201
|
A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects. Nat Rev Microbiol 2012; 10:575-82. [PMID: 22728587 DOI: 10.1038/nrmicro2819] [Citation(s) in RCA: 592] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer has long been considered a genetic disease. However, accumulating evidence supports the involvement of infectious agents in the development of cancer, especially in those organs that are continuously exposed to microorganisms, such as the large intestine. Recent next-generation sequencing studies of the intestinal microbiota now offer an unprecedented view of the aetiology of sporadic colorectal cancer and have revealed that the microbiota associated with colorectal cancer contains bacterial species that differ in their temporal associations with developing tumours. Here, we propose a bacterial driver-passenger model for microbial involvement in the development of colorectal cancer and suggest that this model be incorporated into the genetic paradigm of cancer progression.
Collapse
|
202
|
Mäkivuokko H, Wacklin P, Koenen ME, Laamanen K, Alakulppi N, Venema K, Mättö J. Isolation of bifidobacteria for blood group secretor status targeted personalised nutrition. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2012; 23:18578. [PMID: 23990829 PMCID: PMC3747753 DOI: 10.3402/mehd.v23i0.18578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Background Currently, there is a constant need to find microbial products for maintaining or even improving host microbiota balance that could be targeted to a selected consumer group. Blood group secretor status, determining the ABO status, could be used to stratify the consumer group. Objective We have applied a validated upper intestinal tract model (TIM-1) and culturing methods to screen potential probiotic bacteria from faeces of blood secretor and non-secretor individuals. Design Faecal samples from healthy volunteers were pooled to age- and sex-matched secretor and non-secretor pools. Faecal pools were run through separate TIM-1 simulations, and bacteria were cultivated from samples taken at different stages of simulations for characterisation. Results Microbes in secretor pool survived the transit through TIM-1 system better than microbes of non-secretor pool, especially bifidobacteria and anaerobes were highly affected. The differences in numbers of bifidobacteria and lactobacilli isolates after plate cultivations and further the number of distinct RAPD-genotypes was clearly lower in non-secretor pool than in secretor pool. Conclusions In the present study, we showed that microbiota of secretor and non-secretor individuals tolerate gastrointestinal conditions differently and that a combination of gastrointestinal simulations and cultivation methods proved to be a promising tool for isolating potentially probiotic bacteria.
Collapse
|
203
|
Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M. Host genetic and environmental effects on mouse intestinal microbiota. ISME JOURNAL 2012; 6:2033-44. [PMID: 22695862 DOI: 10.1038/ismej.2012.54] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.
Collapse
Affiliation(s)
- James H Campbell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
204
|
Bucci V, Bradde S, Biroli G, Xavier JB. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol 2012; 8:e1002497. [PMID: 22577356 PMCID: PMC3343147 DOI: 10.1371/journal.pcbi.1002497] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 03/12/2012] [Indexed: 11/19/2022] Open
Abstract
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.
Collapse
Affiliation(s)
- Vanni Bucci
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
| | - Serena Bradde
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
| | - Giulio Biroli
- Institut Physique Théorique (IPhT) CEA Saclay, and CNRS URA, Gif Sur Yvette, France
| | - Joao B. Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (VB); (SB); (JBX)
| |
Collapse
|
205
|
Redford KH, Segre JA, Salafsky N, del Rio CM, McAloose D. Conservation and the microbiome. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2012; 26:195-7. [PMID: 22443125 PMCID: PMC3513825 DOI: 10.1111/j.1523-1739.2012.01829.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- Kent H. Redford
- WCS Institute, Wildlife Conservation Society, Bronx, NY 10460, U.S.A
| | - Julia A. Segre
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892-4442, U.S.A
| | - Nick Salafsky
- Foundations of Success, 4109 Maryland Avenue, Bethesda, MD 20816, U.S.A
| | | | - Denise McAloose
- Wildlife Health, Wildlife Conservation Society, Bronx, NY 10460, U.S.A
| |
Collapse
|
206
|
Nistal E, Caminero A, Herrán AR, Arias L, Vivas S, de Morales JMR, Calleja S, de Miera LES, Arroyo P, Casqueiro J. Differences of small intestinal bacteria populations in adults and children with/without celiac disease: effect of age, gluten diet, and disease. Inflamm Bowel Dis 2012; 18:649-56. [PMID: 21826768 DOI: 10.1002/ibd.21830] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 06/20/2011] [Indexed: 12/13/2022]
Abstract
BACKGROUND Scientific evidence has revealed microecological changes in the intestinal tract of celiac infants. The objective of this work is the study of bacterial differences in the upper small intestine in both adults (healthy, untreated celiac disease [CD], and CD treated with a gluten-free diet) and children (healthy and untreated CD). METHODS Intestinal bacterial communities were identified by 16S rRNA gene sequencing of DNA extracted from duodenal biopsies. RESULTS Analysis of the sequences from adults and children showed that this niche was colonized by bacteria affiliated mainly with three phyla: Firmicutes, Proteobacteria, and Bacteroidetes. In total, 89 different genera were identified in adults and 46 in children. Bacterial richness was significantly lower in the children than in the adults. A global principal component analysis of the bacterial communities of both healthy and untreated CD patient groups (including both children and adults) revealed a strong effect of age in principal component 1--clustering all adults and children separately--and a possible effect of the disease in adults with untreated patients clustering separately. CONCLUSIONS There are bacterial differences in the upper small intestine between untreated children CD patients and untreated CD adults due to age. There are bacterial differences in the upper small bacteria microbiota between treated and untreated CD adults due to treatment with a gluten-free diet.
Collapse
Affiliation(s)
- Esther Nistal
- Área de Microbiología, Facultad de Biología y Ciencias Ambientales, Universidad de León, León, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
207
|
Vítor JMB, Vale FF. Alternative therapies for Helicobacter pylori: probiotics and phytomedicine. ACTA ACUST UNITED AC 2012; 63:153-64. [PMID: 22077218 DOI: 10.1111/j.1574-695x.2011.00865.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Helicobacter pylori is a common human pathogen infecting about 30% of children and 60% of adults worldwide and is responsible for diseases such as gastritis, peptic ulcer and gastric cancer. Treatment against H. pylori is based on the use of antibiotics, but therapy failure can be higher than 20% and is essentially due to an increase in the prevalence of antibiotic-resistant bacteria, which has led to the search for alternative therapies. In this review, we discuss alternative therapies for H. pylori, mainly phytotherapy and probiotics. Probiotics are live organisms or produced substances that are orally administrated, usually in addition to conventional antibiotic therapy. They may modulate the human microbiota and promote health, prevent antibiotic side effects, stimulate the immune response and directly compete with pathogenic bacteria. Phytomedicine consists of the use of plant extracts as medicines or health-promoting agents, but in most cases the molecular mode of action of the active ingredients of these herbal extracts is unknown. Possible mechanisms include inhibition of H. pylori urease enzyme, disruption of bacterial cell membrane, and modulation of the host immune system. Other alternative therapies are also reviewed.
