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1. Full Text Stimulation of TLR2 and TLR4 differentially skews the balance of T cells in a mouse model of arthritis
by Abdollahi-Roodsaz, S and Joosten, L.A.B and Koenders, M.I and Devesa, I and Roelofs, M.F and Radstake, T.R.D.J and Heuvelmans-Jacobs, M and Akira, S and Nicklin, M.J and Ribeiro-Dias, F and Berg, W.B. van den
Journal of Clinical Investigation, ISSN 0021-9738, 2008, Volume 118, Issue 1, pp. 205 - 216
TLRs may contribute to the progression of rheumatoid arthritis through recognition of microbial or host-derived ligands found in arthritic joints. Here, we... 
RHEUMATOID-ARTHRITIS | MEDICINE, RESEARCH & EXPERIMENTAL | TOLL-LIKE RECEPTOR-2 | COLLAGEN-INDUCED ARTHRITIS | ANTAGONIST-DEFICIENT MICE | ACTIVATED PROTEIN-KINASE | HUMAN DENDRITIC CELLS | SYNOVIAL TISSUE | TRANSCRIPTION FACTOR FOXP3 | MEDIATES HEPATIC-INJURY | BACTERIAL-DNA | Germ-Free Life - immunology | Interleukin 1 Receptor Antagonist Protein - immunology | Toll-Like Receptor 2 - genetics | Germ-Free Life - genetics | Humans | Interleukin-17 - immunology | Toll-Like Receptor 9 - genetics | Toll-Like Receptor 4 - genetics | Interleukin 1 Receptor Antagonist Protein - genetics | Toll-Like Receptor 4 - immunology | Arthritis, Rheumatoid - microbiology | Mice, Knockout | T-Lymphocytes, Regulatory - immunology | Toll-Like Receptor 9 - immunology | Arthritis, Rheumatoid - genetics | Lymphocyte Activation - genetics | Lymphocyte Activation - immunology | Animals | Toll-Like Receptor 2 - immunology | Mice | Mice, Inbred BALB C | Arthritis, Rheumatoid - immunology | Disease Models, Animal | Polymerase chain reaction | Receptor antibodies | Prognosis | Rheumatoid arthritis | Research | Diagnosis | Health aspects
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2. Full Text The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia
by Robert M. Brucker and Seth R. Bordenstein
Science, ISSN 0036-8075, 8/2013, Volume 341, Issue 6146, pp. 667 - 669
Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown.... 
Pupae | Biological taxonomies | Microbiota | Insect larvae | REPORTS | Germ free state | Bacteria | Genomes | Hybridity | Larval development | Species | INCOMPATIBILITIES | MULTIDISCIPLINARY SCIENCES | Symbiosis | Species Specificity | Chimera - microbiology | Germ-Free Life - genetics | Chimera - physiology | Gastrointestinal Tract - microbiology | Hymenoptera - microbiology | Phylogeny | Bacteria - genetics | Animals | Bacteria - classification | Hymenoptera - physiology | Germ-Free Life - physiology | Hymenoptera - genetics | Metagenome | Lethal mutation | Origin of species | Genetic aspects | Wasps | Microbiota (Symbiotic organisms) | Somatic hybrids | Hybridization | Microbiology | Insects | Bacteriology
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3. Full Text Impact of the resident microbiota on the nutritional phenotype of drosophila melanogaster
by Ridley, Emma V and Wong, Adam C.-N and Westmiller, Stephanie and Douglas, Angela E
PLoS ONE, ISSN 1932-6203, 05/2012, Volume 7, Issue 5, p. e36765
Background: Animals are chronically infected by benign and beneficial microorganisms that generally promote animal health through their effects on the... 
INSULIN | LIFE-SPAN | LACTOBACILLUS-PLANTARUM | BACTERIA | HOMEOSTASIS | GUT-MICROBIOTA | HEALTHY-SUBJECTS | BLOOD-GLUCOSE | BIOLOGY | COLONIZATION | MECHANISMS | Germ-Free Life - genetics | Metagenome - physiology | Drosophila melanogaster - metabolism | Drosophila melanogaster - microbiology | Fertility - genetics | Metagenome - genetics | Phenotype | Animals | Acetobacter - metabolism | Larva - growth & development | RNA, Ribosomal, 16S - genetics | Female | Larva - genetics | Germ-Free Life - physiology | Host-Pathogen Interactions - physiology | Type 2 diabetes | Microbiota (Symbiotic organisms) | RNA | Drosophila | Physiological aspects | Genetic aspects | Glucose | Health aspects | Dextrose | Metabolic rate | Physiological effects | Senescence | rRNA 16S | Growth rate | Genes | Homeostasis | Eggs | Microorganisms | Microbiota | Bacteria | Physiology | Carbohydrates | Immune response | Nutrition | Metabolism | Insulin | Studies | Energy balance | Nutrition research | Musculoskeletal system | Insects | Animal health | Protein synthesis | Stem cells | Flies | Fecundity | Larval development
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4. Full Text Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development
by Jorge Galindo-Villegas and Diana García-Moreno and Sofia de Oliveira and José Meseguer and Victoriano Mulero
Proceedings of the National Academy of Sciences, ISSN 0027-8424, 09/2012, Volume 109, Issue 39, pp. E2605 - E2614
How fish larvae are protected from infection before the maturation of adaptive immunity, a process which may take up to several weeks in most species, has long... 
