Identification of a Core Bacterial Community within the Large Intestine of the Horse

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.     

Digestive physiology of wild capybara

The capybara (Hydrochaeris hydrochaeris) is a hindgut fermenter whose digestive efficiency is comparable to that of ruminants on similar diets. It is an interesting case for study because it is the largest caecum fermenter and uses coprophagy as part of its digestive strategy. It practices coprophagy in the early morning and forages and defaecates in the evening. Its anatomy is well known but the limited information available about its digestive physiology has been obtained from captive animals. In this work we studied the capybara's digestive physiology, using microbial and chemical information from samples taken from wild capybaras in the early wet season in the morning (0600–0700 hours), noon (1200–1300 hours) and evening (1800–1900 hours), key points in the digestive cycle. Bacteria (cellulolytic and non-cellulolytic) and protozoa were present in high concentrations in the caecum and colon. There were no significant differences in nitrogen concentrations between digestive tract compartments in the coprophagy period (0600 hours), but in the other two periods nitrogen concentrations were significantly higher in the caecum than in the stomach and colon. This is suggestive of selective retention of microbial cells with fluid digesta in the caecum and of cecotrophy (the production of two distinctly different kinds of faeces — one kind called cecotrophes formed from caecal contents and ingested). The capybara hindgut (caecum and colon) with its content, was heavier during the dry season (period of poor diet quality) than in the wet season, but there were no significant seasonal differences between the stomach or small intestine and their contents. This suggests changes in the capacity of the hindgut, the site of microbial fermentation, related to seasonal variation in resource quality.Abbreviations NDF neutral-detergent fibre - SCFA Short-chain fatty acid(s)     

哺乳动物的消化策略（英文）

理解动物的营养生态位是充分理解其整个生态学的基础,对于害兽控制和物种保护也很重要,食肉动物的小肠很发达,这可能与对食物的高消化能力有关;杂食性动物有更复杂的胃肠器官,其后端有可进行发酵的盲肠,消化物的平均滞留时间（mean retention times,MRTs)更长;最长的平均滞留时间见于食草动物,其消化道内高密度的微生物种群对不同滞留区内的消化物进行发酵,但是,并不是所有的食草动物都能够最大程度地消化植物纤维,只有反刍动物、骆驼和个体较大的后肠发酵动物（hindgut fermenter)能够具有这种能力,对比而言,许多其它的食草动物,如前肠发酵的有袋类和小型的后肠发酵动物如兔子、田鼠和负鼠等,它们具备可以使植物纤维消化效率最大的消化系统,可以在食物中的纤维素含量非常高的情况下仍能处理大量的食物。这些不同的消化策略使哺乳动物具有广幅的营养生态位。     

Symbiotic fermentation, digesta passage, and gastrointestinal morphology in bullfrog tadpoles (Rana catesbeiana)

Relative to other herbivorous vertebrates, the nutritional ecology and digestive physiology of anuran larvae remain poorly understood. Our objective was to compare gut structure and inhabitants, digesta passage, and microbial fermentation in bullfrog tadpoles (Rana catesbeiana) to those in other herbivores. Bullfrog tadpole gastrointestinal tracts were long and voluminous, with an enlarged colon that harbored a diverse symbiotic community. The transit time for particulate markers passing through bullfrog tadpoles was 6 h, the median retention time was 8-10 h, and gut clearance was 10-14 h postingestion. Relatively high levels of short-chain fatty acids in the hindgut of tadpoles indicated active microbial fermentation in this gut region. This report represents the first account of gastrointestinal fermentation in the class Amphibia. On the basis of in vitro fermentation assays, we estimated that microbial fermentation in the hindgut provides 20% of the total daily energy requirement of bullfrog tadpoles. These tadpoles also exhibited coprophagy, a practice that provides important nutritive gains in other herbivores. The physiological and behavioral characteristics of these tadpoles are remarkably similar to those of other small-bodied, hindgut-fermenting vertebrates, suggesting convergent digestive strategies among a broad range of herbivorous taxa.     

