Bacteroides Ovatus Research Articles

How Gut Bacteroides Eat Your Veggies

The human gut Bacteroidetes display a greatly expanded capacity for glycan degradation via the expression of multiple outermembrane protein complexes, termed Sus‐like systems. These systems are comprised of proteins that sequentially bind, degrade and import specific carbohydrates. Two classes of carbohydrate‐binding proteins, the SusD‐like proteins and the carbohydrate‐binding lipoproteins (CBLPs) respectively, are functionally conserved within the Bacteroidetes Sus‐like systems and found in all systems. We have recently determined the crystal structures two such cell surface liopoproteins, XgusD, a SusD‐like protein, and XgusE, a CBLP, from Bacteroides ovatus. These proteins are involved in the recognition of xyloglucan, a plant cell wall polysaccharide abundant in many “salad” vegetables including lettuce, tomato and peppers. Xyloglucan is comprised of a beta‐glucan backbone appended with xylose and galactose side chains, and we demonstrate that recognition of this polymer by the XgusD and XgusE proteins is driven by different aspects of the carbohydrate structure. More over, the XgusE protein displays a novel xyloglucan‐binding domain, and likely reflects a new class of carbohydrate‐binding modules. While XgusD is essential for all xyloglucan utilization, mutants of XgusE in B. ovatus are impaired in the uptake of some xyloglucan oligosaccharides. Taken together our data support our previous work demonstrating that the SusD‐like proteins and CBLPs have evolved to play non‐redundant roles in carbohydrate uptake.