Evolution | Epigenetic | Live imaging | Cytokines | Gene regulation | GNOTOBIOTIC ZEBRAFISH | epigenetic | MULTIDISCIPLINARY SCIENCES | evolution | GUT MICROBIOTA | GERM-FREE | T-CELL | MODEL | live imaging | UNSEEN MAJORITY | gene regulation | INFLAMMATION | TOLL-LIKE RECEPTORS | cytokines | HISTONE MODIFICATIONS | NF-KAPPA-B | Chromatin - metabolism | Germ-Free Life - immunology | Zebrafish - immunology | Zebrafish - embryology | Bacteria - immunology | Inflammation - metabolism | Zebrafish - classification | Chromatin - immunology | Myeloid Differentiation Factor 88 - immunology | Zebrafish Proteins - immunology | Toll-Like Receptors - metabolism | Inflammation - microbiology | Histones - immunology | Zebrafish Proteins - metabolism | Germ-Free Life - genetics | Toll-Like Receptors - immunology | Myeloid Differentiation Factor 88 - genetics | Inflammation - immunology | Animals | Histones - genetics | Toll-Like Receptors - genetics | Zebrafish - metabolism | Inflammation - genetics | Histones - metabolism | Zebrafish Proteins - genetics | Chromatin - genetics | Myeloid Differentiation Factor 88 - metabolism | Biological Sciences | PNAS Plus
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5. Full Text Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice
by Tze Guan Tan and Esen Sefik and Naama Geva-Zatorsky and Lindsay Kua and Debdut Naskar and Fei Teng and Lesley Pasman and Adriana Ortiz-Lopez and Ray Jupp and Hsin-Jung Joyce Wu and Dennis L. Kasper and Christophe Benoist and Diane Mathis
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 12/2016, Volume 113, Issue 50, pp. E8141 - E8150
Th17 cells accrue in the intestine in response to particular microbes. In rodents, segmented filamentous bacteria (SFB) induce intestinal Th17 cells, but... 
Probiotic | Microbiota | Intestine | Mucosal immunology | Th17 cells | microbiota | RHEUMATOID-ARTHRITIS | mucosal immunology | intestine | DENDRITIC CELLS | MULTIDISCIPLINARY SCIENCES | HELPER-CELLS | INNATE | SEGMENTED FILAMENTOUS BACTERIA | probiotic | T(H)17 CELLS | INTERLEUKIN-17 | TYPE-2 IMMUNITY | GENOME-WIDE ASSOCIATION | Germ-Free Life - immunology | Humans | Inflammatory Bowel Diseases - immunology | Immunity, Mucosal | Symbiosis - immunology | Male | Arthritis, Experimental - microbiology | Gene Expression Profiling | Symbiosis - genetics | Intestinal Mucosa - cytology | Intestinal Mucosa - immunology | Arthritis, Experimental - etiology | Inflammatory Bowel Diseases - pathology | Female | Th17 Cells - cytology | Bifidobacterium adolescentis - isolation & purification | Germ-Free Life - genetics | Mice, Inbred C57BL | Arthritis, Experimental - immunology | Bifidobacterium adolescentis - immunology | Intestinal Mucosa - microbiology | Probiotics | Animals | Th17 Cells - immunology | Inflammatory Bowel Diseases - microbiology | Mice | Gastrointestinal Microbiome - immunology | Biological Sciences | PNAS Plus
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6. Full Text Restricted microbiota and absence of cognate TCR antigen leads to an unbalanced generation of Th17 cells
by Lochner, Matthias and Bérard, Marion and Sawa, Shinichiro and Hauer, Siona and Gaboriau-Routhiau, Valérie and Fernandez, Tahia Diana and Snel, Johannes and Bousso, Philippe and Cerf-Bensussan, Nadine and Eberl, Gérard
Journal of Immunology, ISSN 0022-1767, 02/2011, Volume 186, Issue 3, pp. 1531 - 1537
Retinoic acid-related orphan receptor (ROR)gamma t(+) TCR alpha beta(+) cells expressing IL-17, termed Th17 cells, are most abundant in the intestinal lamina... 