Collapse
Affiliation(s)
- Jorge M B Vítor
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | | |
Collapse
|
208
|
Boleij A, Tjalsma H. Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer. Biol Rev Camb Philos Soc 2012; 87:701-30. [PMID: 22296522 DOI: 10.1111/j.1469-185x.2012.00218.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A healthy human body contains at least tenfold more bacterial cells than human cells and the most abundant and diverse microbial community resides in the intestinal tract. Intestinal health is not only maintained by the human intestine itself and by dietary factors, but is also largely supported by this resident microbial community. Conversely, however, a large body of evidence supports a relationship between bacteria, bacterial activities and human colorectal cancer. Symbiosis in this multifaceted organ is thus crucial to maintain a healthy balance within the host-diet-microbiota triangle and accordingly, changes in any of these three factors may drive a healthy situation into a state of disease. In this review, the factors that sustain health or drive this complex intestinal system into dysbiosis are discussed. Emphasis is on the role of the intestinal microbiota and related mechanisms that can drive the initiation and progression of sporadic colorectal cancer (CRC). These mechanisms comprise the induction of pro-inflammatory and pro-carcinogenic pathways in epithelial cells as well as the production of (geno)toxins and the conversion of pro-carcinogenic dietary factors into carcinogens. A thorough understanding of these processes will provide leads for future research and may ultimately aid in development of new strategies for CRC diagnosis and prevention.
Collapse
Affiliation(s)
- Annemarie Boleij
- Department of Laboratory Medicine, Nijmegen Institute for Infection, Inflammation and Immunity (N4i) & Radboud University Centre for Oncology (RUCO) of the Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | | |
Collapse
|
209
|
Abstract
Over the last decades the rising occurrence of metabolic diseases throughout the world points to the failure of preventive and therapeutic strategies and of the corresponding molecular and physiological concepts. Therefore, a new paradigm needs to be elucidated. Very recently the intimate cross talk of the intestinal microbiota with the host immune system has opened new avenues. The large diversity of the intestinal microbes' genome, i.e. the metagenome, and the extreme plasticity of the immune system provide a unique balance which, when finely tuned, maintains a steady homeostasis. The discovery that a new microbiota repertoire is one of the causes responsible for the onset of metabolic disease suggests that the relationship with the immune system is impaired. Therefore, we here review the recent arguments that support the view that an alteration in the microbiota to host immune system balance leads to an increased translocation of bacterial antigens towards metabolically active tissues, and could result in a chronic inflammatory state and consequently impaired metabolic functions such as insulin resistance, hepatic fat deposition, insulin unresponsiveness, and excessive adipose tissue development. This imbalance could be at the onset of metabolic disease, and therefore the early treatment of the microbiota dysbiosis or immunomodulatory strategies should prevent and slow down the epidemic of metabolic diseases and hence the corresponding lethal cardiovascular consequences.
Collapse
Affiliation(s)
- Rémy Burcelin
- Institut National de la Santé et de la Recherche Médicale, U1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), BP 84225, 31432 Toulouse, France.
| | | | | |
Collapse
|
210
|
Abstract
The human gastrointestinal tract is divided into sections, allowing digestion and nutrient absorption in the proximal region to be separate from the vast microbial populations in the large intestine, thereby reducing conflict between host and microbes. In the distinct habitats of the gut, environmental filtering and competitive exclusion between microbes are the driving factors shaping microbial diversity, and stochastic factors during colonization history and in situ evolution are likely to introduce intersubject variability. Adaptive strategies of microbes with different niches are genomically encoded: Specialists have smaller genomes than generalists, and microbes with environmental reservoirs have large accessory genomes. A shift toward a Neolithic diet increased loads of simple carbohydrates and selected for their increased breakdown and absorption in the small intestine. Humans who outcompeted microbes for the new substrates obtained more energy from their diets and prospered, an evolutionary process reflected in modern population genetics. The three-way interactions between human genetics, diet, and the microbiota fundamentally shaped modern populations and continue to affect health globally.
Collapse
Affiliation(s)
- Jens Walter
- Department of Food Science, University of Nebraska, Lincoln, Nebraska 68583-0919, USA
| | | |
Collapse
|
211
|
Kim HS. Our Genome and Our other Genome: Understanding humans as Symbionts with Microbes. ACTA ACUST UNITED AC 2012. [DOI: 10.4167/jbv.2012.42.2.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Heenam Stanley Kim
- The Laboratory of Human-Microbial Genomics, Department of Medicine, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| |
Collapse
|
212
|
Advances and perspectives in in vitro human gut fermentation modeling. Trends Biotechnol 2012; 30:17-25. [DOI: 10.1016/j.tibtech.2011.06.011] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 04/19/2011] [Accepted: 06/15/2011] [Indexed: 12/31/2022]
|
213
|
Abstract
Obesity has been and continues to be an epidemic in the United States. Obesity has been addressed in multiple health initiatives, including Healthy People 2010, with no state meeting the proposed goal of a prevalence of obesity < 15% of the adult population. In contrast, obesity rates have continued to increase, with the self-reported prevalence of obesity among adults increasing by 1.1% from 2007 to the present. Indeed, since 2009, 33 states reported obesity prevalences of 25% or more with only 1 state reporting prevalence < 20%. There have been multiple approaches for the treatment of obesity, including fad diets, incentive-based exercise programs, and gastric bypass surgery; none of which have been optimal. In a murine model, it was shown that the majority of the intestinal microbiome consists of two bacterial phyla, the Bacteroidetes and the Firmicutes, and that the relative abundance of these two phyla differs among lean and obese mice; the obese mouse had a higher proportion of Firmicutes to Bacteroidetes (50% greater) than the lean mouse. The same results were appreciated in obese humans compared to lean subjects. The postulated explanation for this finding is that Firmicutes produce more complete metabolism of a given energy source than do Bacteroidetes, thus promoting more efficient absorption of calories and subsequent weight gain. Researchers were able to demonstrate that colonizing germ-free mice with the intestinal microbiome from obese mice led to an increased total body fat in the recipient mice despite a lack of change in diet. The converse, that, colonizing germ-free obese mice with the intestinal microbiome of thin mice causing a decreased total body fat in the recipient mice, has not yet been done. Other possible mechanisms by which the intestinal microbiome affects host obesity include induction of low-grade inflammation with lipopolysaccharide, regulation of host genes responsible for energy expenditure and storage, and hormonal communication between the intestinal microbiome and the host. The following review discusses the microbiome-obesity relationship and proposed mechanisms by which the intestinal microbiota is hypothesized to influence weight gain.
Collapse
Affiliation(s)
- Samuel J Kallus
- Department of Medicine, Georgetown University Hospital, Washington, DC, USA
| | | |
Collapse
|
214
|
Lambert JE, Fellner V. In Vitro Fermentation of Dietary Carbohydrates Consumed by African Apes and Monkeys: Preliminary Results for Interpreting Microbial and Digestive Strategy. INT J PRIMATOL 2011. [DOI: 10.1007/s10764-011-9559-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
215
|
Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis. Mol Biol Rep 2011; 39:5669-76. [DOI: 10.1007/s11033-011-1375-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 12/13/2011] [Indexed: 01/20/2023]
|
216
|
Ahn Y, Linder SW, Veach BT, Steve Yan S, Haydée Fernández A, Pineiro SA, Cerniglia CE. In vitro enrofloxacin binding in human fecal slurries. Regul Toxicol Pharmacol 2011; 62:74-84. [PMID: 22178170 DOI: 10.1016/j.yrtph.2011.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 01/03/2023]
Abstract
Most antibiotic inactivation studies have been conducted through in vitro incubations of human use aminoglycosides, beta-lactams, and fluoroquinolones, usually at fecal concentrations expected with therapeutic dose regimens in humans and animals. Less is known about the inactivation of these molecules when ingested at concentrations consistent with residue levels present in animal-derived foods from antibiotic treated animals. In this investigation, we used the fluoroquinolone, enrofloxacin which is specifically marketed for veterinary medicine as test compound. Fecal suspensions at 10%, 25%, and 50% (w/v) were subjected to physicochemical and molecular characterization and used in the drug binding studies. The fecal binding of enrofloxacin added at concentrations of 0.06, 0.1, 1, 5, 15, 50, and 150 mg/L was determined in various fecal slurry suspensions using analytical chemistry and microbiological assay methods. There was consistent correlation between both assay methods. By the analytical chemistry assay, the 10%, 25% and 50% diluted autoclaved fecal samples dosed with enrofloxacin showed binding of 50±4.6%, 54±6.5% and 56±6.8% of the enrofloxacin, respectively. Binding of enrofloxacin to fecal contents occurred rapidly within 10 min and remained constant over the incubation period. Denaturing gradient gel electrophoreses and pyrosequencing analysis showed varied profiles of the bacterial composition of the human intestinal microbiota for fecal samples from different individuals. This study provided information on methodological questions that have concerned regulatory authorities on in vitro testing to determine if concentrations of veterinary antimicrobial agent residues entering the human colon remain microbiologically active.
