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Human gut microbiome

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https://www.readbyqxmd.com/read/28108392/a-case-of-pyometrocolpos-with-bifidobacterium-species
#1
Maanasa M Bhaskar, Sujatha Sistla, S Kumaravel
Bifidobacterium species, a normal commensal of the human gastrointestinal tract, female genitourinary tract and vagina is usually considered non-pathogenic and is being used therapeutically as probiotic due to its beneficial effects. However, there are several case reports implicating Bifidobacteria as the causative agent in various infectious conditions. Infections with Bifidobacteria are often ignored or underreported as they are part of the normal gut microbiome. Here we discuss a case of pyometrocolpos with Bifidobacterium species...
January 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28105915/spectral-consensus-strategy-for-accurate-reconstruction-of-large-biological-networks
#2
Séverine Affeldt, Nataliya Sokolovska, Edi Prifti, Jean-Daniel Zucker
BACKGROUND: The last decades witnessed an explosion of large-scale biological datasets whose analyses require the continuous development of innovative algorithms. Many of these high-dimensional datasets are related to large biological networks with few or no experimentally proven interactions. A striking example lies in the recent gut bacterial studies that provided researchers with a plethora of information sources. Despite a deeper knowledge of microbiome composition, inferring bacterial interactions remains a critical step that encounters significant issues, due in particular to high-dimensional settings, unknown gut bacterial taxa and unavoidable noise in sparse datasets...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28104778/probiotic-strains-modulate-cytokine-production-and-the-immune-interplay-between-human-peripheral-blood-mononucear-cells-and-colon-cancer-cells
#3
Meir Djaldetti, Hanna Bessler
BACKGROUND: Human health is tightly connected with a great number of gut microbial cells designated as microbiome or microbiota. We have examined the effect of six microbial strains (MS) included in a commercial probiotic on cytokine production by human peripheral blood mononuclear cells (PBMC) and on their immune dialog with colon carcinoma cells. METHODS: Non-stimulated and lipopolysaccharide (LPS) stimulated PBMC were incubated for 24 hours with MS. The secretion of tumor necrosis factor alpha (TNFα), IL-1β, IL-6, interferon gamma (IFNγ), IL-10, and IL-1ra, as well as the effect of MS on the immune interplay between PBMC and cells from HT-29 and RKO colon carcinoma lines were evaluated...
January 18, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28097073/handling-stress-may-confound-murine-gut-microbiota-studies
#4
Cary R Allen-Blevins, Xiaomeng You, Katie Hinde, David A Sela
BACKGROUND: Accumulating evidence indicates interactions between human milk composition, particularly sugars (human milk oligosaccharides or HMO), the gut microbiota of human infants, and behavioral effects. Some HMO secreted in human milk are unable to be endogenously digested by the human infant but are able to be metabolized by certain species of gut microbiota, including Bifidobacterium longum subsp. infantis (B. infantis), a species sensitive to host stress (Bailey & Coe, 2004). Exposure to gut bacteria like B...
2017: PeerJ
https://www.readbyqxmd.com/read/28096483/the-gut-microbiome-of-the-vector-lutzomyia-longipalpis-is-essential-for-survival-of-leishmania-infantum
#5
Patrick H Kelly, Sarah M Bahr, Tiago D Serafim, Nadim J Ajami, Joseph F Petrosino, Claudio Meneses, John R Kirby, Jesus G Valenzuela, Shaden Kamhawi, Mary E Wilson
: The vector-borne disease leishmaniasis, caused by Leishmania species protozoa, is transmitted to humans by phlebotomine sand flies. Development of Leishmania to infective metacyclic promastigotes in the insect gut, a process termed metacyclogenesis, is an essential prerequisite for transmission. Based on the hypothesis that vector gut microbiota influence the development of virulent parasites, we sequenced midgut microbiomes in the sand fly Lutzomyia longipalpis with or without Leishmania infantum infection...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096237/the-human-microbiome-and-cancer
#6
Seesandra V Rajagopala, Sanjay Vashee, Lauren M Oldfield, Yo Suzuki, J Craig Venter, Amalio Telenti, Karen E Nelson
Recent scientific advances have significantly contributed to our understanding of the complex connection between the microbiome and cancer. Our bodies are continuously exposed to microbial cells, both resident and transient, as well as their by-products including toxic metabolites. Circulation of toxic metabolites may contribute to cancer onset or progression at locations distant from where a particular microbe resides. Moreover, microbes may migrate to other locations in the human body and become associated with tumor development...