热应激环境下蛋鸡肠道微生物菌群多样性的分析

PDF HTML阅读 XML下载 导出引用 引用提醒 热应激环境下蛋鸡肠道微生物菌群多样性 DOI: 10.5846/stxb201305050933 作者: 作者单位: 临沂大学生命科学学院,临沂大学生命科学学院,国立冈山大学自然科学研究科,日本冈山- 作者简介: 通讯作者: 中图分类号: 基金项目: 国家高技术研究发展计划 (2013AA102501); 山东省优秀青年科学基金项目(BS2012NY001); 日本学生支援机构归国外国留学生短期研究制度基金(JP22GR037). Diversity analysis of the intestinal microbial flora of laying hens under heat stress Author: Affiliation: College of Life Science,Linyi University,College of Life Science,Linyi University,Laboratory of Animal Genetics Okayama University,Okayama,-,Japan Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:通过分析热应激环境下蛋鸡肠道菌群结构的变化,旨在揭示热应激对肠道微生态环境的影响机理,为探索炎热环境下家禽肠道菌群定植规律提供理论依据。试验选择16周龄济宁百日鸡96只,随机分成对照组[(24±1) ℃,Ⅰ]和热应激[(38±1) ℃]组,分别在2个人工环境气候舱中饲养,各组设6个重复,每个重复8只,试验持续14 d。采用16S rDNA的变性梯度凝胶电泳(Denatured gradient gel electrophoresis, PCR-DGGE)技术和实时荧光定量(Real-time quantitative RT-PCR) 以及多变量统计(Principal Components Analysis,PCA)分析等手段,分析热应激2d(Ⅱ)、7d(Ⅲ)和14 d(Ⅳ)时,对十二指肠、空肠及回肠内容物菌群多样性以及菌群数量变化。PCA分析结果显示,热应激暴露过程中十二指肠部位菌群组成与对照组保持相似的趋势,但热应激2 d时空肠部位菌群组成有分开趋势;到7 d时空肠与回肠部位菌群组成分开明显,而14 d时菌群组成具有明显差异;热应激7、14 d时空肠和回肠部位末检测到敏感乳杆菌(Lactobacillus agilis),回肠部位也末检测到约氏乳杆菌(Lactobacillus johnsonii)、不可培养细菌(Uncultured bacterium)等芽孢杆菌纲,而热应激不同时间段空肠和回肠部位可检测到不可培养细菌(Uncultured Escherichia sp)、溃疡拟杆菌(Bacteroides helcogenes)、卵形拟杆菌(Bacteroides ovatus)和索氏志贺氏菌(Shigella sonnei) 等拟杆菌纲和γ-变形菌纲;其中约氏乳杆菌、敏感乳杆菌数量变化在空肠部位减少最明显(P<0.05),空肠和回肠卵形拟杆菌、不可培养的拟杆菌数量明显上升(P<0.05)。热应激环境下蛋鸡空肠、回肠部位菌群多样性较为丰富,其抑制乳杆菌属、不可培养细菌的增殖,促进卵形拟杆菌的繁殖,而促进卵形拟杆菌的繁殖,导致消化道菌群平衡的破坏。 Abstract:Structural changes in the intestinal microbial flora of laying hens were analyzed to determine the influence of heat stress on the intestinal microbial environment and explore microbial colonization of the poultry intestinal tract in the hot environment. Ninety-six 16-week-old Jining Bairi chickens were randomly allotted into control group Ⅰ (24±1)℃ or the heat stress (38±1)℃ group. Each group was divided into six replicate subgroups, each consisting of eight individuals. The duration of the experiment was 14 days. Denaturing gradient gel electrophoresis combined with multivariate statistical analysis and real-time quantitative analysis of the 16S rDNA were used to analyze the diversity of the microflora in the duodenum, jejunum, and ileum. Changes in the abundance of the microflora were also studied. The effect was examined at 2 days (group Ⅱ), 7 days (group Ⅲ), and 14 days (group Ⅳ) of heat exposure. PCA was carried out and the results showed that the composition of the microflora in parts of the duodenum remained similar between the heat-stressed and control groups, but that the microbial composition of the jejunum area varied between the heat-stressed and control animals after 2 days. At 7 days, significant differences were found in the composition of the microflora in the jejunum and ileum compared with that at 2 days and at 14 days. The influence of heat stress on the bacterial composition in each part of the intestinal tract was most pronounced at the 7-day time point. Bacilli, Lactobacillus agilis in the jejunum and ileum, and Lactobacillus johnsonii and other uncultured bacteria in the ileum, were not detected at the 7- or 14-day time points, while Bacteroidetes and γ-Proteobacteria, uncultured Escherichia sp, Bacteroides helcogenes, Bacteroides ovatus, and Shigella sonnei, were detected in the jejunum and ileum at different time points. Decreases in the overall abundance of L. johnsonii and L. agilis were most obvious in the jejunum (P<0.05), while the abundance of B. ovatus and uncultured Escherichia sp. in the jejunum and ileum was obviously increased (P<0.05). The number of bacterial cells of each of the various strains ranged between 1.76-6.58 lg CFU/g. The results indicated that the proliferation of lactobacilli and uncultured bacteria in the jejunum and ileum of laying hens was inhibited under heat stress, while the growth of B. ovatus in the jejunum and ileum was promoted, resulting in disruption of the digestive tract microflora balance. The intestinal microflora of laying hens under heat stress is relatively abundant, and the diversity of the flora in the jejunum and ileum showed distinct patterns with increasing heat stress exposure time. The effect of heat stress on jejunal microbial flora was most pronounced, followed by the ileum and the duodenum. The types of lactobacilli in the jejunum and ileum were significantly different at the different time points. The effects of thermal stress were detected in the duodenum and jejunum, particularly in reference to four kinds of pathogenic bacteria. The results suggest that heat stress can inhibit Lactobacillus species and promote the proliferation of oval Bacteroidetes, thereby disrupting the balance of the digestive tract microflora. 参考文献 相似文献 引证文献

Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics.