Collapse
Affiliation(s)
- Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079-9502, USA
| | | | | | | | | | | | | |
Collapse
|
217
|
Mikelsaar M, Lazar V, Onderdonk A, Donelli G. Do probiotic preparations for humans really have efficacy? MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2011. [DOI: 10.3402/mehd.v22i0.10128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Marika Mikelsaar
- Department of Microbiology, Medical Faculty, University of Tartu , Tartu, Estonia
| | - Veronica Lazar
- Department of Microbiology, Faculty of Biology, University of Bucharest , Bucharest, Romania
| | - Andrew Onderdonk
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School , Boston MA USA
| | | |
Collapse
|
218
|
Burcelin R, Serino M, Chabo C, Blasco-Baque V, Amar J. Gut microbiota and diabetes: from pathogenesis to therapeutic perspective. Acta Diabetol 2011; 48:257-273. [PMID: 21964884 PMCID: PMC3224226 DOI: 10.1007/s00592-011-0333-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 09/01/2011] [Indexed: 12/13/2022]
Abstract
More than several hundreds of millions of people will be diabetic and obese over the next decades in front of which the actual therapeutic approaches aim at treating the consequences rather than causes of the impaired metabolism. This strategy is not efficient and new paradigms should be found. The wide analysis of the genome cannot predict or explain more than 10-20% of the disease, whereas changes in feeding and social behavior have certainly a major impact. However, the molecular mechanisms linking environmental factors and genetic susceptibility were so far not envisioned until the recent discovery of a hidden source of genomic diversity, i.e., the metagenome. More than 3 million genes from several hundreds of species constitute our intestinal microbiome. First key experiments have demonstrated that this biome can by itself transfer metabolic disease. The mechanisms are unknown but could be involved in the modulation of energy harvesting capacity by the host as well as the low-grade inflammation and the corresponding immune response on adipose tissue plasticity, hepatic steatosis, insulin resistance and even the secondary cardiovascular events. Secreted bacterial factors reach the circulating blood, and even full bacteria from intestinal microbiota can reach tissues where inflammation is triggered. The last 5 years have demonstrated that intestinal microbiota, at its molecular level, is a causal factor early in the development of the diseases. Nonetheless, much more need to be uncovered in order to identify first, new predictive biomarkers so that preventive strategies based on pre- and probiotics, and second, new therapeutic strategies against the cause rather than the consequence of hyperglycemia and body weight gain.
Collapse
Affiliation(s)
- Rémy Burcelin
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France.
- Université de Toulouse, UPS, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432, Toulouse cedex 4, France.
| | - Matteo Serino
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France
- Université de Toulouse, UPS, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432, Toulouse cedex 4, France
| | - Chantal Chabo
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France
- Université de Toulouse, UPS, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432, Toulouse cedex 4, France
| | - Vincent Blasco-Baque
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1048, Toulouse, France
- Université de Toulouse, UPS, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), 31432, Toulouse cedex 4, France
| | - Jacques Amar
- Department of Therapeutics, Rangueil Hospital, Toulouse, France
| |
Collapse
|
219
|
Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants. J Pediatr Gastroenterol Nutr 2011; 53:512-9. [PMID: 21734604 DOI: 10.1097/mpg.0b013e318227e518] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The aim of the study was to investigate the previously unexplored diversity of neonatal intestinal microbiota and monitor early intestinal colonization patterns in Korean preterm infants using high-throughput pyrosequencing technology combined with 16S rDNA-based molecular methods. SUBJECTS AND METHODS A total of 46,369 partial 16S rDNA sequences obtained from 30 fecal samples serially taken from 10 very-low-birth weight preterm infants were analyzed. RESULTS A significant proportion of the molecular species (21.9%) was found to be unclassified. The pathogenic or potentially pathogenic molecular species belonging to the classes Gammaproteobacteria and Bacilli were predominant during the entire observation period. Anaerobic or nonpathogenic molecular species belonging to the class Clostridia (except Clostridium difficile) and phyla Bacteroidetes were ubiquitous even within 72 hours after birth. The proportion of these species increased significantly at 1 month of age. The most ubiquitous and abundant major molecular genera common to all of the postnatal ages were Escherichia, Enterobacter, Enterococcus, Veillonella, Serratia, Staphylococcus, Roseburia, Acinetobacter, Citrobacter, Bacteroides, Faecalibacterium, Blautia, and Streptococcus. CONCLUSIONS The diversity and dynamic nature of intestinal bacterial colonization in very-low-birth weight preterm infants were revealed using pyrosequencing technology. The results of the present pilot study may provide a basis to consider when investigating or interpreting the role of intestinal microbiota in certain preterm infant diseases such as necrotizing enterocolitis or systemic infection.
Collapse
|
220
|
Albesharat R, Ehrmann MA, Korakli M, Yazaji S, Vogel RF. Phenotypic and genotypic analyses of lactic acid bacteria in local fermented food, breast milk and faeces of mothers and their babies. Syst Appl Microbiol 2011; 34:148-55. [PMID: 21300508 DOI: 10.1016/j.syapm.2010.12.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 12/26/2022]
Abstract
Lactic acid bacteria (LAB) are generally accepted as beneficial to the host and their presence is directly influenced by ingestion of fermented food or probiotics. While the intestinal lactic microbiota is well-described knowledge on its routes of inoculation and competitiveness towards selective pressure shaping the intestinal microbiota is limited. In this study, LAB were isolated from faecal samples of breast feeding mothers living in Syria, from faeces of their infants, from breast milk as well as from fermented food, typically consumed in Syria. A total of 700 isolates were characterized by genetic fingerprinting with random amplified polymorphic DNA (RAPD) and identified by comparative 16S rDNA sequencing and Matrix Assisted Laser Desorption Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) analyses. Thirty six different species of Lactobacillus, Enterococcus, Streptococcus, Weissella and Pediococcus were identified. RAPD and MALDI-TOF-MS patterns allowed comparison of the lactic microbiota on species and strain level. Whereas some species were unique for one source, Lactobacillus plantarum, Lactobacillus fermentum, Pediococcus pentosaceus and Lactobacillus brevis were found in all sources. Interestingly, identical RAPD genotypes of L. plantarum, L. fermentum, L. brevis, Enterococcus faecium, Enterococcus faecalis and P. pentosaceus were found in the faeces of mothers, her milk and in faeces of her babies. Diversity of RAPD types found in food versus human samples suggests the importance of host factors in colonization and individual host specificity, and support the hypothesis that there is a vertical transfer of intestinal LAB from the mother's gut to her milk and through the milk to the infant's gut.