Effects of animal or plant protein diets on cecal fermentation in guinea pigs (Cavia porcellus), rats (Rattus norvegicus) and chicks (Gallus gallus domesticus)

Monogastric herbivores such as the guinea pig depend on energy supply from enteric fermentation as short-chain fatty acids (SCFA) corresponding to 30-40% of their maintenance energy requirements. They evolved specific digestive system to adapt their indigenous microflora to plant polysaccharides fermentation. No information has been available about the adaptability of microbial fermentation in hindgut of the monogastric herbivorous to an animal protein diet. We investigated if the guinea pig can fully retrieve energy of an animal protein diet by hindgut fermentation compared with a plant protein diet. For comparison, we also studied two omnivores. End products of in vitro cecal fermentation (SCFA, ammonia and gases) were measured to judge how well an animal protein diet could be fermented. The animal protein diet resulted in the less intensive fermentation with increased feed intake and volume of cecal contents than the plant protein diet only in guinea pigs. This may be due to a limited capacity of the hindgut microflora to adapt to the substrate rich in animal protein. We also found that chick cecal contents produced methane at higher emission rate than ruminants.     

Peptidic soil components are a major dietary resource for the humivorous larvae of Pachnoda spp. (Coleoptera: Scarabaeidae)

Humivorous scarab beetle larvae can thrive exclusively on soil organic matter. Feeding experiments have revealed that the larva of Pachnoda ephippiata mineralizes all major humus components except the polyphenolic fraction. High proteolytic activity in the alkaline midgut fluid and an enormous ammonia production during gut passage suggested that peptidic soil components are an important dietary resource for the larva. By comparing acid-hydrolyzable amino acids in food soil and feces, we showed that a significant fraction of the peptides in soil are removed during gut passage. This agrees well with the high concentrations of free amino acids found the midgut section. Incubation experiments revealed the presence of substantial particle-associated proteolytic activity also in the hindgut, most probably due to microbial activity. High rates of ammonia formation in hindgut homogenates and the conversion of radiolabeled amino acids to acetate and propionate indicated that microbial fermentations of soil peptides play an important role in the hindgut. This was corroborated by viable counts of amino-acid-fermenting bacteria, which formed a substantial fraction of the hindgut microbiota. A complete inventory of organic and inorganic nitrogen species before, during, and after gut passage revealed the formation of nitrite and nitrate in midgut and hindgut, and a substantial nitrogen deficit in the feces, suggesting that part of the ammonia formed by mineralization is subjected to oxidation and subsequent denitrification to N2. Together, the results strongly support the hypothesis that peptidic soil components form a major energy and nutrient source for humivorous insects, supplying the animal with microbial fermentation products and essential amino acids.     

Digestive strategy of the asian colobine genusTrachypithecus

The Asian colobines,Trachypithecus obscurus andT. cirstantus, eat plant-based diets containing 55–80% leaves. The structural polysaccharides in leaves and other plant parts require microbial fermentation before they can be used as an energy source by the monkeys. The major compartments of the gastro-intestinal tract ofTrachypithecus are a voluminous haustrated stomach, a long small itnestine and capacious haustrated hindgut, all of which contribute to the digestive strategy of these two species. Results of digesta marker passage studies indicate there is prolonged retention of digesta for fermentation in both the stomach and haustrated colon. The digestive strategy of these colobines is defined as gastro-colic fermentation, unlike that of other forestomach fermenters in which the hindgut fermentation is of secondary importance.     

More than one way to be an herbivore: convergent evolution of herbivory using different digestive strategies in prickleback fishes (Stichaeidae)

