in preterm birth, and Clostridium difficile infection and gut microbiota.

Pregnancy and birth

Screen Shot 2014-06-23 at 10.51.26 PMA unique gene cluster for the utilization of the mucosal and human milk-associated glycans galacto-N-biose and lacto-N-biose in Lactobacillus casei – Gonzalo N. Bidart – Molecular Microbiology

“The data represent the first characterization of novel metabolic pathways for human milk oligosaccharides and glycoconjugate structures in Firmicutes”

Screen Shot 2014-06-23 at 11.01.13 PMReport from AANP 2014, Nashville, Tennessee: Screening for Bacteria May Help Pregnancy Outcomes – Ed Susman, MedpageToday

“In a single-center study, about 70% of symptomatic women who were screened for vaginal infections with either Mycoplasma Genitalium or Mycoplasma Hominis experienced preterm birth compared with 30% of the asymptomatic women who still underwent screening for the infections at a prenatal visit, reported Allison Phillips, DNP, of Robert Morris University in Pittsburgh, and colleagues.”

Oral microbiome

Screen Shot 2014-06-23 at 10.52.34 PMNew analysis reveals previously ‘hidden diversity’ of mouth bacteria – MBL

“Using a novel computational method called oligotyping, developed by MBL Assistant Research Scientist A. Murat Eren, scientists analyzed gene sequence data from nine sites in the oral cavity. ” “The study will be published in PNAS Online Early Edition the week of June 23-27, 2014”, but is not yet on PNAS website

Screen Shot 2014-06-23 at 10.53.35 PMEffects of pH and Lactate on Hydrogen Sulfide Production by Oral Veillonella spp. – Jumpei Washio – Applied and Environmental Microbiology

“Thus, in the present study, the H2S-producing activity of growing cells, resting cells, and cell extracts of oral Veillonella species and the effects of oral environmental factors, including pH and lactate, were investigated.”

Gut microbiome

Screen Shot 2014-06-23 at 10.54.40 PMStructural and functional changes in the gut microbiota associated to Clostridium difficile infection – Ana E. Pérez-Cobas – Frontiers in Microbiology

“Here, we analyze the composition and functional differences in the gut microbiota of C. difficile infected (CDI) versus non-infected patients, both patient groups having been treated with AB therapy. To do so we used 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. “

Screen Shot 2014-06-23 at 10.58.40 PMThe HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease – M Olivares – Gut

“Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants.”

(Both human and animal)
Screen Shot 2014-06-23 at 10.57.57 PMA single genus in the gut microbiome reflects host preference and specificity – A Murat Eren – The ISME Journal

“In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping.”

Screen Shot 2014-06-23 at 10.57.04 PMMicrobiomes are true to type – Andrew H. Moeller and Howard Ochman – PNAS

“Enter Wang et al. (3), who provide both retrospective and experimental evidence that the maintenance of enterotypes in host populations is driven by dietary variation.”

General human microbiome

Screen Shot 2014-06-23 at 10.56.07 PMMicrobiota and neurodevelopmental windows: implications for brain disorders
– Yuliya E Borre – Trends in Molecular Medicine

“This review compares the parallel early development of the intestinal microbiota and the nervous system.”

Animal models of human microbiome

Screen Shot 2014-06-23 at 11.00.16 PMThe murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression – Sultan Alkadhi – Gut Pathogens

“The appendiceal dysbiosis observed in our Winnie mice is commensurate with, and adds to extant literature data. The presence of Helicobacteraceae (Proteobacteria) only in colitic Winnie mice (but not control mice) is consistent with reports of increased Helicobacter in IBD patients. “

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Human microbiome, June 17

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Gut bacteria swapping DNA segments, what happens after a fecal transplant, intestinal archaea, and more.

Gut microbiome

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut – Michael J. Coyne – mBio

“Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity.”

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation – Anna M. Seekatz – mBio

“Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool.”

The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells – Corinna Bang – PLOS ONE

“Taken together, our findings strongly argue that the archaeal gut inhabitants M. stadtmanae and M. smithii are specifically recognized by the human innate immune system. “

Microbiota and Metabolome Associated with Immunoglobulin A Nephropathy (IgAN) –
Maria De Angelis – PLOS ONE

“This study aimed at investigating the fecal microbiota, and the fecal and urinary metabolome of non progressor (NP) and progressor (P) patients with immunoglobulin A nephropathy (IgAN). “

Respiratory microbiome

Impact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“These data on bacterial associations are the first to be reported surrounding experimental human pneumococcal colonization and show that co-colonizing effects are likely subtle rather than absolute.”