Collapse
Affiliation(s)
- Rima Albesharat
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Weihenstephaner Steig 16, 85350 Freising, Germany
| | | | | | | | | |
Collapse
|
221
|
Ricciardiello L, Bazzoli F, Fogliano V. Phytochemicals and colorectal cancer prevention--myth or reality? Nat Rev Gastroenterol Hepatol 2011; 8:592-6. [PMID: 21894197 DOI: 10.1038/nrgastro.2011.149] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoprevention of colorectal cancer has been the focus of intensive research for more than two decades. Epidemiological evidence has shown a small, but significant association between fruit and vegetable intake and a reduction in colorectal cancer risk. In vitro and animal data have also demonstrated that many dietary phytochemicals have potent chemopreventive activities. However, in humans, single-agent compounds have yielded conflicting results. A key concept is that dietary phytochemicals exert beneficial effects at low concentrations when working in synergy with each other. As the gut microflora evolved in an environment rich in dietary fiber and phytochemicals, the rapid shift towards a Western diet creates an environment in which the gut is more vulnerable to carcinogens, genetic alterations and inflammation. As enforcing dietary interventions on large populations is not realistic, we believe future chemopreventive work should focus on delivering phytochemical mixtures that target the multiple molecular events involved in colorectal carcinogenesis.
Collapse
Affiliation(s)
- Luigi Ricciardiello
- Department of Clinical Medicine, University of Bologna, Via Massarenti 9, Bologna 40138, Italy.
| | | | | |
Collapse
|
222
|
Buhnik-Rosenblau K, Danin-Poleg Y, Kashi Y. Predominant effect of host genetics on levels of Lactobacillus johnsonii bacteria in the mouse gut. Appl Environ Microbiol 2011; 77:6531-8. [PMID: 21803912 PMCID: PMC3187140 DOI: 10.1128/aem.00324-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 07/18/2011] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota is strongly associated with the well-being of the host. Its composition is affected by environmental factors, such as food and maternal inoculation, while the relative impact of the host's genetics have been recently uncovered. Here, we studied the effect of the host genetic background on the composition of intestinal bacteria in a murine model, focusing on lactic acid bacteria (LAB) as an important group that includes many probiotic strains. Based on 16S rRNA gene genotyping, variation was observed in fecal LAB populations of BALB/c and C57BL/6J mouse lines. Lactobacillus johnsonii, a potentially probiotic bacterium, appeared at significantly higher levels in C57BL/6J versus BALB/c mouse feces. In the BALB/c gut, the L. johnsonii level decreased rapidly after oral administration, suggesting that some selective force does not allow its persistence at higher levels. The genetic inheritance of L. johnsonii levels was further tested in reciprocal crosses between the two mouse lines. The resultant F1 offspring presented similar L. johnsonii levels, confirming that mouse genetics plays a major role in determining these levels compared to the smaller maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the LAB population in general and on the persistence of L. johnsonii in the gut in particular. Concentrating on a narrow spectrum of culturable LAB enables the isolation and characterization of such potentially probiotic bacterial strains, which might be specifically oriented to the genetic background of the host as part of a personalized-medicine approach.
Collapse
Affiliation(s)
- Keren Buhnik-Rosenblau
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yael Danin-Poleg
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yechezkel Kashi
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
223
|
Gerritsen J, Smidt H, Rijkers GT, de Vos WM. Intestinal microbiota in human health and disease: the impact of probiotics. GENES & NUTRITION 2011; 6:209-40. [PMID: 21617937 PMCID: PMC3145058 DOI: 10.1007/s12263-011-0229-7] [Citation(s) in RCA: 432] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/20/2011] [Indexed: 02/07/2023]
Abstract
The complex communities of microorganisms that colonise the human gastrointestinal tract play an important role in human health. The development of culture-independent molecular techniques has provided new insights in the composition and diversity of the intestinal microbiota. Here, we summarise the present state of the art on the intestinal microbiota with specific attention for the application of high-throughput functional microbiomic approaches to determine the contribution of the intestinal microbiota to human health. Moreover, we review the association between dysbiosis of the microbiota and both intestinal and extra-intestinal diseases. Finally, we discuss the potential of probiotic microorganism to modulate the intestinal microbiota and thereby contribute to health and well-being. The effects of probiotic consumption on the intestinal microbiota are addressed, as well as the development of tailor-made probiotics designed for specific aberrations that are associated with microbial dysbiosis.
Collapse
Affiliation(s)
- Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands,
| | | | | | | |
Collapse
|
224
|
Mikelsaar M. Human microbial ecology: lactobacilli, probiotics, selective decontamination. Anaerobe 2011; 17:463-7. [PMID: 21787875 DOI: 10.1016/j.anaerobe.2011.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/07/2011] [Indexed: 12/20/2022]
Abstract
Health care-associated infections are closely associated with different medical interventions which interrupt the balance of human microbiota. The occasional predominance of opportunistic pathogens may lead to their translocation into the lymph nodes and bloodstream, causing endogenous (primary or secondary) hospital infections. The question is raised as to if there is a possibility for prevention of the imbalance of GI microbiota during medical interventions in critically ill patients. Prophylactic selective decontamination of the digestive tract (SDD) simultaneously applies three to four different antimicrobials for the suppression of enteric aerobic microbes, which are potentially pathogenic microorganisms. However, there is no convincing evidence that the indigenous beneficial intestinal microbiota are preserved, resulting in reduced mortality of high-risk patients. In this overview, we have evaluated the antimicrobial treatment guidelines of the Infectious Diseases Society of America (IDSA) for intra-abdominal infections in adults and seniors according to their safety for different Lactobacillus spp. The data from our group and in the literature have shown that all tested lactobacilli strains (nearly one hundred) were insusceptible to metronidazole while different species of lactobacilli of the three fermentation groups expressed particular antibiotic susceptibility to vancomycin, cefoxitin, ciprofloxacin and some new tetracyclines. We have relied on microbial ecology data showing that the GI tracts of adults and the elderly are simultaneously colonised at least with several (four to a maximum of 12) Lactobacillus species expressing variable intrinsic insusceptibility to the aforementioned antimicrobials, according to the provided data in table. This finding offers the possibility of preserving the colonisation of the intestine with some beneficial lactobacilli during antimicrobial treatment in critically ill patients with health care-associated infections. Several probiotic Lactobacillus spp. strains are intrinsically resistant to antimicrobials and can be used during antibacterial therapy, however, their application as an additive to antimicrobial treatment in critically ill patients needs to be investigated in well-designed clinical trials.
Collapse
Affiliation(s)
- Marika Mikelsaar
- Department of Microbiology, Medical Faculty, University of Tartu, Tartu 50411, Estonia.
| |
Collapse
|
225
|
McLaughlin RW, Zheng JS, Chen MM, Zhao QZ, Wang D. Detection of Helicobacter in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. DISEASES OF AQUATIC ORGANISMS 2011; 95:241-245. [PMID: 21932536 DOI: 10.3354/dao02364] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In animals, infection by the Epsilonproteobacteria Helicobacter spp. and H. cetorum is widespread. It has been suggested that H. cetorum may cause gastritis in cetaceans. The aim of our study was to investigate the presence of Helicobacter spp. in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. The fecal material of 12 porpoises living in the wild in Poyang Lake and 1 porpoise living in captivity at the Wuhan Baiji Dolphinarium were examined by PCR for the presence of Helicobacter spp. The fecal material of 8 of 12 wild porpoises and the captive porpoise were positive for Helicobacter spp. as determined by PCR using Helicobacter-specific primers, which target the 16S rRNA gene. A 16S rRNA clone library was then prepared from 1 sample isolated from a female porpoise living in the wild. DNA sequence analysis from 3 of the clones showed 98 to 99% identity to the H. cetorum 16S rRNA gene. These results demonstrate the prevalence of Helicobacter spp. and H. cetorum in endangered freshwater finless porpoises.