In fishes, the evolution of herbivory has occured within a spectrum of digestive strategies, with two extremes on opposite ends: (i) a rate-maximization strategy characterized by high intake, rapid throughput of food through the gut, and little reliance on microbial digestion or (ii) a yield-maximization strategy characterized by measured intake, slower transit of food through the gut, and more of a reliance on microbial digestion in the hindgut. One of these strategies tends to be favored within a given clade of fishes. Here, we tested the hypothesis that rate or yield digestive strategies can arise in convergently evolved herbivores within a given lineage. In the family Stichaeidae, convergent evolution of herbivory occured in Cebidichthys violaceus and Xiphister mucosus, and despite nearly identical diets, these two species have different digestive physiologies. We found that C. violaceus has more digesta in its distal intestine than other gut regions, has comparatively high concentrations (>11 mM) of short-chain fatty acids (SCFA, the endpoints of microbial fermentation) in its distal intestine, and a spike in β-glucosidase activity in this gut region, findings that, when coupled to long retention times (>20 h) of food in the guts of C. violaceus, suggest a yield-maximizing strategy in this species. X. mucosus showed none of these features and was more similar to its sister taxon, the omnivorous Xiphister atropurpureus, in terms of digestive enzyme activities, gut content partitioning, and concentrations of SCFA in their distal intestines. We also contrasted these herbivores and omnivores with other sympatric stichaeid fishes, Phytichthys chirus (omnivore) and Anoplarchus purpurescens (carnivore), each of which had digestive physiologies consistent with the consumption of animal material. This study shows that rate- and yield-maximizing strategies can evolve in closely related fishes and suggests that resource partitioning can play out on the level of digestive physiology in sympatric, closely related herbivores.     

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change

Faeces could be used for evaluating the balance of the equine hindgut microbial ecosystem, which would offer a practical method for assessing gut health and how this relates to disease. However, previous studies concluded that faeces microbial ecosystem was not representative of the proximal hindgut (caecum and ventral colon). This study aimed to evaluate if variations of the faecal microbial ecosystem were similar to those observed in the proximal hindgut. Six horses, fistulated in the caecum and right ventral (RV) colon, were subjected to a gradual change of diet, from a 100% hay (high fibre) diet (2.2 DM kg/day per 100 kg BW) to a 57% hay+43% barley (high starch) diet (0.8 DM kg/day per 100 kg BW hay and 0.6 DM kg/day per 100 kg BW barley). The two diets were iso-energetic and fed over a 3-week trial period. Samples of digesta from the caecum, RV colon and faeces were collected two times on the 10th and 20th day of the trial, for each diet to assess the microbial ecosystem parameters by both classical culture technics and biochemical methods. The variations observed in the caecal and colonic bacterial composition (increase in total anaerobic, amylolytic and lactate-utilizing and decrease in cellulolytic bacteria concentrations) and microbial activity (changes in volatile fatty acids concentrations and increase in lactate concentrations) demonstrated that the hay+barley diet caused changes in the hindgut microbial ecosystem. Similar variations were observed in the faecal microbial ecosystem. Feeding the hay+barley diet resulted in higher concentrations of faecal lipopolysaccharides. The functional bacterial group concentrations (cellulolytics, amylolytics and lactate utilizers) were significantly correlated between caecum and faeces and between colon and faeces. From analyses of the metabolites produced from microbial activity, only valerate concentration in the caecum and the proportion of propionate were significantly correlated with the same parameters in the faeces. Results of the principal component analysis performed between all the caecal/faecal and colonic/faecal parameters revealed that the total anaerobic and cellulolytic bacteria concentrations, as well as valerate, l-lactate and lipopolysaccharide concentrations were strongly correlated with several microbial parameters in the caecum (P<0.027; r>|0.45|) and in the colon (P<0.013; r>|0.50|). This demonstrated that faecal samples and their bacterial analyses could be used to represent caecum and RV colon hindgut microbial ecosystem in terms of variations during a change from a high-fibre to a high-starch diet, and thus could be markers of particular interest to diagnostic proximal hindgut microbial disturbances.     

Enumeration of anaerobic bacterial microflora of the equine gastrointestinal tract.