ObjectivesTo identify β-lactamase genes in gut commensal Bacteroides species and to assess the impact of these enzymes, when carried by outer membrane vesicles (OMVs), in protecting enteric pathogens and commensals.MethodsA deletion mutant of the putative class A β-lactamase gene (locus tag BT_4507) found in the genome of the human commensal Bacteroides thetaiotaomicron was constructed and a phenotypic analysis performed. A phylogenetic tree was built from an alignment of nine Bacteroides cephalosporinase protein sequences, using the maximum likelihood method. The rate of cefotaxime degradation after incubation with OMVs produced by different Bacteroides species was quantified using a disc susceptibility test. The resistance of Salmonella Typhimurium and Bifidobacterium breve to cefotaxime in liquid culture in the presence of B. thetaiotaomicron OMVs was evaluated by measuring bacterial growth.ResultsThe B. thetaiotaomicron BT_4507 gene encodes a β-lactamase related to the CepA cephalosporinase of Bacteroides fragilis. OMVs produced by B. thetaiotaomicron and several other Bacteroides species, except Bacteroides ovatus, carried surface-associated β-lactamases that could degrade cefotaxime. β-Lactamase-harbouring OMVs from B. thetaiotaomicron protected Salmonella Typhimurium and B. breve from an otherwise lethal dose of cefotaxime.ConclusionsThe production of membrane vesicles carrying surface-associated β-lactamases by Bacteroides species, which constitute a major part of the human colonic microbiota, may protect commensal bacteria and enteric pathogens, such as Salmonella Typhimurium, against β-lactam antibiotics.

Antimicrobial resistance among anaerobes isolated from clinical specimens in Kuwait hospitals: Comparative analysis of 11-year data

Our objective was to compare the antimicrobial resistance trends among clinically relevant anaerobes against 9 different antibiotics over two periods, 2008–2012 and 2002–2007. Antimicrobial susceptibility testing was performed by determining the MICs using E test method. The interpretation of results was according to the breakpoints recommended by the Clinical Laboratory and Standard Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST). A total of 2240 clinically significant isolates were collected between 2008 and 2012 in four teaching hospitals in Kuwait. The commonest isolates were Bacteroides fragilis (40.4%), Prevotella bivia (18.6%), Peptostreptococcus spp. (13.8%) and Bacteroides ovatus (11.1%). According to CLSI and EUCAST breakpoints used for the 2008–2012 and 2002–2007 isolates, high resistance rates to amoxicillin–clavulanic acid, clindamycin, penicillin and piperacillin were noted among the Gram-negative isolates. They ranged between 0 and 0–62.1 and 62.1%, and 0 and 0–59.1 and 62.1%, respectively against clindamycin, 0 and 0–34.5 and 45.3%, and 0 and 0–45 and 57.5%, respectively against piperacillin and 0 and 0–24.2 and 24.2%, and 0 and 0–23.1 and 30.6%, respectively against amoxicillin–clavulanic acid. The mean interpretative results by both CLSI and EUCAST during the 2008–2012 and 2002–2007 periods showed that the B. fragilis isolates were highly resistant to penicillin (100 vs 100%), clindamycin (43.7 vs 44.2%), piperacillin (35.8 vs 42.7%) and amoxicillin–clavulanic acid (13.2 vs 14%), respectively. When compared with 2002–2007, the CLSI, but not EUCAST, demonstrated statistically significant decreased resistance to clindamycin (P < 0.03). However, both interpretative criteria showed demonstrable statistically significant decrease in resistance rates to imipenem (P < 0.00097 vs P < 0.00074), meropenem (P < 0.000006 vs P < 0.0407) and piperacillin (P < 0.000017 vs P < 0.0461). Our data shows that there is a need for periodic monitoring of the susceptibility testing for anaerobic bacteria in the face of increasing resistance rates as well as to guide in the empirical therapy of anaerobic infections.

Antibiotic susceptibility profiles of anaerobic pathogens in The Netherlands

The antibiotic susceptibility profile of the Bacteroides fragilis group, Gram-positive anaerobic cocci (GPAC), Fusobacterium spp., Prevotella spp., Veillonella spp. and Bilophila wadsworthia for amoxicillin, amoxicillin–clavulanic acid, clindamycin and metronidazole was determined. Human clinical isolates were isolated between 2011 and 2013 at the Microbiological Diagnostic Laboratory of the University Medical Center Groningen, The Netherlands and subjected to MALDI-TOF MS identification and susceptibility testing using E-test for MIC determination.Differences in clindamycin susceptibility between species of the B. fragilis group and GPAC were observed, with Bacteroides ovatus and Peptoniphilus harei having the highest resistance rates. Compared to other European countries, in The Netherlands the MIC90 for clindamycin of fusobacteria is low. Metronidazole resistance was first encountered in the genus Prevotella in 2013, but not in species of GPAC as reported in Belgium and Bulgaria. The differences in clindamycin resistance between the different European countries and reports of metronidazole resistance within the genera Prevotella and GPAC warrant more extensive susceptibility studies on anaerobic pathogens.