Collapse
Affiliation(s)
- R W McLaughlin
- Biology Department, Saint Mary's University of Minnesota, Winona, Minnesota 55987-1399, USA
| | | | | | | | | |
Collapse
|
226
|
Prakash S, Rodes L, Coussa-Charley M, Tomaro-Duchesneau C. Gut microbiota: next frontier in understanding human health and development of biotherapeutics. Biologics 2011; 5:71-86. [PMID: 21847343 PMCID: PMC3156250 DOI: 10.2147/btt.s19099] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Indexed: 12/29/2022]
Abstract
The gut microbiota is a remarkable asset for human health. As a key element in the development and prevention of specific diseases, its study has yielded a new field of promising biotherapeutics. This review provides comprehensive and updated knowledge of the human gut microbiota, its implications in health and disease, and the potentials and limitations of its modification by currently available biotherapeutics to treat, prevent and/or restore human health, and future directions. Homeostasis of the gut microbiota maintains various functions which are vital to the maintenance of human health. Disruption of the intestinal ecosystem equilibrium (gut dysbiosis) is associated with a plethora of human diseases, including autoimmune and allergic diseases, colorectal cancer, metabolic diseases, and bacterial infections. Relevant underlying mechanisms by which specific intestinal bacteria populations might trigger the development of disease in susceptible hosts are being explored across the globe. Beneficial modulation of the gut microbiota using biotherapeutics, such as prebiotics, probiotics, and antibiotics, may favor health-promoting populations of bacteria and can be exploited in development of biotherapeutics. Other technologies, such as development of human gut models, bacterial screening, and delivery formulations eg, microencapsulated probiotics, may contribute significantly in the near future. Therefore, the human gut microbiota is a legitimate therapeutic target to treat and/or prevent various diseases. Development of a clear understanding of the technologies needed to exploit the gut microbiota is urgently required.
Collapse
Affiliation(s)
- Satya Prakash
- Biomedical Technology and Cell Therapy Research Laboratory, Department of Biomedical Engineering and Artificial Cells and Organs Research Centre, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | | | | | | |
Collapse
|
227
|
Rosenberg E, Zilber-Rosenberg I. Symbiosis and development: the hologenome concept. ACTA ACUST UNITED AC 2011; 93:56-66. [PMID: 21425442 DOI: 10.1002/bdrc.20196] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
All animals and plants establish symbiotic relationships with microorganisms; often the combined genetic information of the diverse microbiota exceeds that of the host. How the genetic wealth of the microbiota affects all aspects of the holobiont's (host plus all of its associated microorganisms) fitness (adaptation, survival, development, growth and reproduction) and evolution is reviewed, using selected coral, insect, squid, plant, and human/mouse published experimental results. The data are discussed within the framework of the hologenome theory of evolution, which demonstrates that changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont in the short term but also can be transmitted to offspring and lead to long lasting cooperations. As acquired characteristics (microbes) are heritable, consideration of the holobiont as a unit of selection in evolution leads to neo-Lamarckian principles within a Darwinian framework. The potential application of these principles can be seen in the growing fields of prebiotics and probiotics.
Collapse
Affiliation(s)
- Eugene Rosenberg
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Givat Shmuel, Israel.
| | | |
Collapse
|
228
|
Swann JR, Tuohy KM, Lindfors P, Brown DT, Gibson GR, Wilson ID, Sidaway J, Nicholson JK, Holmes E. Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats. J Proteome Res 2011; 10:3590-603. [PMID: 21591676 DOI: 10.1021/pr200243t] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces; antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.
Collapse
Affiliation(s)
- Jonathan R Swann
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
229
|
Abstract
Microbial ecology is revealing the vast diversity of strains and species that coexist in many environments, ranging from free-living communities to the symbionts that compose the human microbiome. In parallel, there is growing evidence of the importance of cooperative phenotypes for the growth and behavior of microbial groups. Here we ask: How does the presence of multiple species affect the evolution of cooperative secretions? We use a computer simulation of spatially structured cellular groups that captures key features of their biology and physical environment. When nutrient competition is strong, we find that the addition of new species can inhibit cooperation by eradicating secreting strains before they can become established. When nutrients are abundant and many species mix in one environment, however, our model predicts that secretor strains of any one species will be surrounded by other species. This "social insulation" protects secretors from competition with nonsecretors of the same species and can improve the prospects of within-species cooperation. We also observe constraints on the evolution of mutualistic interactions among species, because it is difficult to find conditions that simultaneously favor both within- and among-species cooperation. Although relatively simple, our model reveals the richness of interactions between the ecology and social evolution of multispecies microbial groups, which can be critical for the evolution of cooperation.
Collapse
Affiliation(s)
- Sara Mitri
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
- Oxford Centre for Integrative Systems Biology, Oxford University, Oxford OX1 3QU, United Kingdom; and
| | - João B. Xavier
- Program in Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Kevin R. Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
- Oxford Centre for Integrative Systems Biology, Oxford University, Oxford OX1 3QU, United Kingdom; and
| |
Collapse
|
230
|
Li Q, Zhang Q, Wang C, Tang C, Zhang Y, Li N, Li J. Fish oil enhances recovery of intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplant. PLoS One 2011; 6:e20460. [PMID: 21698145 PMCID: PMC3117781 DOI: 10.1371/journal.pone.0020460] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/23/2011] [Indexed: 01/10/2023] Open
Abstract
Background The intestinal chronic rejection (CR) is the major limitation to long-term survival of transplanted organs. This study aimed to investigate the interaction between intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplantation, and to find out whether fish oil enhances recovery of intestinal microbiota and epithelial integrity. Methods/Principal Findings The luminal and mucosal microbiota composition of CR rats were characterized by DGGE analysis at 190 days after intestinal transplant. The specific bacterial species were determined by sequence analysis. Furthermore, changes in the localization of intestinal TJ proteins were examined by immunofluorescent staining. PCR-DGGE analysis revealed that gut microbiota in CR rats had a shift towards Escherichia coli, Bacteroides spp and Clostridium spp and a decrease in the abundance of Lactobacillales bacteria in the intestines. Fish oil supplementation could enhance the recovery of gut microbiota, showing a significant decrease of gut bacterial proportions of E. coli and Bacteroides spp and an increase of Lactobacillales spp. In addition, CR rats showed pronounced alteration of tight junction, depicted by marked changes in epithelial cell ultrastructure and redistribution of occuldin and claudins as well as disruption in TJ barrier function. Fish oil administration ameliorated disruption of epithelial integrity in CR, which was associated with an improvement of the mucosal structure leading to improved tight junctions. Conclusions/Significance Our study have presented novel evidence that fish oil is involved in the maintenance of epithelial TJ integrity and recovery of gut microbiota, which may have therapeutic potential against CR in intestinal transplantation.