Samples from the duodenum, jejunum, and ileum, as well as from the cecum and colon, were obtained from 11 mature grass-fed horses. Viable counts of total culturable and proteolytic bacteria were made on habitat-simulating media containing 40% clarified ruminal fluid. The mean pHs in the duodenum, jejunum, and ileum were 6.32, 7.10, and 7.47, respectively; the mean pH decreased to 6.7 in the hindgut. The acetate concentration increased along the length of the small intestine and was the only volatile fatty acid present in this gut segment. Molar proportions of acetate, propionate, and butyrate in the hindgut were 85:10:3. Differences in bacterial counts on habitat-simulating media containing equine cecal fluid or clarified ruminal fluid were negligible. Bacterial counts showed a substantial population in the duodenum (ca. 2.9 x 10(6) per g [wet weight] of sample), and this increased to 29.0 x 10(6) in the jejunum and 38.4 x 10(6) in the ileum. Proteolytic bacteria formed a high proportion of the total culturable bacteria, especially in duodenal samples. Counts of proteolytic bacteria per gram (wet weight) of sample were 3.0 x 10(6), 15.6 x 10(6), and 22.0 x 10(6) in the duodenum, jejunum, and ileum, respectively. There was a close relationship between lumenal and mucosal bacterial counts, although actual values were lower in mucosal samples. The mucosal bacterial population in the duodenum was high relative to the lumenal population. Although the comparison of bacterial populations in the hindgut of the horse and white rhino was limited to a single animal, the results were of interest. Counts were higher in the cecum than in the colon for both the horse and the white rhino.(ABSTRACT TRUNCATED AT 250 WORDS)     

Enumeration of anaerobic bacterial microflora of the equine gastrointestinal tract

Samples from the duodenum, jejunum, and ileum, as well as from the cecum and colon, were obtained from 11 mature grass-fed horses. Viable counts of total culturable and proteolytic bacteria were made on habitat-simulating media containing 40% clarified ruminal fluid. The mean pHs in the duodenum, jejunum, and ileum were 6.32, 7.10, and 7.47, respectively; the mean pH decreased to 6.7 in the hindgut. The acetate concentration increased along the length of the small intestine and was the only volatile fatty acid present in this gut segment. Molar proportions of acetate, propionate, and butyrate in the hindgut were 85:10:3. Differences in bacterial counts on habitat-simulating media containing equine cecal fluid or clarified ruminal fluid were negligible. Bacterial counts showed a substantial population in the duodenum (ca. 2.9 x 10(6) per g [wet weight] of sample), and this increased to 29.0 x 10(6) in the jejunum and 38.4 x 10(6) in the ileum. Proteolytic bacteria formed a high proportion of the total culturable bacteria, especially in duodenal samples. Counts of proteolytic bacteria per gram (wet weight) of sample were 3.0 x 10(6), 15.6 x 10(6), and 22.0 x 10(6) in the duodenum, jejunum, and ileum, respectively. There was a close relationship between lumenal and mucosal bacterial counts, although actual values were lower in mucosal samples. The mucosal bacterial population in the duodenum was high relative to the lumenal population. Although the comparison of bacterial populations in the hindgut of the horse and white rhino was limited to a single animal, the results were of interest. Counts were higher in the cecum than in the colon for both the horse and the white rhino.(ABSTRACT TRUNCATED AT 250 WORDS)     

The functional significance of the browser-grazer dichotomy in African ruminants

The allometric relationships for the fermentation rate of dry matter, the total energy concentration of volatile fatty acids (VFAs), the energy supplied from VFA production and the mass of the digesta contents within the rumen or caecum and proximal colon (hindgut) were used to test whether the digestive strategies of grazing and browsing African ruminants differ. The wet and dry mass of the contents of the rumen and hindgut were allometrically related to body mass (BM). These relationships did not differ between browsing and grazing ruminants. The fermentation rates in the rumen were strongly allometric and the intercepts of the relationships did not differ between browsers and grazers. The fermentation rates in the hindgut were not allometrically related to BM and did not differ between ruminants with different feeding habits. Likewise, the total energy concentration of the VFAs in the rumen and hindgut showed no allometric scaling and did not differ between browsing and grazing ruminants. The energy supplied by VFA production in both the rumen and hindgut of African ruminants scaled at around 0.8 with BM. Only in the case of the energy supplied by VFAs in the rumen were there significantly different intercepts for browsing and grazing ruminants. The energy supplied by VFA production in the rumen was inadequate to meet the energy requirements for maintenance of browsers and small grazers. The retention time of digesta in the alimentary tract was positively related to BM although there was no difference in the allometric relationships for grazers and browsers. The results of these analyses suggest that, after controlling for the effects of body mass, there is little difference in digestive strategy between African ruminants with different morphological adaptations of the gut.     