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Crystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight-stranded, calycin-like, β-barrel fold and bind an endogenous unknown ligand at one end of the β-barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.

Persistence of Bacteroides ovatus under simulated sunlight irradiation.

BackgroundBacteroides ovatus, a member of the genus Bacteroides, is considered for use in molecular-based methods as a general fecal indicator. However, knowledge on its fate and persistence after a fecal contamination event remains limited. In this study, the persistence of B. ovatus was evaluated under simulated sunlight exposure and in conditions similar to freshwater and seawater. By combining propidium monoazide (PMA) treatment and quantitative polymerase chain reaction (qPCR) detection, the decay rates of B. ovatus were determined in the presence and absence of exogenous photosensitizers and in salinity up to 39.5 parts per thousand at 27°C.ResultsUVB was found to be important for B. ovatus decay, averaging a 4 log10 of decay over 6 h of exposure without the presence of extracellular photosensitizers. The addition of NaNO2, an exogenous sensitizer producing hydroxyl radicals, did not significantly change the decay rate of B. ovatus in both low and high salinity water, while the exogenous sensitizer algae organic matter (AOM) slowed down the decay of B. ovatus in low salinity water. At seawater salinity, the decay rate of B. ovatus was slower than that in low salinity water, except when both NaNO2 and AOM were present.ConclusionThe results of laboratory experiments suggest that if B. ovatus is released into either freshwater or seawater environment in the evening, 50% of it may be intact by the next morning; if it is released at noon, only 50% may be intact after a mere 5 min of full spectrum irradiation on a clear day. This study provides a mechanistic understanding to some of the important environmental relevant factors that influenced the inactivation kinetics of B. ovatus in the presence of sunlight irradiation, and would facilitate the use of B. ovatus to indicate the occurrence of fecal contamination.

Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer.

Bacterial colonisation of the gut is involved in the development of colitis-associated colorectal cancer. However, it remains unclear how the gut microbiota dynamically shifts correlating with colorectal carcinogenesis. Here, we reveal the longitudinal shifts in the microbial community that occur with colitis-associated colorectal cancer. High-throughput sequencing results for the bacterial 16S rRNA gene (V3 region) were compared for azoxymethane/dextran sodium sulphate-treated mice and control mice. We found that microbial community structure was significantly altered by chronic colitis. Microbes in the species Streptococcus luteciae, Lactobacillus hamster, Bacteroides uniformis and Bacteroides ovatus were increased during colorectal carcinogenesis. Histological measurements for a molecular network including six interconnected key factors from inflammation to cancer, namely p65, p53, COX-2, PPARγ, CCR2 and β-catenin, indicated that the microbiome modifications were correlated with molecular pathogenesis of colitis-associated colorectal cancer. Phylotype modifications after each AOM/DSS cycle were identified. A longitudinal microbial network was then constructed for the gut microbiome and showed that the phylotype shifts during this process were complex and highly dynamic. This work may provide a deeper understanding of the role of the microbiota and microbe-host interactions in colitis-associated colorectal cancer.

Structures of Complexes of a Metal-independent Glycosyltransferase GT6 from Bacteroides ovatus with UDP-N-Acetylgalactosamine (UDP-GalNAc) and Its Hydrolysis Products

Mammalian members of glycosyltransferase family 6 (GT6) of the CAZy database have a GT-A fold containing a conserved Asp-X-Asp (DXD) sequence that binds an essential metal cofactor. Bacteroides ovatus GT6a represents a GT6 clade found in more than 30 Gram-negative bacteria that is similar in sequence to the catalytic domains of mammalian GT6, but has an Asn(95)-Ala-Asn(97) (NXN) sequence substituted for the DXD motif and metal-independent catalytic activity. Co-crystals of a low activity mutant of BoGT6a (E192Q) with UDP-GalNAc contained protein complexes with intact UDP-GalNAc and two forms with hydrolysis products (UDP plus GalNAc) representing an initial closed complex and later open form primed for product release. Two cationic residues near the C terminus of BoGT6a, Lys(231) and Arg(243), interact with the diphosphate moiety of UDP-GalNAc, but only Lys(231) interacts with the UDP product and may function in leaving group stabilization. The amide group of Asn(95), the first Asn of the NXN motif, interacts with the ribose moiety of the substrate. This metal-independent GT6 resembles its metal-dependent homologs in undergoing conformational changes on binding UDP-GalNAc that arise from structuring the C terminus to cover this substrate. It appears that in the GT6 family, the metal cofactor functions specifically in binding the UDP moiety in the donor substrate and transition state, actions that can be efficiently performed by components of the polypeptide chain.