Collapse
Affiliation(s)
- Qiurong Li
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qiang Zhang
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chenyang Wang
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chun Tang
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yanmei Zhang
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ning Li
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jieshou Li
- Department of Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- * E-mail:
| |
Collapse
|
231
|
Mai V, Young CM, Ukhanova M, Wang X, Sun Y, Casella G, Theriaque D, Li N, Sharma R, Hudak M, Neu J. Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS One 2011; 6:e20647. [PMID: 21674011 PMCID: PMC3108958 DOI: 10.1371/journal.pone.0020647] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/05/2011] [Indexed: 12/12/2022] Open
Abstract
Intestinal luminal microbiota likely contribute to the etiology of necrotizing enterocolitis (NEC), a common disease in preterm infants. Microbiota development, a cascade of initial colonization events leading to the establishment of a diverse commensal microbiota, can now be studied in preterm infants using powerful molecular tools. Starting with the first stool and continuing until discharge, weekly stool specimens were collected prospectively from infants with gestational ages ≤32 completed weeks or birth weights≤1250 g. High throughput 16S rRNA sequencing was used to compare the diversity of microbiota and the prevalence of specific bacterial signatures in nine NEC infants and in nine matched controls. After removal of short and low quality reads we retained a total of 110,021 sequences. Microbiota composition differed in the matched samples collected 1 week but not <72 hours prior to NEC diagnosis. We detected a bloom (34% increase) of Proteobacteria and a decrease (32%) in Firmicutes in NEC cases between the 1 week and <72 hour samples. No significant change was identified in the controls. At both time points, molecular signatures were identified that were increased in NEC cases. One of the bacterial signatures detected more frequently in NEC cases (p<0.01) matched closest to γ-Proteobacteria. Although this sequence grouped to the well-studied Enterobacteriaceae family, it did not match any sequence in Genbank by more than 97%. Our observations suggest that abnormal patterns of microbiota and potentially a novel pathogen contribute to the etiology of NEC.
Collapse
Affiliation(s)
- Volker Mai
- Department of Microbiology and Cell Sciences and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
232
|
Abstract
Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.
Collapse
|
233
|
Marchesi JR, Dutilh BE, Hall N, Peters WHM, Roelofs R, Boleij A, Tjalsma H. Towards the human colorectal cancer microbiome. PLoS One 2011; 6:e20447. [PMID: 21647227 PMCID: PMC3101260 DOI: 10.1371/journal.pone.0020447] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 04/22/2011] [Indexed: 12/12/2022] Open
Abstract
Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.
Collapse
Affiliation(s)
| | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for
Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen,
The Netherlands
- Departments of Computer Science and Biology, San Diego State University,
San Diego, California, United States of America
| | - Neil Hall
- Centre for Genomic Research, School of Biological Sciences, University of
Liverpool, Liverpool, United Kingdom
| | - Wilbert H. M. Peters
- Department of Gastroenterology, Nijmegen Institute for Infection,
Inflammation and Immunity (N4i) & Radboud University Centre for Oncology
(RUCO) of the Radboud University Nijmegen Medical Centre, Nijmegen, The
Netherlands
| | - Rian Roelofs
- Department of Laboratory Medicine, Nijmegen Institute for Infection,
Inflammation and Immunity (N4i) & Radboud University Centre for Oncology
(RUCO) of the Radboud University Nijmegen Medical Centre, Nijmegen, The
Netherlands
| | - Annemarie Boleij
- Department of Laboratory Medicine, Nijmegen Institute for Infection,
Inflammation and Immunity (N4i) & Radboud University Centre for Oncology
(RUCO) of the Radboud University Nijmegen Medical Centre, Nijmegen, The
Netherlands
| | - Harold Tjalsma
- Department of Laboratory Medicine, Nijmegen Institute for Infection,
Inflammation and Immunity (N4i) & Radboud University Centre for Oncology
(RUCO) of the Radboud University Nijmegen Medical Centre, Nijmegen, The
Netherlands
| |
Collapse
|
234
|
Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 2011; 9:279-90. [PMID: 21407244 DOI: 10.1038/nrmicro2540] [Citation(s) in RCA: 989] [Impact Index Per Article: 76.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To what extent do host genetics control the composition of the gut microbiome? Studies comparing the gut microbiota in human twins and across inbred mouse lines have yielded inconsistent answers to this question. However, candidate gene approaches, in which one gene is deleted or added to a model host organism, show that a single host gene can have a tremendous effect on the diversity and population structure of the gut microbiota. Now, quantitative genetics is emerging as a highly promising approach that can be used to better understand the overall architecture of host genetic influence on the microbiota, and to discover additional host genes controlling microbial diversity in the gut. In this Review, we describe how host genetics and the environment shape the microbiota, and how these three factors may interact in the context of chronic disease.
Collapse
|
235
|
Reisz RR, Scott DM, Pynn BR, Modesto SP. Osteomyelitis in a Paleozoic reptile: ancient evidence for bacterial infection and its evolutionary significance. Naturwissenschaften 2011; 98:551-5. [DOI: 10.1007/s00114-011-0792-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/18/2011] [Accepted: 03/20/2011] [Indexed: 01/29/2023]
|
236
|
Skin microbiota: microbial community structure and its potential association with health and disease. INFECTION GENETICS AND EVOLUTION 2011; 11:839-48. [PMID: 21463709 DOI: 10.1016/j.meegid.2011.03.022] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/24/2011] [Accepted: 03/25/2011] [Indexed: 12/22/2022]
Abstract
Skin, the largest human organ, is a complex and dynamic ecosystem inhabited by a multitude of microorganisms. Host demographics and genetics, human behavior, local and regional environmental characteristics, and transmission events may all potentially drive human skin microbiota variability, resulting in an alteration of microbial community structure. This alteration may have important consequences regarding health and disease outcomes among individuals. More specifically, certain diversity patterns of human microbiota may be predictive or diagnostic of disease. The purpose of this review is to briefly describe the skin microbiota, outline the potential determining factors driving its variability, posit the likelihood of an association between the resulting microbial community structure on the skin with disease outcomes among individuals, and finally, to present some challenges and implications for studying the skin microbiota.
Collapse
|
237
|
Gómez-Doñate M, Payán A, Cortés I, Blanch AR, Lucena F, Jofre J, Muniesa M. Isolation of bacteriophage host strains of Bacteroides species suitable for tracking sources of animal faecal pollution in water. Environ Microbiol 2011; 13:1622-31. [PMID: 21443742 DOI: 10.1111/j.1462-2920.2011.02474.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Microbial source tracking (MST) methods allow the identification of specific faecal sources. The aim is to detect the sources of faecal pollution in a water body to allow targeted, efficient and cost-effective remediation efforts in the catchment. Bacteriophages infecting selected host strains of Bacteroides species are used as markers to track faecal contaminants in water. By using a suitable Bacteroides host from a given faecal origin, it is possible to specifically detect bacteriophages of this faecal origin. It can thus be used to detect specific phages of Bacteroides for MST. With this objective, we isolated several Bacteroides strains from pig, cow and poultry faeces by applying a previously optimized methodology used to isolate the host strains from humans. The isolated strains belonged to Bacteroides fragilis and Bacteroides thetaiotaomicron. These strains, like most Bacteroides species, detected phages of the Siphoviridae morphology. Using the newly isolated host strains for phage enumeration in a range of samples, we showed that these detect phages in faecal sources that coincide with their own origin (70-100% of the samples), and show no detection or very low percentages of detection of phages from other animal origins (from 0 to 20% of the samples). Only strains isolated from pig wastewater detected phages in 50% of human sewage samples. Nevertheless, those strains detecting phages from faecal origins other than their own detected fewer phages (2-3 log₁₀ pfu·100 ml⁻¹) than the phages detected by the specific strain of the same origin. On the basis of our results, we propose that faecal source tracking with phages infecting specific Bacteroides host strains is a useful method for MST. In addition, the method presented here is feasible in laboratories equipped with only basic microbiological equipment, it is more rapid and cost-effective than other procedures and it does not require highly qualified staff.