Physicochemical conditions and microbial activities in the highly alkaline gut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae)

The soil macrofauna plays an important role in the carbon and nitrogen cycle of terrestrial ecosystems. In order to gain more insight into the role of the intestinal microbiota in transformation and mineralization of organic matter during gut passage, we characterized the physicochemical conditions, microbial activities, and community structure in the gut of our model organism, the humus-feeding larva of the cetoniid beetle Pachnoda ephippiata. Microsensor measurements revealed an extreme alkalinity in the midgut, with highest values (pH > 10) between the second and third crown of midgut ceca. Both midgut and hindgut were largely anoxic, but despite the high pH, the redox potential of the midgut content was surprisingly high even in the largest instar. However, reducing conditions prevailed in the hindgut paunch of all instars (E(h) approximately -100 mV). Both gut compartments possessed a pronounced gut microbiota, with highest numbers in the hindgut, and microbial fermentation products were present in high concentrations. The stimulation of hindgut methanogenesis by exogenous electron donors, such as H(2), formate, and methanol, together with considerable concentrations of formate in midgut and hemolymph, suggests that midgut fermentations are coupled to methanogenesis in the hindgut by an intercompartmental transfer of reducing equivalents via the hemolymph. The results of a cultivation-based enumeration of the major metabolic groups in midgut and hindgut, which yielded high titers of lactogenic, propionigenic, and acetogenic bacteria, are in good agreement not only with the accumulation of microbial fermentation products in the respective compartments but also with the results of a cultivation-independent characterization of the bacterial communities reported in the companion paper (M. Egert, B. Wagner, T. Lemke, A. Brune, and M. W. Friedrich, Appl. Environ. Microbiol. 69:6659-6668, 2003).     

Changes in microbiota population during fermentation of narezushi as revealed by pyrosequencing analysis

Modern Japanese sushi is derived from an archetype, narezushi, which is made by the fermentation of salted fish with rice. Several studies have demonstrated that lactic acid bacteria are dominantly present in narezushi, but no studies have addressed how microbial composition changes during fermentation. In this study, we examined changes in the microbial population in aji (horse mackerel)-narezushi during fermentation by pyrosequencing the 16S ribosomal RNA gene (rDNA). Ribosomal Database Project Classifier analysis revealed that among the 53 genera present, the Lactobacillus population drastically increased during fermentation, while the populations of other bacteria remained unchanged. Basic Local Alignment Search Tool analysis revealed that L. plantarum and L. brevis were the major species. Comparison with other fermented food microbiota indicated high product-dependency of the bacterial composition, which might have been due to the starter-free fermentation process.     

Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA)

The horse’s hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp® DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples.     

光唇鱼消化道的形态结构特征

采用解剖及石蜡切片显微技术,观察研究了光唇鱼消化道的形态结构特征。消化道由口咽腔、食道、肠构成。口下位、马蹄形,无颌齿,具咽齿,齿式为4/4。舌较小,前端游离,舌粘膜表层为复层鳞状上皮,有较多的杯状细胞和味蕾。食道及肠均由粘膜层、粘膜下层、肌层及外膜构成。食道内皱襞发达,粘膜层有大量杯状细胞。肠道盘曲,由前、中、后肠组成,肠长/体长为1.84±0.24;前肠管腔较大,中、后肠管腔渐变小;前、中肠皱襞及纹状缘比后肠发达;前肠及后肠杯状细胞较少,中肠杯状细胞较多。光唇鱼消化道的形态结构特征与其食性相适应。     

In vitro degradation of the flavonol quercetin and of quercetin glycosides in the porcine hindgut