January 17, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28095919/ancient-bacteria-of-the-%C3%A3-tzi-s-microbiome-a-genomic-tale-from-the-copper-age
#7
Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
BACKGROUND: Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS: Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28095889/evolution-of-gut-microbiota-composition-from-birth-to-24-weeks-in-the-infantmet-cohort
#8
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Touhy, R Paul Ross, C Anthony Ryan, Paul W O' Toole, Catherine Stanton
BACKGROUND: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age. METHODS: V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS. RESULTS: Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28092309/microbiota-targeted-therapies-on-the-intensive-care-unit
#9
Bastiaan W Haak, Marcel Levi, W Joost Wiersinga
PURPOSE OF REVIEW: The composition and diversity of the microbiota of the human gut, skin, and several other sites is severely deranged in critically ill patients on the ICU, and it is likely that these disruptions can negatively affect outcome. We here review new and ongoing studies that investigate the use of microbiota-targeted therapeutics in the ICU, and provide recommendations for future research. RECENT FINDINGS: Practically every intervention in the ICU as well as the physiological effects of critical illness itself can have a profound impact on the gut microbiota...
January 13, 2017: Current Opinion in Critical Care
https://www.readbyqxmd.com/read/28091525/a-fibrolytic-potential-in-the-human-ileum-mucosal-microbiota-revealed-by-functional-metagenomic
#10
Orlane Patrascu, Fabienne Béguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, Anne-Laure Abraham, Marion Leclerc, Christophe Klopp, Nicolas Terrapon, Bernard Henrissat, Hervé M Blottière, Joël Doré, Christel Béra-Maillet
The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090466/microbiome-linked-crosstalk-in-the-gastrointestinal-exposome-towards-host-health-and-disease
#11
REVIEW
Yuseok Moon
The gastrointestinal exposome represents the integration of all xenobiotic components and host-derived endogenous components affecting the host health, disease progression and ultimately clinical outcomes during the lifespan. The human gut microbiome as a dynamic exposome of commensalism continuously interacts with other exogenous exposome as well as host sentineling components including the immune and neuroendocrine circuit. The composition and diversity of the microbiome are established on the basis of the luminal environment (physical, chemical and biological exposome) and host surveillance at each part of the gastrointestinal lining...
December 2016: Pediatric Gastroenterology, Hepatology & Nutrition
https://www.readbyqxmd.com/read/28079170/growth-and-morbidity-of-gambian-infants-are-influenced-by-maternal-milk-oligosaccharides-and-infant-gut-microbiota
#12
Jasmine C C Davis, Zachery T Lewis, Sridevi Krishnan, Robin M Bernstein, Sophie E Moore, Andrew M Prentice, David A Mills, Carlito B Lebrilla, Angela M Zivkovic
Human milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother's HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3'-sialyllactose was found to be a good indicator of infant weight-for-age...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078319/gut-microbiota-inflammation-and-colorectal-cancer
#13
Jun Sun, Ikuko Kato
Although genes contribute to colorectal cancer, the gut microbiota are an important player. Accumulating evidence suggests that chronic infection and the ensuing inflammation contributes to tumor initiation and tumor progression. A variety of bacterial species and tumor-promoting virulence mechanisms have been investigated. Significant advances have been made in understanding the composition and functional capabilities of the gut microbiota and its roles in cancer. In the current review, we discuss the novel roles of microbiota in the progression of colon cancer...
June 2016: Genes & Diseases
https://www.readbyqxmd.com/read/28077947/asthma-and-the-microbiome-defining-the-critical-window-in-early-life
#14
REVIEW
Leah T Stiemsma, Stuart E Turvey
Asthma is a chronic inflammatory immune disorder of the airways affecting one in ten children in westernized countries. The geographical disparity combined with a generational rise in prevalence, emphasizes that changing environmental exposures play a significant role in the etiology of this disease. The microflora hypothesis suggests that early life exposures are disrupting the composition of the microbiota and consequently, promoting immune dysregulation in the form of hypersensitivity disorders. Animal model research supports a role of the microbiota in asthma and atopic disease development...