Collapse
Affiliation(s)
- Marta Gómez-Doñate
- Department of Microbiology, University of Barcelona-Institut de l'aigua, Diagonal 645, E-08028, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
238
|
Van den Abbeele P, Van de Wiele T, Verstraete W, Possemiers S. The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiol Rev 2011; 35:681-704. [PMID: 21361997 DOI: 10.1111/j.1574-6976.2011.00270.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Along the human gastrointestinal tract, microorganisms are confronted with multiple barriers. Besides selective physical conditions, the epithelium is regularly replaced and covered with a protective mucus layer trapping immune molecules. Recent insights into host defense strategies show that the host selects the intestinal microbiota, particularly the mucosa-associated microbial community. In this context, humans coevolved with thousands of intestinal microbial species that have adapted to provide host benefits, while avoiding pathogenic behavior that might destabilize their host interaction. While mucosal microorganisms would be crucial for immunological priming, luminal microorganisms would be important for nutrient digestion. Further, we propose that the intestinal microorganisms also coevolved with each other, leading to coherently organized, resilient microbial associations. During disturbances, functionally redundant members become more abundant and are crucial for preserving community functionality. The outside of the mucus layer, where host defense molecules are more diluted, could serve as an environment where microorganisms are protected from disturbances in the lumen and from where they can recolonize the lumen after perturbations. This might explain the remarkable temporal stability of microbial communities. Finally, commensals that become renegade or a decreased exposure to essential coevolved microorganisms may cause particular health problems such as inflammatory bowel diseases, obesity or allergies.
Collapse
|
239
|
Booijink CCGM, El-Aidy S, Rajilić-Stojanović M, Heilig HGHJ, Troost FJ, Smidt H, Kleerebezem M, De Vos WM, Zoetendal EG. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 2011; 12:3213-27. [PMID: 20626454 DOI: 10.1111/j.1462-2920.2010.02294.x] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 10⁷ -10⁸ bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9-28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.
Collapse
Affiliation(s)
- Carien C G M Booijink
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
240
|
Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in Bifidobacteria. GENES AND NUTRITION 2011; 6:285-306. [PMID: 21484167 DOI: 10.1007/s12263-010-0206-6] [Citation(s) in RCA: 485] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 12/15/2010] [Indexed: 12/17/2022]
Abstract
Members of the genus Bifidobacterium can be found as components of the gastrointestinal microbiota, and are believed to play an important role in maintaining and promoting human health by eliciting a number of beneficial properties. Bifidobacteria can utilize a diverse range of dietary carbohydrates that escape degradation in the upper parts of the intestine, many of which are plant-derived oligo- and polysaccharides. The gene content of a bifidobacterial genome reflects this apparent metabolic adaptation to a complex carbohydrate-rich gastrointestinal tract environment as it encodes a large number of predicted carbohydrate-modifying enzymes. Different bifidobacterial strains may possess different carbohydrate utilizing abilities, as established by a number of studies reviewed here. Carbohydrate-degrading activities described for bifidobacteria and their relevance to the deliberate enhancement of number and/or activity of bifidobacteria in the gut are also discussed in this review.
Collapse
Affiliation(s)
- Karina Pokusaeva
- Alimentary Pharmabiotic Centre, Department of Microbiology, University College Cork, Western Road, Cork, Ireland
| | | | | |
Collapse
|
241
|
Karasov WH, Martínez del Rio C, Caviedes-Vidal E. Ecological physiology of diet and digestive systems. Annu Rev Physiol 2011; 73:69-93. [PMID: 21314432 DOI: 10.1146/annurev-physiol-012110-142152] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The morphological and functional design of gastrointestinal tracts of many vertebrates and invertebrates can be explained largely by the interaction between diet chemical constituents and principles of economic design, both of which are embodied in chemical reactor models of gut function. Natural selection seems to have led to the expression of digestive features that approximately match digestive capacities with dietary loads while exhibiting relatively modest excess. Mechanisms explaining differences in hydrolase activity between populations and species include gene copy number variations and single-nucleotide polymorphisms. In many animals, both transcriptional adjustment and posttranscriptional adjustment mediate phenotypic flexibility in the expression of intestinal hydrolases and transporters in response to dietary signals. Digestive performance of animals depends also on their gastrointestinal microbiome. The microbiome seems to be characterized by large beta diversity among hosts and by a common core metagenome and seems to differ flexibly among animals with different diets.
Collapse
Affiliation(s)
- William H Karasov
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, 53706, USA.
| | | | | |
Collapse
|
242
|
Kovacs A, Ben-Jacob N, Tayem H, Halperin E, Iraqi FA, Gophna U. Genotype is a stronger determinant than sex of the mouse gut microbiota. MICROBIAL ECOLOGY 2011; 61:423-8. [PMID: 21181142 DOI: 10.1007/s00248-010-9787-2] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Accepted: 12/03/2010] [Indexed: 05/09/2023]
Abstract
The mammalian gut microbiota is considered to be determined mostly by diet, while the effect of genotype is still controversial. Here, we examined the effect of genotype on the gut microbiota in normal populations, exhibiting only natural polymorphisms, and evaluated this effect in comparison to the effect of sex. DNA fingerprinting approaches were used to profile the gut microbiota of eight different recombinant inbred mouse lines of the collaborative cross consortium, whose level of genetic diversity mimics that of a natural human population. Analyses based on automated ribosomal internal transcribed spacer analysis demonstrated significant higher similarity of the gut microbiota composition within mouse lines than between them or within same-gender groups. Thus, genetic background significantly impacts the microbiota composition and is a stronger determinant than gender. These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases.
Collapse
Affiliation(s)
- Amir Kovacs
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | | | | | | | | | | |
Collapse
|
243
|
Trosvik P, Rudi K, Straetkvern KO, Jakobsen KS, Naes T, Stenseth NC. Web of ecological interactions in an experimental gut microbiota. Environ Microbiol 2011; 12:2677-87. [PMID: 20482738 DOI: 10.1111/j.1462-2920.2010.02236.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The dynamics of all ecosystems are dictated by intrinsic, density-dependent mechanisms and by density-independent environmental forcing. In spite of the importance of the gastrointestinal microbiota in health and disease, the ecology of this system remains largely unknown. Here, we take an ecological approach to gut microbial community analysis, with statistical modelling of time series data from chemostats. This approach removes effects of host forcing, allowing us to describe a network of intrinsic interactions determining the dynamic structure of an experimental gut microbiota. Surprisingly, the main colonization pattern in this simplified model system resembled that of the human infant gut, suggesting a potentially important role of density-dependent interactions in the early gut microbiota. Knowledge of ecological structures in microbial systems may provide us with a means of controlling such systems by modifying the strength and nature of interactions among microbes and between the microbes and their environment.
Collapse
Affiliation(s)
- Pål Trosvik
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo N-0316, Norway
| | | | | | | | | | | |
Collapse
|
244
|
Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 2011; 11:7. [PMID: 21219646 PMCID: PMC3032643 DOI: 10.1186/1471-2180-11-7] [Citation(s) in RCA: 508] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/10/2011] [Indexed: 12/11/2022] Open
Abstract
Background The gut microbiota is thought to play a key role in the development of the inflammatory bowel diseases Crohn's disease (CD) and ulcerative colitis (UC). Shifts in the composition of resident bacteria have been postulated to drive the chronic inflammation seen in both diseases (the "dysbiosis" hypothesis). We therefore specifically sought to compare the mucosa-associated microbiota from both inflamed and non-inflamed sites of the colon in CD and UC patients to that from non-IBD controls and to detect disease-specific profiles. Results Paired mucosal biopsies of inflamed and non-inflamed intestinal tissue from 6 CD (n = 12) and 6 UC (n = 12) patients were compared to biopsies from 5 healthy controls (n = 5) by in-depth sequencing of over 10,000 near full-length bacterial 16S rRNA genes. The results indicate that mucosal microbial diversity is reduced in IBD, particularly in CD, and that the species composition is disturbed. Firmicutes were reduced in IBD samples and there were concurrent increases in Bacteroidetes, and in CD only, Enterobacteriaceae. There were also significant differences in microbial community structure between inflamed and non-inflamed mucosal sites. However, these differences varied greatly between individuals, meaning there was no obvious bacterial signature that was positively associated with the inflamed gut. Conclusions These results may support the hypothesis that the overall dysbiosis observed in inflammatory bowel disease patients relative to non-IBD controls might to some extent be a result of the disturbed gut environment rather than the direct cause of disease. Nonetheless, the observed shifts in microbiota composition may be important factors in disease maintenance and severity.
