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Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe 2015; 17:385-391. [PMID: 25732063 DOI: 10.1016/j.chom.2015.01.015] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/23/2014] [Accepted: 01/09/2015] [Indexed: 12/13/2022]
Abstract
The gut microbiome is widely studied by fecal sampling, but the extent to which stool reflects the commensal composition at intestinal sites is poorly understood. We investigated this relationship in rhesus macaques by 16S sequencing feces and paired lumenal and mucosal samples from ten sites distal to the jejunum. Stool composition correlated highly with the colonic lumen and mucosa and moderately with the distal small intestine. The mucosal microbiota varied most based on location and was enriched in oxygen-tolerant taxa (e.g., Helicobacter and Treponema), while the lumenal microbiota showed inter-individual variation and obligate anaerobe enrichment (e.g., Firmicutes). This mucosal and lumenal community variability corresponded to functional differences, such as nutrient availability. Additionally, Helicobacter, Faecalibacterium, and Lactobacillus levels in stool were highly predictive of their abundance at most other gut sites. These results quantify the composition and biogeographic relationships between gut microbial communities in macaques and support fecal sampling for translational studies.
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Affiliation(s)
- Koji Yasuda
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA
| | - Keunyoung Oh
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Boyu Ren
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Timothy L Tickle
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Lynn M Wachtman
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Boston, MA 02139, USA
| | - Andrew D Miller
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Biomedical Sciences, Section of Anatomic Pathology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | - Susan V Westmoreland
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA
| | - Keith G Mansfield
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA
| | - Eric J Vallender
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Gregory M Miller
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Pharmaceutical Sciences, Bouvé College of Health Science, Northeastern University, Boston, MA 02115, USA
| | - James K Rowlett
- New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | | | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
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Tangney M, Mitchell WJ. Characterisation of a glucose phosphotransferase system in Clostridium acetobutylicum ATCC 824. Appl Microbiol Biotechnol 2006; 74:398-405. [PMID: 17096120 DOI: 10.1007/s00253-006-0679-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Revised: 09/11/2006] [Accepted: 09/13/2006] [Indexed: 11/24/2022]
Abstract
The transport of glucose by the solventogenic anaerobe Clostridium acetobutylicum was investigated. Glucose phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) activity was detected in extracts prepared from cultures grown on glucose and extract fractionation revealed that both soluble and membrane components are required for activity. Glucose PTS activity was inhibited by the analogue methyl alpha-glucoside, indicating that the PTS enzyme II belongs to the glucose-glucoside (Glc) family of proteins. Consistent with this conclusion, labelled methyl alpha-glucoside was phosphorylated by PEP in cell-free extracts and this activity was inhibited by glucose. A single gene encoding a putative enzyme II of the glucose family, which we have designated glcG, was identified from the C. acetobutylicum ATCC 824 genome sequence. In common with certain other low-GC gram-positive bacteria, including Bacillus subtilis, the C. acetobutylicum glcG gene appears to be associated with a BglG-type regulator mechanism, as it is preceded by a transcription terminator that is partially overlapped by a typical ribonucleic antiterminator (RAT) sequence, and is downstream of an open reading frame that appears to encode a transcription antiterminator protein. This is the first report of a glucose transport mechanism in this industrially important organism.
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Affiliation(s)
- Martin Tangney
- School of Life Sciences, Merchiston Campus, Napier University, Edinburgh EH10 5DT, UK.
