Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome--a longitudinal study in IBS and control subjects

Irritable bowel syndrome (IBS) is a common intestinal disorder that includes continuous or recurrent intestinal pain and discomfort and altered bowel habits. The pathophysiology of IBS is incompletely understood, but it may involve an altered intestinal microbiota. The aim of the present study was to compare the composition and temporal stability of faecal microbiota of IBS patients and healthy controls by applying culture-based techniques and PCR-DGGE analysis. No difference in the prevalence or mean culturable manners of bacteroides, bifidobacteria, spore-forming bacteria, lactobacilli, enterococci or yeasts were observed between the IBS and the control groups, whereas slightly higher numbers of coliforms as well as an increased aerobe:anaerobe ratio was observed in the IBS group. PCR-DGGE revealed more temporal instability in the predominant bacterial population of IBS subjects than in controls. In 9 out of 21 IBS subjects and 5 out of 17 controls the PCR-DGGE profiles obtained from the samples of the same individual on different occasions (sampling points 0, 3 and 6 months) were clearly different. However, the instability in some of the IBS subjects could partly be explained by the antibiotic consumption during the study. The present study suggests that instability of intestinal microbiota may be involved in IBS. However, further studies are needed to associate the instability with specific IBS symptoms or with specific bacterial groups and species.     

茶多酚对ApoE~(-/-)小鼠肠道菌群多样性的影响

目的以高脂饲料饲养的SPF级C57 BL/6 ApoE-/-小鼠作为动物模型,研究茶多酚采食对其肠道菌群多样性的影响。方法通过随机饮水的方式给予ApoE-/-小鼠0.4、0.8和1.6 g/L的茶多酚,处理14 d时用PCR-DGGE分析对照组(CK)和茶多酚组小鼠新鲜粪便中肠道菌群的相似性和多样性。结果 UPGMA聚类分析表明,低剂量茶多酚组(LTP)、中剂量茶多酚组(MTP)这两组与对照组(CK)、高剂量茶多酚组(HTP)聚为两大簇。PCA分析显示,LTP组与CK组、MTP组、HTP组分别聚集在不同位置,有明显界限;多样性数据分析显示:CK组DGGE图谱的丰富度和Shannon-Wiener指数(H')与茶多酚组差异无统计学意义(P0.05);CK组与MTP组的均匀度(E)差异存在统计学意义(P0.05,P=0.015),说明中剂量茶多酚作用14 d后与对照组肠道菌群的菌群分配相比均一性显著下降。结论连续处理14 d时CK组与LTP组、MTP组小鼠肠道菌群差异有统计学意义,即茶多酚对ApoE-/-小鼠肠道菌群多样性有显著影响。     

Intestinal microbiota in human health and disease: the impact of probiotics

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.     

肠道微生物群落与炎症性肠病关系研究进展

目的炎症性肠病（IBD）包括克罗恩病（CD）和溃疡性结肠炎（UC）,以持续性肠道非特异性炎症为特征,通常反复发作、迁延不愈,临床上仍无特效性的治疗手段。IBD确切的发病机制尚不清楚,涉及免疫、环境及遗传等因素,这些因素共同诱导肠道炎症、黏膜损伤和修复。肠道微生物群落及其代谢产物、宿主基因易感性及肠道黏膜免疫三方面共同参与了IBD的发病机制。本文从消化道微生态角度出发,对目前IBD相关的肠道微生物群落研究现状、宿主-微生物间免疫应答及益生菌治疗等内容进行探讨。     

Anaerobic gram-negative faecal flora in patients with Crohn's Disease and healthy subjects

The anaerobic gram-negative faecal flora of five patients with Crohn's Disease (CD) was identified and compared with that of healthy subjects. For isolation and cultivation of the anaerobic gram-negative rods a non-selective medium was used. There were no significant differences in numbers of Bacteroides and Fusobacterium spp. between patients with CD and healthy subjects. However, the numbers of the "Bacteroides fragilis" group were significantly higher in patients than in controls. The high numbers of the "B. fragilis" group in the faeces of patients were particularly due to B. vulgatus which was 6 times more frequent in patients than in healthy subjects. This indicated that B. vulgatus was responsible for the higher numbers of anaerobic gram-negative rods in the faecal flora of patients with CD.     