LINEAGE COMMITMENT | ADAPTIVE IMMUNITY | RETINOIC ACID | ROR-GAMMA-T | HELPER-CELLS | REGULATORY T-CELLS | INTESTINAL IMMUNE-RESPONSES | PROINFLAMMATORY IL-17(+) | NKP46(+) CELLS | IMMUNOLOGY | FILAMENTOUS BACTERIA | T-Lymphocytes, Helper-Inducer - microbiology | Gram-Positive Bacterial Infections - immunology | Cell Proliferation | Germ-Free Life - immunology | Molecular Sequence Data | Male | Green Fluorescent Proteins - genetics | Cell Differentiation - genetics | Lymphocyte Activation - genetics | Lymphocyte Activation - immunology | Intestinal Mucosa - immunology | T-Lymphocytes, Helper-Inducer - immunology | Female | Nuclear Receptor Subfamily 1, Group F, Member 3 - deficiency | T-Lymphocytes, Helper-Inducer - pathology | Forkhead Transcription Factors - deficiency | Nuclear Receptor Subfamily 1, Group F, Member 3 - genetics | Amino Acid Sequence | Forkhead Transcription Factors - biosynthesis | Germ-Free Life - genetics | Interleukin-17 - genetics | Mice, Transgenic | CD4 Lymphocyte Count | Interleukin-17 - biosynthesis | Intestinal Mucosa - microbiology | Forkhead Transcription Factors - genetics | Receptors, Antigen, T-Cell - physiology | Mice, Knockout | Gram-Positive Bacterial Infections - pathology | Cell Differentiation - immunology | Animals | Green Fluorescent Proteins - biosynthesis | Nuclear Receptor Subfamily 1, Group F, Member 3 - biosynthesis | Mice | Receptors, Antigen, T-Cell - genetics | Receptors, Antigen, T-Cell - deficiency | Intestinal Mucosa - pathology | Life Sciences | Immunology
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7. Full Text A critical role for regulatory T cell-mediated control of inflammation in the absence of commensal microbiota
by Chinen, Takatoshi and Volchkov, Pavel Y and Chervonsky, Alexander V and Rudensky, Alexander Y
Journal of Experimental Medicine, ISSN 0022-1007, 10/2010, Volume 207, Issue 11, pp. 2323 - 2330
Suppression mediated by regulatory T cells (T reg cells) represents a unique, cell-extrinsic mechanism of in-trans negative regulation that restrains multiple... 
MEDICINE, RESEARCH & EXPERIMENTAL | IMMUNITY | HOMEOSTASIS | BACTERIA | NOD MICE | PROTEIN | AUTOIMMUNITY | TRANSCRIPTION FACTOR FOXP3 | IMMUNOLOGY | MATURATION | Inflammation - microbiology | Germ-Free Life - immunology | Germ-Free Life - genetics | Intestine, Small - microbiology | Enteritis - genetics | Immunity, Innate - genetics | Inflammation - immunology | Lymphocyte Depletion | Adaptive Immunity - genetics | Mice, Knockout | T-Lymphocytes, Regulatory - immunology | Immunity, Innate - immunology | Pancreatitis - genetics | Bacteria - immunology | Animals | Enteritis - microbiology | Enteritis - immunology | Inflammation - genetics | Pancreatitis - immunology | Mice | Adaptive Immunity - immunology | Pancreatitis - microbiology | Intestine, Small - immunology | Brief Definitive Report
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8. Full Text Antibiotics impair murine hematopoiesis by depleting the intestinal microbiota
by Josefsdottir, Kamilla S and Baldridge, Megan T and Kadmon, Claudine S and King, Katherine Y
Blood, ISSN 0006-4971, 02/2017, Volume 129, Issue 6, pp. 729 - 739
Bone marrow suppression is an adverse effect associated with many antibiotics, especially when administered for prolonged treatment courses. Recent advances in... 
