The eco-evolutionary dynamics of microbial populations by Vanlnsberghe, David(David Stephen)

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Ecological insights from bacterial networks by Smith, Mark Burnham

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A holobiont view of island biogeography: unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates by Armstrong, Ellie E., Perez-Lamarque, Benoît, Bi, Ke, Chen, Cerise, Becking, Leontine E., Lim, Jun Ying, Linderoth, Tyler, Krehenwinkel, Henrik, Gillespie, Rosemary G.

“…The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. …”
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Expression of NOD2 in Paneth cells: a possible link to Crohn's ileitis. by Ogura, Y, Lala, S, Xin, W, Smith, E, Dowds, T, Chen, F, Zimmermann, E, Tretiakova, M, Cho, J, Hart, J, Greenson, J, Keshav, S, Nuñez, G

“…The impaired capacity of CD associated mutations to sense luminal bacteria may result in increased susceptibility to certain gut microbes.…”

Roles of fermented plant-, dairy- and meat-based foods in the modulation of allergic responses by Abd Rahim, Muhamad Hafiz, Hazrin-Chong, Nur Hazlin, Harith, Hanis Hazeera, Wan-Mohtar, Wan Abd Al Qadr Imad, Sukor, Rashidah

“…Positive outcomes on AR through fermented foods could be linked to microbial hydrolysis of food allergens, improvement in gut microbiota robustness, and modulation of the immune system that promotes a balance between T helper 1 (Th1) and Th2 cells. …”

Visualizing Attack of Escherichia coli by the Antimicrobial Peptide Human Defensin 5 by Chileveru, Haritha Reddy, Lim, Shion A., Chairatana, Phoom, Wommack, Andrew, Chiang, I-Ling, Nolan, Elizabeth Marie

“…Human α-defensin 5 (HD5) is a 32-residue cysteine-rich host-defense peptide that exhibits broad-spectrum antimicrobial activity and contributes to innate immunity in the human gut and other organ systems. Despite many years of investigation, its antimicrobial mechanism of action remains unclear. …”
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Microbial Co-occurrence Relationships in the Human Microbiome by Faust, Karoline, Sathirapongsasuti, Jarupon, Izard, Jacques, Segata, Nicola, Gevers, Dirk, Raes, Jeroen, Huttenhower, Curtis

“…Comparing phylogenetic versus functional similarities among bacteria, we show that dominant commensal taxa (such as Prevotellaceae and Bacteroides in the gut) often compete, while potential pathogens (e.g. …”
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In between empathy and wonder lies the contamination that makes us human by Hsu, Yuping, S.M. Massachusetts Institute of Technology.

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Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals by Chang, W, Lai, A

“… <h4>Background</h4> <p>Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. …”

Enzymatic hydrolysis of lignocellulosis biomass using extract from the termite Coptotermes curvignathus holmgren by Wong, Sin-Yee

“…To disintegrate the tough linear chains of cellulose, termites are loaded with different species of microorganisms in their relatively tiny guts. These gut microbes would collaborate to produce digestive enzymatic juice for degrading wood into consumable end products such as sugars, hydrogen, ethanol and acetate. …”
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Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation by Hegazy, AN, West, NR, Stubbington, MJT, Wendt, E, Suijker, KIM, Datsi, A, This, S, Danne, C, Campion, S, Duncan, SH, Owens, BMJ, Uhlig, HH, McMichael, A, Bergthaler, A, Teichmann, SA, Keshav, S, Powrie, F

“…<h3>Background &amp; Aims</h3> <p>Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. …”

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations by Chu, Nathaniel David, Smith, Mark Burnham, Perrotta, Allison, Kassam, Zain, Alm, Eric J

“…Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial communities—believed to be the therapeutic agent—can complicate or undermine treatment efficacy. …”
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A single-cell survey of the small intestinal epithelium by Haber, Adam L., Biton, Moshe, Rogel, Noga, Herbst, Rebecca H., Shekhar, Karthik, Smillie, Christopher, Burgin, Grace, Delorey, Toni M., Howitt, Michael R., Katz, Yarden, Tirosh, Itay, Beyaz, Semir, Dionne, Danielle, Zhang, Mei, Raychowdhury, Raktima, Garrett, Wendy S., Rozenblatt-Rosen, Orit, Shi, Hai Ning, Yilmaz, Omer, Xavier, Ramnik J., Regev, Aviv

“…Intestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. …”
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DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome by Sun, Yihua, Kong, Lingxin, Wu, Guojun, Cao, Bo, Pang, Xiaoyan, Deng, Zixin, Dedon, Peter C, Zhang, Chenhong, You, Delin

“…To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. …”
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The airway microbiome: present and future applications by Aogáin, Micheál Mac, Jaggi, Tavleen Kaur, Chotirmall, Sanjay Haresh

“…As a complex organ system, with varying topology and a mucosal surface area exceeding that of the gut, the respiratory tract is recognized as a key site of host-microbe interaction. …”
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Helicobacter hepaticus polysaccharide induces an anti-inflammatory response in intestinal macrophages by Danne, C, Powrie, F

“…A high density of microbes inhabits the intestine, helping with food digestion, vitamin synthesis, xenobiotic detoxification, pathogen resistance and immune system maturation. …”

The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins ( Pygoscelis papua ) in their natural environment by Kaczvinsky, C, Levy, H, Preston, S, Youngflesh, C, Clucas, G, Lynch, HJ, Hart, T, Smith, AL

“…This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. …”

MAIT cells and the microbiome by Jabeen, MF, Hinks, TSC

“…Moreover, we speculate whether manipulation of the microbiota, or harnessing MAIT cell ligands within the gut or disease-specific sites could offer novel therapeutic strategies.…”

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life by Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric Steven, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.

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Dichotomous regulation of group 3 innate lymphoid cells by nongastric Helicobacter species by Shen, Zeli, Fox, James G.

“…Intestinal innate lymphoid cells (ILCs) contribute to the protective immunity and homeostasis of the gut, and the microbiota are critically involved in shaping ILC function. …”
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