B acteroides isolated from four mammalian hosts lack host‐specific 16S rRNA gene phylogeny and carbon and nitrogen utilization patterns

One-hundred-and-three isolates of Bacteroides ovatus,B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human, and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using 16S rRNA gene sequencing, repetitive sequence-based polymerase chain reaction (rep-PCR), and phenotypic microarrays. Analysis of 16S rRNA gene sequences revealed high sequence identity in these Bacteroides; with distinct phylogenetic groupings by bacterial species but not host origin. Phenotypic microarray analysis demonstrated these Bacteroides shared the ability to utilize many of the same carbon substrates, without differences due to species or host origin, indicative of their broad carbohydrate fermentation abilities. Limited nitrogen substrates were utilized; in addition to ammonia, guanine, and xanthine, purine derivatives were utilized by most isolates followed by a few amino sugars. Only rep-PCR analysis demonstrated host-specific patterns, indicating that genomic changes due to coevolution with host did not occur by mutation in the 16S rRNA gene or by a gain or loss of carbohydrate utilization genes within these Bacteroides. This is the first report to indicate that host-associated genomic differences are outside of 16S rRNA gene and carbohydrate utilization genes and suggest conservation of specific bacterial species with the same functionality across mammalian hosts for this Bacteroidetes clade.

Evidence That GH115 α-Glucuronidase Activity, Which Is Required to Degrade Plant Biomass, Is Dependent on Conformational Flexibility

The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan.

Isolation ofBacteroidesfrom fish and human fecal samples for identification of unique molecular markers

Bacteroides molecular markers have been used to identify human fecal contamination in natural waters, but recent work in our laboratory confirmed cross-amplification of several human-specific Bacteroides spp. assays with fecal DNA from fish. For identification of unique molecular markers, Bacteroides from human (n = 4) and fish (n = 7) fecal samples were cultured and their identities were further confirmed using Rapid ID 32A API strips. The 16S rDNA from multiple isolates from each sample was PCR amplified, cloned, and sequenced to identify unique markers for development of more stringent human-specific assays. In human feces, Bacteroides vulgatus was the dominant species (75% of isolates), whereas in tilapia feces, Bacteroides eggerthii was dominant (66%). Bacteroides from grass carp, channel catfish, and blue catfish may include Bacteroides uniformis, Bacteroides ovatus, or Bacteroides stercoris. Phylogenic analyses of the 16S rRNA gene sequences showed distinct Bacteroides groupings from each fish species, while human sequences clustered with known B. vulgatus. None of the fish isolates showed significant similarity to Bacteroides sequences currently deposited in NCBI (National Center for Biotechnology Information). This study expands the current sequence database of cultured fish Bacteroides. Such data are essential for identification of unique molecular markers in human Bacteroides that can be utilized in differentiating fish and human fecal contamination in water samples.