2017: Allergy, Asthma, and Clinical Immunology
https://www.readbyqxmd.com/read/28077565/mahmi-database-a-comprehensive-metahit-based-resource-for-the-study-of-the-mechanism-of-action-of-the-human-microbiota
#15
Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28074537/neuroblastoma-causes-alterations-of-the-intestinal-microbiome-gut-hormones-inflammatory-cytokines-and-bile-acid-composition
#16
Christoph Castellani, Georg Singer, Margarita Kaiser, Thomas Kaiser, Jianfeng Huang, Daniela Sperl, Karl Kashofer, Guenter Fauler, Barbara Guertl-Lackner, Gerald Höfler, Holger Till
OBJECTIVE: To assess the effect of neuroblastoma (NB) on the intestinal microbiome, metabolism, and inflammatory parameters in a murine model. MATERIALS AND METHODS: Athymic Hsd:Fox1nu mice received subperitoneal implantation of human NB cells (MHH-NB11) (tumor group, TG) or culture medium (sham group). Following 10 weeks of tumor growth, all animals were sacrificed to collect total white adipose tissue (WAT). Luminex assays were performed for gut hormone and inflammation marker analysis...
January 11, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28070563/gut-microbiome-of-the-canadian-arctic-inuit
#17
Catherine Girard, Nicolas Tromas, Marc Amyot, B Jesse Shapiro
Diet is a major determinant of community composition in the human gut microbiome, and "traditional" diets have been associated with distinct and highly diverse communities, compared to Western diets. However, most traditional diets studied have been those of agrarians and hunter-gatherers consuming fiber-rich diets. In contrast, the Inuit of the Canadian Arctic have been consuming a traditional diet low in carbohydrates and rich in animal fats and protein for thousands of years. We hypothesized that the Inuit diet and lifestyle would be associated with a distinct microbiome...
January 2017: MSphere
https://www.readbyqxmd.com/read/28069756/inside-out-hiv-the-gut-microbiome-and-the-mucosal-immune-system
#18
REVIEW
Jay Liu, Brett Williams, Daniel Frank, Stephanie M Dillon, Cara C Wilson, Alan L Landay
The components of the human gut microbiome have been found to influence a broad array of pathologic conditions ranging from heart disease to diabetes and even to cancer. HIV infection upsets the delicate balance in the normal host-microbe interaction both through alterations in the taxonomic composition of gut microbial communities as well as through disruption of the normal host response mechanisms. In this article we review the current methods of gut microbiome analysis and the resulting data regarding how HIV infection might change the balance of commensal bacteria in the gut...
January 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28069754/the-influence-of-the-microbiome-on-type-1-diabetes
#19
REVIEW
Alexandra Paun, Christopher Yau, Jayne S Danska
Type 1 diabetes (T1D) is characterized by the autoimmune destruction of pancreatic β cells. The rapid rise in T1D incidence during the past 50 y suggests environmental factors contribute to the disease. The trillion symbiotic microorganisms inhabiting the mammalian gastrointestinal tract (i.e., the microbiota) influence numerous aspects of host physiology. In this study we review the evidence linking perturbations of the gut microbiome to pancreatic autoimmunity. We discuss data from rodent models demonstrating the essential role of the gut microbiota on the development and function of the host's mucosal and systemic immune systems...
January 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28065879/structural-zeros-in-high-dimensional-data-with-applications-to-microbiome-studies
#20
Abhishek Kaul, Ori Davidov, Shyamal D Peddada
SUMMARYThis paper is motivated by the recent interest in the analysis of high-dimensional microbiome data. A key feature of these data is the presence of "structural zeros" which are microbes missing from an observation vector due to an underlying biological process and not due to error in measurement. Typical notions of missingness are unable to model these structural zeros. We define a general framework which allows for structural zeros in the model and propose methods of estimating sparse high-dimensional covariance and precision matrices under this setup...
January 8, 2017: Biostatistics
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