Collapse
Affiliation(s)
- Alan W Walker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
245
|
Barboza PS, Bennett A, Lignot JH, Mackie RI, McWhorter TJ, Secor SM, Skovgaard N, Sundset MA, Wang T. Digestive challenges for vertebrate animals: microbial diversity, cardiorespiratory coupling, and dietary specialization. Physiol Biochem Zool 2010; 83:764-74. [PMID: 20578844 DOI: 10.1086/650472] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The digestive system is the interface between the supply of food for an animal and the demand for energy and nutrients to maintain the body, to grow, and to reproduce. Digestive systems are not morphologically static but rather dynamically respond to changes in the physical and chemical characteristics of the diet and the level of food intake. In this article, we discuss three themes that affect the ability of an animal to alter digestive function in relation to novel substrates and changing food supply: (1) the fermentative digestion in herbivores, (2) the integration of cardiopulmonary and digestive functions, and (3) the evolution of dietary specialization. Herbivores consume, digest, and detoxify complex diets by using a wide variety of enzymes expressed by bacteria, predominantly in the phyla Firmicutes and Bacteroidetes. Carnivores, such as snakes that feed intermittently, sometimes process very large meals that require compensatory adjustments in blood flow, acid secretion, and regulation of acid-base homeostasis. Snakes and birds that specialize in simple diets of prey or nectar retain their ability to digest a wider selection of prey. The digestive system continues to be of interest to comparative physiologists because of its plasticity, both phenotypic and evolutionary, and because of its widespread integration with other physiological systems, including thermoregulation, circulation, ventilation, homeostasis, immunity, and reproduction.
Collapse
Affiliation(s)
- P S Barboza
- Department of Biology and Wildlife, University of Alaska, Fairbanks, AK 99775, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
246
|
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc Natl Acad Sci U S A 2010; 108 Suppl 1:4592-8. [PMID: 20937873 DOI: 10.1073/pnas.1011383107] [Citation(s) in RCA: 783] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Periodontal disease has been associated with atherosclerosis, suggesting that bacteria from the oral cavity may contribute to the development of atherosclerosis and cardiovascular disease. Furthermore, the gut microbiota may affect obesity, which is associated with atherosclerosis. Using qPCR, we show that bacterial DNA was present in the atherosclerotic plaque and that the amount of DNA correlated with the amount of leukocytes in the atherosclerotic plaque. To investigate the microbial composition of atherosclerotic plaques and test the hypothesis that the oral or gut microbiota may contribute to atherosclerosis in humans, we used 454 pyrosequencing of 16S rRNA genes to survey the bacterial diversity of atherosclerotic plaque, oral, and gut samples of 15 patients with atherosclerosis, and oral and gut samples of healthy controls. We identified Chryseomonas in all atherosclerotic plaque samples, and Veillonella and Streptococcus in the majority. Interestingly, the combined abundances of Veillonella and Streptococcus in atherosclerotic plaques correlated with their abundance in the oral cavity. Moreover, several additional bacterial phylotypes were common to the atherosclerotic plaque and oral or gut samples within the same individual. Interestingly, several bacterial taxa in the oral cavity and the gut correlated with plasma cholesterol levels. Taken together, our findings suggest that bacteria from the oral cavity, and perhaps even the gut, may correlate with disease markers of atherosclerosis.
Collapse
|
247
|
Robinson CJ, Bohannan BJM, Young VB. From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev 2010; 74:453-76. [PMID: 20805407 PMCID: PMC2937523 DOI: 10.1128/mmbr.00014-10] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.
Collapse
Affiliation(s)
- Courtney J. Robinson
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
| | - Brendan J. M. Bohannan
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
| | - Vincent B. Young
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
| |
Collapse
|
248
|
Ofiţeru ID, Lunn M, Curtis TP, Wells GF, Criddle CS, Francis CA, Sloan WT. Combined niche and neutral effects in a microbial wastewater treatment community. Proc Natl Acad Sci U S A 2010; 107:15345-50. [PMID: 20705897 PMCID: PMC2932620 DOI: 10.1073/pnas.1000604107] [Citation(s) in RCA: 352] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It has long been assumed that differences in the relative abundance of taxa in microbial communities reflect differences in environmental conditions. Here we show that in the economically and environmentally important microbial communities in a wastewater treatment plant, the population dynamics are consistent with neutral community assembly, where chance and random immigration play an important and predictable role in shaping the communities. Using dynamic observations, we demonstrate a straightforward calibration of a purely neutral model and a parsimonious method to incorporate environmental influence on the reproduction (or birth) rate of individual taxa. The calibrated model parameters are biologically plausible, with the population turnover and diversity in the heterotrophic community being higher than for the ammonia oxidizing bacteria (AOB) and immigration into AOB community being relatively higher. When environmental factors were incorporated more of the variance in the observations could be explained but immigration and random reproduction and deaths remained the dominant driver in determining the relative abundance of the common taxa. Consequently we suggest that neutral community models should be the foundation of any description of an open biological system.
Collapse
Affiliation(s)
- Irina Dana Ofiţeru
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
- Chemical Engineering Department, University Politehnica of Bucharest, Bucharest RO 011061, Romania
| | - Mary Lunn
- Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, United Kingdom
| | - Thomas P. Curtis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - George F. Wells
- Department of Civil and Environmental Engineering, Yang and Yamazaki Building, 473 Via Ortega MC-4020, Stanford University, Stanford, CA 94305
| | - Craig S. Criddle
- Department of Civil and Environmental Engineering, Yang and Yamazaki Building, 473 Via Ortega MC-4020, Stanford University, Stanford, CA 94305
| | - Christopher A. Francis
- Environmental Earth System Science, Y2E2 Building, 473 Via Ortega, Stanford University, Stanford, CA 94305-4216; and
| | - William T. Sloan
- Department of Civil Engineering, University of Glasgow, Glasgow G12 8LT, United Kingdom
| |
Collapse
|
249
|
Understanding the Extent and Sources of Variation in Gut Microbiota Studies; a Prerequisite for Establishing Associations with Disease. DIVERSITY-BASEL 2010. [DOI: 10.3390/d2091085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
250
|
Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA. Bacterial diversity in the oral cavity of 10 healthy individuals. THE ISME JOURNAL 2010; 4:962-74. [PMID: 20336157 PMCID: PMC2941673 DOI: 10.1038/ismej.2010.30] [Citation(s) in RCA: 438] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An 11th pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S ribosomal RNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11,368 high-quality, nonchimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacterial phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences with near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis showed significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health.
Collapse
Affiliation(s)
- Elisabeth M. Bik
- Departments of Microbiology & Immunology, and of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Clara Davis Long
- Departments of Microbiology & Immunology, and of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Gary C. Armitage
- School of Dentistry, University of California, San Francisco, CA
| | - Peter Loomer
- School of Dentistry, University of California, San Francisco, CA
| | | | - Emmanuel F. Mongodin
- Institute For Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | | | - Steven R. Gill
- Department of Oral Biology, State University of New York, Buffalo, NY
| | | | - David A. Relman
- Departments of Microbiology & Immunology, and of Medicine, Stanford University School of Medicine, Stanford, CA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA
| |
Collapse
|