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation

Fecal microbiota transplantation (FMT) from healthy donors, which is an effective alternative for treatment of Clostridium difficile-associated disease, is being considered for several disorders such as inflammatory bowel disease, irritable bowel syndrome, and metabolic syndrome. Disease remission upon FMT is thought to be facilitated by an efficient colonization of healthy donor microbiota, but knowledge of the composition and temporal stability of patient microbiota after FMT is lacking. Five patients with moderately to severely active ulcerative colitis (Mayo score ≥6) and refractory to standard therapy received FMT via nasojejunal tube and enema. In addition to clinical activity and adverse events, the patients' fecal bacterial communities were monitored at multiple time points for up to 12 weeks using 16S rRNA gene-targeted pyrosequencing. FMT elicited fever and a temporary increase of C-reactive protein. Abundant bacteria from donors established in recipients, but the efficiency and stability of donor microbiota colonization varied greatly. A positive clinical response was observed after 12 weeks in one patient whose microbiota had been effectively augmented by FMT. This augmentation was marked by successive colonization of donor-derived phylotypes including the anti-inflammatory and/or short-chain fatty acid-producing Faecalibacterium prausnitzii, Rosebura faecis, and Bacteroides ovatus. Disease severity (as measured by the Mayo score) was associated with an overrepresentation of Enterobacteriaceae and an underrepresentation of Lachnospiraceae. This study highlights the value of characterizing temporally resolved microbiota dynamics for a better understanding of FMT efficacy and provides potentially useful diagnostic indicators for monitoring FMT success in the treatment of ulcerative colitis.

Species differentiation of Bacteroides dorei from Bacteroides vulgatus and Bacteroides ovatus from Bacteroides xylanisolvens – Back to basics

We present the results from 16S sequencing and phenotypic tests for differentiation of Bacteroides dorei from Bacteroides vulgatus and Bacteroides ovatus from Bacteroides xylanisolvens, which was not possible with MALDI-TOF MS. Testing with β-glucosidase could differentiate B. dorei from B. vulgatus and a negative catalase reaction could identify B. xylanisolvens.

Novel xylan-controlled delivery of therapeutic proteins to inflamed colon by the human anaerobic commensal bacterium

Growth factors such as keratinocyte growth factor-2 (KGF-2) and transforming growth factor-beta (TGF-β) are important immunoregulatory and epithelial growth factors. They are also potential therapeutic proteins for inflammatory bowel disease. However, owing to protein instability in the upper gastrointestinal tract, it is difficult to achieve therapeutic levels of these proteins in the injured colon when given orally. Furthermore, the short half-life necessitates repeated dosage with large amounts of the growth factor, which may have dangerous side effects, hence the importance of temporal and spatial control of growth factor delivery. The human commensal gut bacterium, Bacteroides ovatus, was genetically engineered to produce human KGF-2 or TGF-β1 (BO-KGF or BO-TGF) in a regulated manner in response to the dietary polysaccharide, xylan. The successful application of BO-KGF or BO-TGF in the prevention of dextran sodium sulphate induced murine colitis is presented here. This novel drug delivery system had a significant prophylactic effect, limiting the development of intestinal inflammation both clinically and histopathologically. The ability to regulate heterologous protein production by B ovatus using xylan is both unique and an important safety feature of this drug delivery system. The use of genetically engineered B ovatus for the controlled and localised delivery of epithelial growth promoting and immunomodulatory proteins has potential clinical applications for the treatment of various diseases targeting the colon.

Ethnic diversity of gut microbiota: Species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects

The composition of the human gut microbiota is related to host health, and it is thought that dietary habits may play a role in shaping this composition. Here, we examined the population size and prevalence of six predominant bacterial genera and the species compositions of genus Bifidobacterium (g-Bifid) and Bacteroides fragilis group (g-Bfra) in 42 healthy Belgian adults by quantitative PCR (qPCR) over a period of one month. The population sizes and prevalence of these bacteria were basically stable throughout the study period. The predominant g-Bifid species were Bifidobacterium adolescentis and Bifidobacterium longum ss. longum, and the predominant g-Bfra species were Bacteroides vulgatus, Bacteroides uniformis, and Bacteroides ovatus. The Belgian gut microbiota data were then compared with gut microbiota data from 46 Japanese subjects collected according to the same protocol (Matsuki etal., Appl. Environ. Microbiol. 70, 167-173, 2004). The population size and prevalence of Bifidobacterium catenulatum group were significantly lower in the Belgian gut microbiota than in the Japanese gut microbiota (P<0.001); however, the population size and prevalence of g-Bifid did not differ. This species-level qPCR analysis will be helpful for investigating the diversity of gut microbiota among ethnic groups.