GRANULOPOIESIS | STEM-CELLS | HEMATOLOGY | NEUTROPENIA | T-CELLS | DISEASE | CD8-Positive T-Lymphocytes - pathology | STAT1 Transcription Factor - deficiency | Hematopoietic Stem Cells - pathology | Anemia - pathology | Gastrointestinal Microbiome - physiology | Leukopenia - therapy | Hematopoiesis - drug effects | Granulocytes - drug effects | Leukopenia - chemically induced | CD8-Positive T-Lymphocytes - metabolism | Thrombocytosis - microbiology | Bone Marrow Cells - drug effects | Granulocytes - pathology | Anti-Bacterial Agents - adverse effects | B-Lymphocytes - pathology | Granulocytes - metabolism | Thrombocytosis - pathology | B-Lymphocytes - metabolism | Hematopoietic Stem Cells - drug effects | Gene Expression | Leukopenia - microbiology | Macrophages - pathology | Signal Transduction | Germ-Free Life - genetics | Mice, Inbred C57BL | Bone Marrow Cells - pathology | Anemia - chemically induced | Anemia - therapy | Hematopoiesis - genetics | Hematopoietic Stem Cells - metabolism | Germ-Free Life - drug effects | STAT1 Transcription Factor - genetics | Leukopenia - pathology | Fecal Microbiota Transplantation | Thrombocytosis - chemically induced | Mice, Knockout | B-Lymphocytes - drug effects | Macrophages - metabolism | Animals | Gastrointestinal Microbiome - drug effects | CD8-Positive T-Lymphocytes - drug effects | Macrophages - drug effects | Mice | Anemia - microbiology | Thrombocytosis - therapy | Bone Marrow Cells - metabolism | Hematopoiesis and Stem Cells
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9. Full Text RNA-Seq Quantification of Hepatic Drug Processing Genes in Germ-Free Mice
by Selwyn, FP and Cui, JY and Klaassen, CD
DRUG METABOLISM AND DISPOSITION, ISSN 0090-9556, 10/2015, Volume 43, Issue 10, pp. 1572 - 1580
Intestinal bacteria have been shown to be important in regulating host intermediary metabolism and contributing to obesity. However, relatively less is known... 
CYTOCHROME-P450 | PHARMACOLOGY & PHARMACY | BIOTRANSFORMATION | MICROBIOTA | GUT FLORA | EXPRESSION | Germ-Free Life - genetics | Liver - metabolism | Mice, Inbred C57BL | Cytochrome P-450 Enzyme System - metabolism | Male | RNA - genetics | Sequence Analysis, RNA - methods | Pharmaceutical Preparations - metabolism | Animals | Liver - drug effects | Cytochrome P-450 Enzyme System - genetics | Mice | Pharmaceutical Preparations - administration & dosage | Special Section on Drug Metabolism and the Microbiome
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10. Full Text Nature of bacterial colonization influences transcription of mucin genes in mice during the first week of life
by Bergström, Anders and Kristensen, Matilde B and Bahl, Martin I and Metzdorff, Stine B and Fink, Lisbeth N and Frøkiær, Hanne and Licht, Tine R
BMC Research Notes, ISSN 1756-0500, 2012, Volume 5, Issue 1, pp. 402 - 402
Postnatal regulation of the small intestinal mucus layer is potentially important in the development of adult gut functionality. We hypothesized that the... 
16S rRNA | Postnatal transcription onset | Probiotics | Escherichia coli Nissle | Lactobacillus acidophilus NCFM | Germ free mice | LinRegPCR | qPCR | Monocolonized | Mucin-2 - genetics | Metagenome - physiology | Gene Expression Regulation, Developmental | Mucins - metabolism | Trefoil Factor-3 | Mucus - metabolism | Transcription, Genetic | Microbial Consortia - genetics | Escherichia coli - physiology | Real-Time Polymerase Chain Reaction | Mucin-3 - genetics | Animals, Newborn | Mucin-2 - metabolism | Mucin-1 - metabolism | Mucin-3 - metabolism | Lactobacillus acidophilus - physiology | Germ-Free Life - genetics | Intestine, Small - microbiology | Mucin-4 - metabolism | Mucin-4 - genetics | Mucus - microbiology | Animals | RNA, Ribosomal, 16S - genetics | Mice | Intestine, Small - metabolism | Mucins - genetics | Mucin-1 - genetics | Dams | Microbiota (Symbiotic organisms) | RNA | Genes | Escherichia coli | Mucins | Genetic transcription | Microbial colonies | Protein binding | Microbiology | E coli | Efficiency | Colleges & universities | Bacteria | Software | Life sciences | Gene expression | Experiments | Manuscripts | Food
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11. Full Text Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets
by Chowdhury, Shankar R and King, Dale E and Willing, Benjamin P and Band, Mark R and Beever, Jonathan E and Lane, Adrienne B and Loor, Juan J and Marini, Juan C and Rund, Laurie A and Schook, Lawrence B and Van Kessel, Andrew G and Rex, H. Rex
BMC Genomics, ISSN 1471-2164, 07/2007, Volume 8, Issue 1, pp. 215 - 215
To gain insight into host-microbe interactions in a piglet model, a functional genomics approach was used to address the working hypothesis that... 