黄瓜香等山野菜对糖尿病大鼠脂质代谢及肠道正常菌群的影响

目的观察黄瓜香等对糖尿病大鼠脂质代谢的影响,并进一步探讨其调脂机制。方法选取糖尿病大鼠灌胃给予黄瓜香提取液120mg/（kg.d）,共8周,检测其空腹血脂变化,及其肠道菌群变化。结果（1）经黄瓜香提取物治疗后,治疗组较糖尿病组,甘油三脂、低密度脂蛋白和胆固醇明显降低（P〈0.01）;（2）糖尿病组肠道菌群较正常组有明显变化（P〈0.01）,尤其双歧杆菌、乳杆菌等明显减少,而治疗后肠道菌群得到调整。结论黄瓜香提取物可能通过扶植肠道菌群生长繁殖,对脂质代谢发挥作用,从而达到其调脂目的。     

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

Despite a long-suspected role in the development of human colorectal cancer (CRC), the composition of gut microbiota in CRC patients has not been adequately described. In this study, fecal bacterial diversity in CRC patients (n=46) and healthy volunteers (n=56) were profiled by 454 pyrosequencing of the V3 region of the 16S ribosomal RNA gene. Both principal component analysis and UniFrac analysis showed structural segregation between the two populations. Forty-eight operational taxonomic units (OTUs) were identified by redundancy analysis as key variables significantly associated with the structural difference. One OTU closely related to Bacteroides fragilis was enriched in the gut microbiota of CRC patients, whereas three OTUs related to Bacteroides vulgatus and Bacteroides uniformis were enriched in that of healthy volunteers. A total of 11 OTUs belonging to the genera Enterococcus, Escherichia/Shigella, Klebsiella, Streptococcus and Peptostreptococcus were significantly more abundant in the gut microbiota of CRC patients, and 5 OTUs belonging to the genus Roseburia and other butyrate-producing bacteria of the family Lachnospiraceae were less abundant. Real-time quantitative PCR further validated the significant reduction of butyrate-producing bacteria in the gut microbiota of CRC patients by measuring the copy numbers of butyryl-coenzyme A CoA transferase genes (Mann–Whitney test, P<0.01). Reduction of butyrate producers and increase of opportunistic pathogens may constitute a major structural imbalance of gut microbiota in CRC patients.     

Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects

Patients with atopic dermatitis (AD) are highly susceptible to viral, bacterial, and fungal skin infections because their skin is dry and this compromises the barrier function of the skin. Therefore, the skin microbiota of patients with AD is believed to be different from that of healthy individuals. In the present study, the skin fungal microbiota of nine patients with mild, moderate, or severe AD and ten healthy subjects were compared using an rRNA clone library. Fungal D1/D2 large subunit analysis of 3647 clones identified 58 species and seven unknown phylotypes in face scale samples from patients with AD and healthy subjects. Malassezia species were predominant, accounting for 63%-86% of the clones identified from each subject. Overall, the non-Malassezia yeast microbiota of the patients was more diverse than that of the healthy individuals. In the AD samples 13.0 ± 3.0 species per case were detected, as compared to 8.0 ± 1.9 species per case in the samples taken from healthy individuals. Notably, Candida albicans, Cryptococcus diffluens, and Cryptococcus liquefaciens were detected in the samples from the patients with AD. Of the filamentous fungal microbiota, Cladosporium spp. and Toxicocladosporium irritans were the predominant species in these patients. Many pathogenic fungi, including Meyerozyma guilliermondii (anamorphic name, Candida guilliermondii), and Trichosporon asahii, and allergenic microorganisms such as Alternaria alternata and Aureobasidium pullulans were found on the skin of the healthy subjects. When the fungal microbiota of the samples from patients with mild/moderate to severe AD and healthy individuals were clustered together by principal coordinates analysis they were found to be clustered according to health status.     

Building the microbiome in health and disease: niche construction and social conflict in bacteria

Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of ‘niche construction’. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.     