The xylan utilization system of the plant pathogen Xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts

Xylan is a major structural component of plant cell wall and the second most abundant plant polysaccharide in nature. Here, by combining genomic and functional analyses, we provide a comprehensive picture of xylan utilization by Xanthomonas campestris pv campestris (Xcc) and highlight its role in the adaptation of this epiphytic phytopathogen to the phyllosphere. The xylanolytic activity of Xcc depends on xylan-deconstruction enzymes but also on transporters, including two TonB-dependent outer membrane transporters (TBDTs) which belong to operons necessary for efficient growth in the presence of xylo-oligosaccharides and for optimal survival on plant leaves. Genes of this xylan utilization system are specifically induced by xylo-oligosaccharides and repressed by a LacI-family regulator named XylR. Part of the xylanolytic machinery of Xcc, including TBDT genes, displays a high degree of conservation with the xylose-regulon of the oligotrophic aquatic bacterium Caulobacter crescentus. Moreover, it shares common features, including the presence of TBDTs, with the xylan utilization systems of Bacteroides ovatus and Prevotella bryantii, two gut symbionts. These similarities and our results support an important role for TBDTs and xylan utilization systems for bacterial adaptation in the phyllosphere, oligotrophic environments and animal guts.

Specific humoral immune response to the Thomsen-Friedenreich tumor antigen (CD176) in mice after vaccination with the commensal bacterium Bacteroides ovatus D-6.

The tumor-specific Thomsen-Friedenreich antigen (TFα, CD176) is an attractive target for a cancer vaccine, especially as TF-directed antibodies play an important role in cancer immunosurveillance. However, synthetic TF vaccines have not overcome the low intrinsic immunogenicity of TF. Since natural TF-directed antibodies present in human sera are generated in response to microbes found in the gastrointestinal tract, microbial TF structures are obviously more immunogenic than synthetic TF. We recently isolated a new strain (D-6) of the human gut bacterium Bacteroides ovatus, which carries the true TFα antigen. Here, we present experimental data on the immunogenicity of this strain. Mice immunized with B. ovatus D-6 in the absence of adjuvants developed specific anti-TFα IgM and IgG antibodies which also bound to human cancer cells carrying TFα. Our data suggest that B. ovatus D-6 presents a unique TFα-specific immunogenicity based on a combination of several inherent properties including: expression of the true TFα antigen, clustering and accessible presentation of TFα as repetitive side chains on a capsular polysaccharide, and intrinsic adjuvant properties. Therefore, B. ovatus strain D-6 is an almost perfect candidate for the development of the first adjuvant-free TFα-specific anti-tumor vaccine.

Broad Diversity and Newly Cultured Bacterial Isolates from Enrichment of Pig Feces on Complex Polysaccharides

One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.

Major phenylpropanoid‐derived metabolites in the human gut can arise from microbial fermentation of protein

Plant secondary metabolites, such as phenolic acids are commonly associated with benefits for human health. Two of the most abundant phenylpropanoid-derived compounds detected in human faecal samples are phenylacetic acid (PAA) and 4-hydroxylphenylacetic acid (4-hydroxyPAA). Although they have the potential to be derived from diets rich in plant-based foods, evidence suggests that these compounds can be derived from the microbial fermentation of aromatic amino acids (AAAs) in the colon. To identify the bacteria responsible, 26 strains representing 25 of the dominant human colonic species were screened for phenyl metabolite formation. Seven strains produced significant amounts of both PAA and 4-hydroxyPAA. These included five out of seven Bacteroidetes (Bacteroides thetaiotaomicron, Bacteroides eggerthii, Bacteroides ovatus, Bacteroides fragilis, Parabacteroides distasonis), and two out of 17 Firmicutes (Eubacterium hallii and Clostridium bartlettii). These species also produced indole-3-acetic acid (IAA), the corresponding tryptophan metabolite, but C. bartlettii showed 100 times higher IAA production than the other six strains. Four strains were further tested and PAA formation was substantially increased by phenylalanine, 4-hydroxyPAA by tyrosine and IAA by tryptophan. This study demonstrates that certain microbial species have the ability to ferment all three AAAs and that protein fermentation is the likely source of major phenylpropanoid-derived metabolites in the colon.