Animals, Newborn | Intestinal Mucosa - metabolism | Cell Proliferation | Oligonucleotide Array Sequence Analysis | Electron Transport - genetics | Germ-Free Life - genetics | Intestine, Small - microbiology | Gene Expression Profiling | Signal Transduction - genetics | Intestinal Mucosa - microbiology | Gene Regulatory Networks | Intestinal Mucosa - cytology | Cell Differentiation - genetics | Host-Parasite Interactions - genetics | Metabolic Networks and Pathways - genetics | Animals | Intestinal Mucosa - immunology | Swine | Transcription, Genetic | Intestine, Small - metabolism | Immunity, Mucosal - genetics | Principal Component Analysis | Intestine, Small - immunology | Messenger RNA | Intestine, Small | Physiological aspects | Genetic aspects | Genetic transcription | Research | Properties | Epithelium
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12. Full Text A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development
by Yamamoto, Masahiro and Yamaguchi, Rui and Munakata, Kaori and Takashima, Kiyoe and Nishiyama, Mitsue and Hioki, Kyoji and Ohnishi, Yasuyuki and Nagasaki, Masao and Imoto, Seiya and Miyano, Satoru and Ishige, Atsushi and Watanabe, Kenji
BMC Genomics, ISSN 1471-2164, 07/2012, Volume 13, Issue 1, pp. 335 - 335
Background: Epidemiological studies have suggested that the encounter with commensal microorganisms during the neonatal period is essential for normal... 
Hygiene hypothesis | Metagene profiler | Germ-free | Type 1 interferon | Toll-like receptor | ADJUVANT-INDUCED ARTHRITIS | GENE SET ENRICHMENT | COMMENSAL BACTERIA | TOLERANCE | ONTOLOGY TERMS | COLONIZATION | GUT MICROBIOTA | AUTOIMMUNE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | EXPRESSION | MetaGene Profiler | Germ-Free Life - immunology | Gene Expression Profiling | Immune System - growth & development | Liver - growth & development | Organ Specificity - genetics | Gene Expression Regulation, Developmental | Intestine, Small - growth & development | Toll-Like Receptors - metabolism | Spleen - growth & development | Animals, Newborn | Multigene Family - genetics | Bacteria - metabolism | Immune System - microbiology | Oligonucleotide Array Sequence Analysis - methods | Germ-Free Life - genetics | Liver - metabolism | Signal Transduction - genetics | Reverse Transcriptase Polymerase Chain Reaction | Animals | Spleen - metabolism | Models, Biological | Toll-Like Receptors - genetics | Mice | Intestine, Small - metabolism | Cluster Analysis | Usage | DNA microarrays | Perinatal infection | Genetic aspects | Research | Health aspects | Risk factors | Immune system | Infants (Newborn) | Analysis | Sunscreens (Cosmetics) | Liver | Genes | Interferon | B cells | Biological response modifiers | Studies | Microorganisms | Algorithms | Cytokines | Statistical methods | Gene expression | Experiments | Thermal cycling
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13. Full Text The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community
by Wymore Brand, Meghan and Wannemuehler, Michael J and Phillips, Gregory J and Proctor, Alexandra and Overstreet, Anne-Marie and Jergens, Albert E and Orcutt, Roger P and Fox, James G
ILAR Journal, ISSN 1084-2020, 08/2015, Volume 56, Issue 2, pp. 169 - 178
The gastrointestinal (GI) microbiota forms a mutualistic relationship with the host through complex and dynamic interactions. Because of the complexity and... 
ASF | Gnotobiotic | Microbiota | microbiota | OLIGONUCLEOTIDE PROBES | GERMFREE MICE | INTESTINAL MICROBIOTA | GASTROINTESTINAL-TRACT | BACTERIAL FLORA | INFLAMMATORY-BOWEL-DISEASE | T-CELL RESPONSES | gnotobiotic | VETERINARY SCIENCES | LYMPHATIC TISSUE | HELICOBACTER-HEPATICUS | IMMUNE REACTIVITY | Bacteria - metabolism | Animals | Germ-Free Life - genetics | Humans | Gastrointestinal Microbiome - physiology | Mice | Germ-Free Life - physiology | Gastrointestinal Microbiome - genetics
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