Vaginal microbiome

Diversity and stability of cultured vaginal lactobacilli in pregnant women from a multi-ethnic urban UK population – S.M. Husain – Journal of Applied Microbiology

“Self-collected vaginal swabs at 13 and 20 weeks gestation were obtained from women attending for routine antenatal care and cultured for lactobacilli.”

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Human microbiome digest, June 3, 2014

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Antimicrobial proteins in saliva, Lactobacillus spp and preterm birth, and probiotics. It’s been a long day, so no pictures today.

Oral microbiome

Salivary antimicrobial proteins associate with age related changes in streptococcal composition in dental plaque – Jennifer Malcolm – Molecular Oral Microbiology

“Dental plaque and saliva were collected from 57 children aged 12-24 months at baseline, of whom 23 children were followed-up at three-years of age. At each time, saliva was assessed for LL37, HNPs 1-3, calprotectin, lactoferrin, salivary IgA, total plaque bacteria and Streptococcus mutans.”

Pregnancy and birth

Characterisation of the vaginal Lactobacillus microbiota associated with preterm delivery – Ljubomir Petricevic – Nature Scientific Reports

“This study suggests that dominating L. iners alone detected in vaginal smears of healthy women in early pregnancy might be associated with preterm delivery”

Development of the preterm gut microbiota in infants at risk of necrotising enterocolitis and sepsis – Christopher Stewart – Doctoral thesis, Northumbria University

Intestinal Microbial Community Profiles of a Newborn Preterm Infant Using Pyrosequencing Analysis: Pilot Study (in Korean)- Jong-Geol Kim – Neonatal Medicine

“The bacterial community in the newborn’s meconium was quite similar to that in the AF, which was dominated by Sphingomonas (45.2%). “

Gut microbiome

Relating the metatranscriptome and metagenome of the human gut – Eric A. Franzosa with Curtis Huttenhower – PNAS

“Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods.”

Defining the diversity of microbial eukaryotic communities in the mammalian gut within the context of environmental eukaryotic diversity – Laura W. Parfrey – Frontiers in Microbiology

“We show that adults from non-western populations harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. “

General human microbiome

Culturing For Cures – UCSF Scientists Explore the Bacterial Communities that Live In and On Our Bodies to Find Treatments for Disease – Claire Conway – UCSF News

“Scientists are hard at work trying to leverage the extraordinary healing powers of the microbiome, mining it for treatments of a variety of conditions, including asthma, irritable bowel syndrome and obesity.”

Probiotics

Autoinducer-2 Plays a Crucial Role in Gut Colonization and Probiotic Functionality of Bifidobacterium breve UCC2003 – Steven E. A. Christiaen – PLOS ONE

“we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition”

Urinary metabolomic fingerprinting after consumption of a probiotic strain in women with mastitis – Rosa Vázquez-Fresno – Pharmacological Research

“The application of NMR-based metabolomics enabled the identification of the overall effects of probiotic consumption among women suffering from mastitis and highlighted the potential of this approach in evaluating the outcomes of probiotics consumption.”

Animal models of gut microbiota

Effects of subchronic exposure of silver nanoparticles on intestinal microbiota and gut-associated immune responses in the ileum of Sprague-Dawley rats – Katherine Williams – Nanotoxicology

“This study evaluated changes in the populations of intestinal-microbiota and intestinal-mucosal gene expression in Sprague-Dawley rats (both male and female) that were gavaged orally with discrete sizes of AgNP (10, 75 and 110 nm) and silver acetate.”

Metabolomics

Oral Abstract: The high colon cancer risk in African Americans can be reduced by dietary modification – Stephen O’Keefe – Cancer & Metabolism

“dietary switch between these two populations produces reciprocal changes in the microbiome, metabolome, and mucosal biomarkers of risk within 2 weeks”

Strategies in Discovery Metabolomics – Kate Marusina – GenEngNews

Microbiome conferences

2nd World Congress on Targeting Microbiota – Institut Pasteur, Paris, France – October 16-17, 2014

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