The present study investigated the microbial degradation of the plant flavonol quercetin and its naturally occurring glycosides isoquercitrin and rutin in the porcine hindgut. The experiments were carried out with the semicontinuous colon-simulation technique. The fluid and particle phase of pig hindgut contents from freshly slaughtered animals were used for the in vitro incubations. Following a five-day equilibration period, quercetin, isoquercitrin or rutin were administered to fermentation vessels and their turnover rate was determined. None of the flavonols affected parameters of microbial fermentation like pH, redox potential or VFA production. The turnover rate for isoquercitrin was seven times higher than the turnover for the fermentation fluid. The turnover rates for quercetin and rutin were four and twofold higher than fluid turnover, respectively. After administration of isoquercitrin or rutin, their aglycone quercetin was detected as an intermediary metabolite. Under sterile conditions using autoclaved incubation fluids and hindgut contents, turnover rates for quercetin and rutin were still higher than the fluid turnover in the fermentation vessels. This indicates a certain chemical instability of the flavonols and/or adsorption to ingesta particles. Thus, flavonols are subjected to microbial metabolism in the porcine hindgut. The glycosidic structure strongly influences the rate of metabolism.     

虎纹蛙消化道淀粉酶和脂肪酶活力研究

以酶学分析方法研究了虎纹蛙消化道淀粉酶和脂肪酶的分布以及pH和温度对这两种消化酶活力的影响。结果表明：在各自生理pH值条件下,虎纹蛙消化道不同部位淀粉酶活力大小顺序依次为前肠〉中肠〉后肠〉食道〉胃,胃和肠淀粉酶最适pH值分别为8．6和7．0,最适温度分别为35℃和40℃。脂肪酶活力大小顺序依次为中肠〉后肠〉前肠〉胃〉食道,各部位之间差异显著（P〈0．05）,胃和肠脂肪酶的最适pH值均为9．0,最适温度分别为50℃和55℃。     

草鱼肠道纤维素降解细菌的分离与鉴定

为更好地弄清草鱼（Ctenopharyngodon idella）肠道纤维素降解细菌的种类,采用羧甲基纤维素（CMC）作为唯一碳源的选择性培养基,分别从草鱼肠道内容物和肠道黏膜中分离到了40株产纤维素酶细菌。16S rRNA基因序列的分析结果显示,大多数产纤维素酶细菌为气单胞菌属（Aeromonas）的种类,其次为肠杆菌属（Enterobacter）的细菌以及未经分离纯培养的细菌（Uncultured bacterium）。进一步研究细菌产纤维素酶能力发现,纤维素酶活性显著性高于其他菌株的分别是A. veronii MC2、A. veronii BC6、肠杆菌科（Enterobacteriaceae）中一种未经分离纯培养的细菌BM3（Uncultured bacterium BM3）和A. jandaei HC9。草鱼肠道中简答气单胞菌（A. jandaei）、类志贺邻单胞菌（Plesiomonas shigelloides）、阴沟肠杆菌（E. cloacae）以及产气肠杆菌（E. aerogenes）是被作为产纤维素酶细菌的首次报道。       

Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris)

The capybara (Hydrochoerus hydrochaeris) is the world's largest living rodent. Native to South America, this hindgut fermenter is herbivorous and coprophagous and uses its enlarged cecum to digest dietary plant material. The microbiota of specialized hindgut fermenters has remained largely unexplored. The aim of this work was to describe the composition of the bacterial community in the fermenting cecum of wild capybaras. The analysis of bacterial communities in the capybara cecum is a first step towards the functional characterization of microbial fermentation in this model of hindgut fermentation. We sampled cecal contents from five wild adult capybaras (three males and two females) in the Venezuelan plains. DNA from cecal contents was extracted, the 16S rDNA was amplified, and the amplicons were hybridized onto a DNA microarray (G2 PhyloChip). We found 933 bacterial operational taxonomic units (OTUs) from 182 families in 21 bacterial phyla in the capybara cecum. The core bacterial microbiota (present in at least four animals) was represented by 575 OTUs. About 86% of the cecal bacterial OTUs belong to only five phyla, namely, Firmicutes (322 OTUs), Proteobacteria (301 OTUs), Bacteroidetes (76 OTUs), Actinobacteria (69 OTUs), and Sphirochaetes (37 OTUs). The capybara harbors a diverse bacterial community that includes lineages involved in fiber degradation and nitrogen fixation in other herbivorous animals.