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Coconnier-Polter MH, Liévin-Le Moal V, Servin AL. A Lactobacillus acidophilus strain of human gastrointestinal microbiota origin elicits killing of enterovirulent Salmonella enterica Serovar Typhimurium by triggering lethal bacterial membrane damage. Appl Environ Microbiol 2005; 71:6115-20. [PMID: 16204528 PMCID: PMC1265971 DOI: 10.1128/aem.71.10.6115-6120.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human gastrointestinal microbiota produces antagonistic activities against gastrointestinal bacterial pathogens. We undertook a study to investigate the mechanism(s) by which a Lactobacillus acidophilus strain of human microbiota origin antagonizes the gram-negative enteroinvasive pathogen Salmonella enterica serovar Typhimurium. We showed that the cell-free culture supernatant of L. acidophilus strain LB (LB-CFCS) induced the following effects in S. enterica SL1344: (i) a decrease in intracellular ATP that paralleled bacterial death, (ii) the release of lipopolysaccharide, (iii) permeabilization of the bacterial membrane, and (iv) an increase in the sensitivity of Salmonella to the lytic action of sodium dodecyl sulfate. Finally, we showed using two mutant strains of Salmonella, PhoP MS7953s and PmrA JKS1170, that the two-component regulatory systems PhoP-PhoQ and PmrA-PmrB that regulate the mechanisms of resistance to antibacterial agents in Salmonella did not influence the anti-Salmonella effect of LB-CFCS.
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Villarino A, Bouvet OM, Regnault B, Martin-Delautre S. Exploring the frontier between life and death in Escherichia coli: evaluation of different viability markers in live and heat- or UV-killed cells. Res Microbiol 2000; 151:755-68. [PMID: 11130866 DOI: 10.1016/s0923-2508(00)01141-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A number of methods have been proposed to assess the viability of cells without culture. Each method is based on criteria that reflect different levels of cellular integrity or functionality. As a consequence, the interpretation of viability is often ambiguous. The purposes of this work were to evaluate the capacity of current viability markers to distinguish between live and dead Escherichia coli K-12 cells. Methods that assess 'viability' by the demonstration of metabolic activities (esterase activity, active electron transport chain, transport of glucose), cellular integrity (membrane integrity, presence of nucleic acids) or the building up of cellular material (cell elongation) have been evaluated in live and UV- or heat-killed cells. With live cells, viability markers detected cells in counts similar to the colony count. However, these so-called viability markers could stain dead cells for some time after the lethal treatment. For the UV-killed cells, residual activities were detected even after 48 h of storage at 20 degrees C. However, for heat-treated cells, these activities disappeared within hours after heat treatment. Only a combination of fluorescence in situ hybridization with rRNA probes and cell elongation in response to nutrients (in the presence of an inhibitor of cell division) had the ability to differentiate live from dead cells. Problems in the definition of a viable but nonculturable state are in part due to the lack of a clear definition of bacterial death. We consider death as an irreversible state where no growth, cell elongation or protein synthesis may occur.
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Affiliation(s)
- A Villarino
- Aquabiolab, Unité des entérobactéries, Institut Pasteur, Paris, France.
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Rager MN, Binet MR, Bouvet OM. 31P and 13C nuclear magnetic resonance studies of metabolic pathways in Pasteurella multocida characterization of a new mannitol-producing metabolic pathway. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 263:695-701. [PMID: 10469132 DOI: 10.1046/j.1432-1327.1999.00540.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glucose metabolism of Pasteurella multocida was examined in resting cells in vivo using 13C NMR spectroscopy, in cell-free extracts in vitro using 31P NMR spectroscopy and using enzyme assays. The NMR data indicate that glucose is converted by the Embden-Meyerhof and pentose phosphate pathways. The P. multocida fructose 6-phosphate phosphotransferase activity (the key enzyme of the Embden-Meyerhof pathway) was similar to that of Escherichia coli. Nevertheless, and in contrast to that of E. coli, its activity was inhibited by alpha glycerophosphate. This inhibition is consistent with the very low fructose 6-phosphate phosphotransferase activity found in cell-free extracts of P. multocida using a spectrophotometric method. The dominant end products of glucose metabolism were mannitol, acetate and succinate. Under anaerobic conditions, P. multocida was able to constitutively produce mannitol from glucose, mannose, fructose, sucrose, glucose 6-phosphate and fructose 6-phosphate. We propose a new metabolic pathway in P. multocida where fructose 6-phosphate is reduced to mannitol 1-phosphate by fructose 6-phosphate reductase. Mannitol 1-phosphate produced is then converted to mannitol by mannitol 1-phosphatase.
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Affiliation(s)
- M N Rager
- Service de Résonance Magnétique Nucléaire UMR 7576, Ecole Nationale Supérieure de Chimie de Paris, France
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