Diversity of the human gastrointestinal tract microbiota revisited

Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.     

Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract

A metaproteomics approach comprising two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time of flight (mass spectrometry) was applied to the largely uncultured infant fecal microbiota for the first time. The fecal microbial metaproteome profiles changed over time, and one protein spot contained a peptide sequence that showed high similarity to those of bifidobacterial transaldolases.     

肝硬化自发性腹膜炎患者肠道优势菌群分析初探

目的 探讨肝硬化自发性腹膜炎(SBP)患者肠道优势菌群多样性变化的规律.方法 采集肝硬化SBP初始诊治患者和健康受试者各30例,收集粪便样本,进行PCR-DGGE优势菌群结构分析,并应用定量PCR技术检测肠道内乳杆菌属、双歧杆菌属和肠杆菌科细菌的含量.结果 肝硬化SBP患者肠道优势菌群结构复杂程度明显增多,SBP组和健康对照组患者分别能够聚类到不同的簇中,提示两组受试者肠道优势菌群结构明显不同.定量PCR检测结果发现,肠道优势细菌中双歧杆菌的含量明显下降(7.90±0.96 vs.9.15±1.21),而肠杆菌科细菌的数量明显增多(8.95 ±0.88 vs.7.31±0.40),两组间比较差异具有统计学意义(P＜0.05),这与SBP常见的病原菌有一定的相关性.结论 肝硬化SBP患者肠道优势菌群结构明显变化,双歧杆菌属细菌明显减少,肠杆菌科细菌明显增加,肠道微生态失衡可能是SBP发生的内在原因.     

Dynamics of morphometric indicators of rat testes during adaptation to high-altitude in the Antarctic regions with subsequent dysadaptation

In the experiments performed on 100 white non-inbred male rats (some of them have been kept at the altitude of 3.488 m in the station Vostok, and others--at the coastal level in the station Mirny) testes have been studied, as well as morphometric analysis of convoluted seminiferous tubules and estimation of spermatogenesis activity. During the first month of living at the altitude the section area of the convoluted seminiferous tubules decreases, while the area of their lumen increases. During subsequent periods in the animals, living at the altitude, differences in the parameters, in comparison with the control, disappear. During the first 6 months of their living at the altitude a sharp decrease in spermatogenesis activity is observed. A month of life at the coastal level (after 10 months of hypoxic effect) does not result in normalization of the spermatogenesis activity.     

Variation of the microbiota and metabolome along the canine gastrointestinal tract

Introduction

The fecal microbiota are relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiota and metabolome at other sites along the gastrointestinal tract remains deficient.

Objective

To analyze the gastrointestinal microbiota and metabolome of healthy domestic dogs at four anatomical sites.

Methods

Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods.

Results

Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include relative concentrations of amino acids, which decreased from the small to large intestine; pyruvate, which peaked in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine.

Conclusion

The microbiota and metabolome vary significantly at different sites along the canine gastrointestinal tract.

     

人类正常胃肠道组织基因表达谱特征的生物信息学分析

目的:筛选人类正常胃肠道组织特异性高表达基因.方法:以公开发表的人类正常组织基因表达数据库资料为研究对象,应用单侧 Student T检验筛选胃、回肠和结肠组织的特异性高表达基因.Ingenuity软件和KEGG分析特异性高表达基因相关的生理功能;Cluster软件分析胃特异性高表达基因谱在胃癌基因数据库中的表达特征.结果:筛选出胃高表达基因196个,回肠高表达基因203个,结肠高表达基因224个,高表达基因的功能与胃肠道的主要生理功能相吻合.筛选出的正常胃肠高表达基因中含有一些癌基因和抑癌基因.系统聚类分析发现胃特异性高表达基因在胃癌数据库的胃正常组织中高表达,而相应的胃癌组织低表达,癌组织和正常组织可以完好聚类分组,并且可以区分中分化和低分化胃癌.结论:人类正常胃、回肠和结肠具有组织特异的与生理功能密切相关的高表达基因群.     

Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants

The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.     

Ghrelin receptors in human gastrointestinal tract during prenatal and early postnatal development

The aim of our study was to investigate the appearance, density and distribution of ghrelin cells and GHS-R1a and GHS-R1b in the human stomach and duodenum during prenatal and early postnatal development. We examined chromogranin-A and ghrelin cells in duodenum, and GHS-R1a and GHS-R1b expression in stomach and duodenum by immunohistochemistry in embryos, fetuses, and infants. Chromogranin-A and ghrelin cells were identified in the duodenum at weeks 10 and 11 of gestation. Ghrelin cells were detected individually or clustered within the base of duodenal crypts and villi during the first trimester, while they were presented separately within the basal and apical parts of crypts and villi during the second and third trimesters. Ghrelin cells were the most numerous during the first (∼11%) and third (∼10%) trimesters of gestation development. GHS-R1a and GHS-R1b were detected at 11 and 16 weeks of gestation, showed the highest level of expression in Brunner's gland and in lower parts of duodenal crypts and villi during the second trimester in antrum, and during the third trimester in corpus and duodenum. Our findings demonstrated for the first time abundant duodenal expression of ghrelin cells and ghrelin receptors during human prenatal development indicating a role of ghrelin in the regulation of growth and differentiation of human gastrointestinal tract.     