Comparison of populations of human faecal bacteria before and after in vitro incubation with plant cell wall substrates

Human faecal slurries were incubated anaerobically with larchwood xylan, oat spelt xylan, wheat bran, apple cell walls or sugar beet pulp as sole carbon sources. The populations which developed during incubation were different from the inoculum, the most marked changes being an increase in the number of Bacteroides species and a decrease in the number of Fusobacterium species for all carbon sources tested. With a water-soluble preparation of larchwood xylan the population was dominated by species able to ferment this substrate, in contrast to the population which developed with the insoluble substrates. The ability to use one plant cell wall substrate appeared to be related to the ability to use others. Strains capable of using plant cell wall substrates included Bacteroides spp., Clostridium clostridiiforme, Bifidobacterium longum, Fusobacterium spp. and Escherichia coli. When incubation with two contrasting substrates (bran and larchwood xylan) was replicated, the populations which developed were reproducibly different from the inoculum and from each other.     

Comparison of populations of human faecal bacteria before and after in vitro incubation with plant cell wall substrates

Human faecal slurries were incubated anaerobically with larchwood xylan, oat spelt xylan, wheat bran, apple cell walls or sugar beet pulp as sole carbon sources. The populations which developed during incubation were different from the inoculum, the most marked changes being an increase in the number of Bacteroides species and a decrease in the number of Fusobacterium species for all carbon sources tested. With a water-soluble preparation of larchwood xylan the population was dominated by species able to ferment this substrate, in contrast to the population which developed with the insoluble substrates. The ability to use one plant cell wall substrate appeared to be related to the ability to use others. Strains capable of using plant cell wall substrates included Bacteroides spp., Clostridium clostridiiforme, Bifidobacterium longum, Fusobacterium spp. and Escherichia coli. When incubation with two contrasting substrates (bran and larchwood xylan) was replicated, the populations which developed were reproducibly different from the inoculum and from each other.     

Anti-bacteroides lipopolysaccharide IgG levels in healthy adults and sepsis patients

Abstract Members of the genus Bacteroides greatly outnumber enterobacteria in the human colon and therefore represent a vast potential pool of biologically active LPS. An enzyme-linked immunosorbent assay was developed to estimate the distribution of IgG levels to LPS from B. fragilis, B. vulgatus, B. thetaiotaomicron and to a mixture of rough LPS from three enterobacteria and Pseudomonas aeruginosa in sera from 641 adult blood donors. By inhibition ELISA some cross-reactivity was demonstrated between the different anti-bacteroides LPS IgG, but with very little between the anti-bacteroides LPS IgG and the anti-enterobacterial/ Pseudomonas LPS IgG. Serum IgG was measured daily over 5–9-day periods in 12 sepsis patients (6 survivors, 6 non-survivors) and in a healthy individual. In all patients IgG levels fluctuated to a greater extent than levels in a healthy subject. Variations all followed similar overall trends and indicated that exposure to bacteroides LPS had occurred. In 5 out of 6 survivors, IgG levels were rising at the end of the period, while 4 of the 6 non-survivors showed falls, with an exception showing increasing levels to B. fragilis LPS. In 5 out of 6 non-survivors, IgG levels against B. fragilis LPS were substantially higher than those against the other LPSs. In this small sample some trends in antibody kinetics have been recognised which suggest bacteroides LPS may be significant in sepsis, and indicate that this study should be extended.     

Use of superoxide dismutase and catalase producing lactic acid bacteria in TNBS induced Crohn's disease in mice

Reactive oxygen species are involved in various aspects of intestinal inflammation and tumor development. Decreasing their levels using antioxidant enzymes, such as catalase (CAT) or superoxide dismutase (SOD) could therefore be useful in the prevention of certain diseases. Lactic acid bacteria (LAB) are ideal candidates to deliver these enzymes in the gut. In this study, the anti-inflammatory effects of CAT or SOD producing LAB were evaluated using a trinitrobenzenesulfonic acid (TNBS) induced Crohn's disease murine model. Engineered Lactobacillus casei BL23 strains producing either CAT or SOD, or the native strain were given to mice before and after intrarectal administration of TNBS. Animal survival, live weight, intestinal morphology and histology, enzymatic activities, microbial translocation to the liver and cytokines released in the intestinal fluid were evaluated. The mice that received CAT or SOD-producing LAB showed a faster recovery of initial weight loss, increased enzymatic activities in the gut and lesser extent of intestinal inflammation compared to animals that received the wild-type strain or those that did not receive bacterial supplementation. Our findings suggest that genetically engineered LAB that produce antioxidant enzymes could be used to prevent or decrease the severity of certain intestinal pathologies.