Microbial biofilms in the human gastrointestinal tract

The human gastrointestinal tract contains rich and diverse microbiotas along its length. However, while extensive studies have been made on lumenal bacterial communities in the gut, less work has been carried out on organisms growing in biofilms, where individual groups of bacteria exist in a multiplicity of different microhabitats and metabolic niches associated with the mucosa, the mucus layer and particulate surfaces in the gut lumen. Bacteria and yeasts also occur in biofilms attached to artificial surfaces and devices implanted in the host, such as in patients being fed via enteral tubes. Although we are just beginning to investigate the composition and metabolic activities of these structures, increasing evidence suggests that they are important to the host in both health and disease. There is mounting interest in mucosal biofilms in the colon, especially with respect to their role in inflammatory bowel disease. Because bacteria growing in biofilms are more resistant to antibiotics than unattached organisms, it is often difficult to modify the structure and composition of these communities, or to eradicate them from the body. However, recent work has shown that there is considerable potential to alter the species composition of mucosal biofilms in a beneficial way using synbiotics.     

Bacterial biofilms in the human gastrointestinal tract

Microbial biofilms were first described in 1936 and subsequent research has unveiled their ubiquity and physiological distinction from free-living (planktonic) microorganisms. In light of their emerging significance this review examines the bacterial biofilms within the human gastrointestinal tract. Attention is paid to the nature of these mucosally- associated populations, focusing on the protected environment afforded by the continual secretion of mucus by host epithelial cells. It also examines the attributes possessed by various bacterial species that facilitate habitation of this microenvironment. Additionally, contrasts are drawn between planktonic bacteria of the lumen and sessile (biofilm) bacteria growing in close association with host cells and food particles. In particular the different fermentation profiles exhibited by these two fractions are discussed. The potential role of these communities in host health and disease, as well as the stabilisation of the lumenal population, is also considered. Reference is made to the state of mutualism that exists between these little understood populations and the host epithelia, thus highlighting their ecological significance in terms of gastrointestinal health.     

Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited

The phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16S ribosomal DNA (rDNA) sequence analysis. Samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. A library comprising 4,270 cloned 16S rDNA sequences obtained directly by PCR from 52 samples of either the ileum, the cecum, or the colon was constructed. In total, 375 phylotypes were identified using a 97% similarity criterion. Three hundred nine of the phylotypes (83%) had a <97% sequence similarity to any sequences in the database and may represent yet-uncharacterized bacterial genera or species. The phylotypes were affiliated with 13 major phylogenetic lineages. Three hundred four phylotypes (81%) belonged to the low-G+C gram-positive division, and 42 phylotypes (11.2%) were affiliated with the Bacteroides and Prevotella group. Four clusters of phylotypes branching off deeply within the low-G+C gram-positive bacteria and one in the Mycoplasma without any cultured representatives were found. The coverage of all the samples was 97.2%. The relative abundance of the clones approximated a lognormal distribution; however, the phylotypes detected and their abundance varied between two libraries from the same sample. The results document that the intestinal microbial community is very complex and that the majority of the bacterial species colonizing the gastrointestinal tract in pigs have not been characterized.     

Mining the microbiota of the neonatal gastrointestinal tract for conjugated linoleic acid-producing bifidobacteria

This study was designed to isolate different strains of the genus Bifidobacterium from the fecal material of neonates and to assess their ability to produce the cis-9, trans-11 conjugated linoleic acid (CLA) isomer from free linoleic acid. Fecal material was collected from 24 neonates aged between 3 days and 2 months in a neonatal unit (Erinville Hospital, Cork, Ireland). A total of 46 isolates from six neonates were confirmed to be Bifidobacterium species based on a combination of the fructose-6-phosphate phosphoketolase assay, RAPD [random(ly) amplified polymorphic DNA] PCR, pulsed-field gel electrophoresis (PFGE), and partial 16S ribosomal DNA sequencing. Interestingly, only 1 of the 11 neonates that had received antibiotic treatment produced bifidobacteria. PFGE after genomic digestion with the restriction enzyme XbaI demonstrated that the bifidobacteria population displayed considerable genomic diversity among the neonates, with each containing between one and five dominant strains, whereas 11 different macro restriction patterns were obtained. In only one case did a single strain appear in two neonates. All genetically distinct strains were then screened for CLA production after 72 h of incubation with 0.5 mg of free linoleic acid ml(-1) by using gas-liquid chromatography. The most efficient producers belonged to the species Bifidobacterium breve, of which two different strains converted 29 and 27% of the free linoleic acid to the cis-9, trans-11 isomer per microgram of dry cells, respectively. In addition, a strain of Bifidobacterium bifidum showed a conversion rate of 18%/microg dry cells. The ability of some Bifidobacterium strains to produce CLA could be another human health-promoting property linked to members of the genus, given that this metabolite has demonstrated anticarcinogenic activity in vitro and in vivo.     

Activity of phenolsulfotransferases in the human gastrointestinal tract

Sulfate conjugation by sulfotransferase enzymes is an important pathway for the detoxication of xenobiotics and endogenous compounds. The large surface area of the gastrointestinal tract exposes the body to a range of potential toxins, and hence local metabolism is likely to be important. The ability of different regions of the gut to sulfate micromolar concentrations of simple phenols and catecholamines has been determined throughout the gut using 4-nitrophenol and dopamine as standard substrates. The pattern of sulfation of both compounds was similar, with activity highest in the small bowel >right colon >left colon >rectum >stomach >esophagus. High concentrations of sulfotransferases in the reservoir areas of the right and left colon indicate possible importance in detoxication by sulfation and also perhaps in activating mutagens in the same areas. Nutritional factors, such as a high-fat diet may, however, alter sulfotransferase activity.     

Changes in conditioned reflex activity during adaptation of the rat to pressure-chamber and high-altitude hypoxia

A group of rats with a stereotype of conditioned reflexes was preliminarily trained to hypoxia effects during 30 days (at the "altitude" of 6000 m, time of exhibition--from 10 to 60 min, for 18 days--only 60 min). Adaptive changes in the process of training consisted in a weakening of differentiation inhibition, partial amnesia of the conditioned reaction of active avoidance and appearance of phasic states (equalization and paradoxical phases) in the cerebral cortex. The following adaptation of hypoxia "trained" rats to new natural conditions of Alpine altitude (3200 m) proceeded favourably, without disturbance of differentiation inhibition and without phasic states. Rats without preliminary training to altitude chamber hypoxia, in mountains (3200 m) were subjected to moderate tension resulting in protective inhibition, partial amnesia and transient disturbance of differentiation inhibition.     

Mechanical properties of the human gastrointestinal tract

The tensile properties of the human esophagus, stomach, small and large bowel were examined on an Instron 1221 tensiometer. The values of maximal stress and destructive strain were the following: for esophagus-1.2 MPa and 140%, respectively, for stomach axial specimens-0.7 MPa and 190%, for stomach transversal specimens-0.5 MPa and 190%, for small bowel transversal specimens-0.9 MPa and 140% and for large bowel transversal specimens-0.9 MPa and 180%. Tests conducted on small and large bowel axial specimens permitted examination of the intestinal wall as a multi-layered structure. The mechanical properties of tested bowels in axial and transversal directions were qualitatively different. The submucosa and muscular layers condition the mechanical strength of bowel wall, while the serosa and mucosa showed no significant strength. Reproducible results were generated for cadaveric and surgically removed stomach and small intestine, which showed their mechanical properties similar under certain storage conditions. The data received could be used for monitoring of the mechanical properties of bowel wall layers under different conditions and for checking of bowel distension sequences.     

Simultaneous assessment of luminal integrity and vascular perfusion of the gastrointestinal tract using dual-channel near-infrared fluorescence

Anastomotic complications such as stenosis and leakage in the gastrointestinal (GI) tract can cause high patient morbidity and mortality. To identify the potential preconditions of these complications intraoperatively, we explored the use of two 700 nm near-infrared (NIR) fluorophores administered intraluminally: (1) chlorella, an over-the-counter herbal supplement containing high concentrations of chlorophyll, and (2) methylene blue (MB). In parallel, we administered the 800 nm NIR fluorophore indocyanine green (ICG) intravenously to assess vascular function. Dual-channel, real-time intraoperative imaging and quantitation of the contrast to background ratio (CBR) were performed under normal conditions or after anastomosis or leakage of the stomach and intestines in 35 kg Yorkshire pigs using the Fluorescence-Assisted Resection and Exploration (FLARE) imaging system. Luminal integrity could be assessed with relatively high sensitivity with either chlorella or MB, although chlorella provided significantly higher CBR. ICG angiography provided assessment of blood perfusion of normal, ischemic, and anastomotic areas of the GI tract. Used simultaneously, 700 nm (chlorella or MB) and 800 nm (ICG) NIR fluorescence permitted independent assessment of luminal integrity and vascular perfusion of the GI tract intraoperatively and in real time. This technology has the potential to identify critical complications, such as anastomotic leakage, intraoperatively, when correction is still possible.