室内饲养对高原鼠兔肠道微生物群落构建过程的影响

群落生态构建过程是近年来微生物群落生态学的研究热点。室内饲养可引起肠道菌群的剧烈变化,这种改变是否会影响群落的构建过程,一直未见报道。本文以高原鼠兔(Ochotona curzoniae)为对象,采用16S rRNA测序技术,探讨室内饲养和野生高原鼠兔肠道微生物群落在结构、功能以及群落构建过程等方面的差异。结果表明,在繁殖季节,室内饲养组的群落多样性指数和均匀度指数均显著低于野外组;群落丰度指数和群落覆盖度指数在非繁殖季节显著高于繁殖季节。拟杆菌门(Bacteroidetes)在室内饲养组显著富集,而厚壁菌门(Firmicute)和浮霉菌门(Planctomycetes)在野外组显著富集;在野外组,Epsilonbacteraeota和软壁菌门(Tenericutes)在繁殖季节显著富集。菌群功能分析显示,室内饲养组与野生组在细胞通讯和心血管疾病通路存在显著差异;野外组繁殖季节与非繁殖季节肠道菌群功能在氨基酸代谢、碳水化合物代谢和脂质代谢等通路存在显著差异。中性模型拟合结果表明,室内饲养明显降低了菌群构建的随机过程。野外组生理状态也会降低菌群构建的随机性。本研究证明室内饲养和宿主生理状...     

Use of leaves as cushions to sit on wet ground by wild chimpanzees

A new type of tool use, leaf cushion, by wild chimpanzees (Pan troglodytes verus) at Bossou, Guinea, was found. We report two cases: one is indirect evidence; the other is direct observation of a chimpanzee who used the tool. Both cases indicate that chimpanzees used a set of leaves as a cushion while sitting on wet ground. Chimpanzees at Bossou show various kinds of tool use, some of which are unique to the community. Most of these behavioral patterns are subsistence tool use for obtaining food, as at other study sites. The use of leaves as a cushion adds to the few instances of nonsubsistence, elementary technology seen used by wild chimpanzees. Am. J. Primatol. 44:215–220, 1998. © 1998 Wiley-Liss, Inc.     

富硒猴头菇对小鼠肠道菌群的调节作用

目的以昆明小鼠为实验对象,观察富硒猴头菇对小鼠肠道菌群的影响。方法设高、中和低3个剂量组和1个普通猴头菇对照组,1个蒸馏水对照组,搜集粪便,用细菌16S rDNA荧光定量PCR法测定3大类肠道菌的数量。结果富硒猴头菇冻干粉灌胃后,中剂量组和高剂量组小鼠肠道中大肠埃希菌明显减少,低、中剂量组双歧杆菌增多,高剂量组乳酸菌增多,差异有统计学意义(P0.05)。且断药3 d后,中剂量组的大肠埃希菌、双歧杆菌数量,高剂量组的大肠埃希菌、乳酸菌数量与正常对照组相比差异仍有统计学意义。结论富硒猴头菇对小鼠肠道菌群有明显调节作用。     

一株中度嗜热嗜酸细菌的分离与分子鉴定

用稀释分离法,从云南某温泉分离得到一株中度嗜热嗜酸细菌YN06。该菌株短杆状,革兰氏阴性,菌体大小为(0．3-0．5)μm x(1-2．2)μm。16S rDNA和16S—23S间隔区序列分析表明,YN06与嗜酸硫杆菌属的喜温硫杆菌处于同一进化树分支中,相似性均高达99%以上,因此该菌株被鉴定为喜温硫杆菌。     

家蚕肠道产蛋白酶细菌的分离筛选与分子鉴定

目的肠道细菌对家蚕具有重要的生理作用,探明家蚕肠道产蛋白酶细菌菌群对家蚕肠道细菌的高效开发与利用具有十分重要的意义。方法从菁松×皓月品种4龄家蚕肠液中分离与纯化肠道细菌,获得一株产高活力蛋白酶细菌,对该菌菌落进行形态学鉴定及菌体的显微镜检并结合16S rDNA方法进行了鉴定。结果该菌为革兰阴性杆菌,属于嗜麦芽寡养单胞菌(Stenotrophom onas maltophilia)。结论该产蛋白酶细菌产酶能力较高,可进一步开发研究并用作微生态制剂。     

Assessing the effects of cognitive experiments on the welfare of captive chimpanzees (Pan troglodytes) by direct comparison of activity budget between wild and captive chimpanzees

We investigated the effects of cognitive experiments by direct comparison of activity budgets between wild and captive chimpanzees. One goal of captive management is to ensure that the activity budgets of captive animals are as similar as possible to those of their wild counterparts. However, such similarity has rarely been achieved. We compared the activity budget among three groups of chimpanzees: wild chimpanzees in Bossou (Guinea, n = 10), and captive chimpanzees who participated in cognitive experiments (experimental chimpanzees, n = 6) or did not participate in the experiments (nonexperimental chimpanzees, n = 6) at the Primate Research Institute (Japan). The experimental chimpanzees voluntarily participated in computer‐controlled cognitive tasks and small pieces of fruits were provided as rewards. The data from captivity were obtained on the experimental days (weekdays) and nonexperimental days (weekends). In both study sites, we followed each chimpanzee from about 7 a.m. until the time when chimpanzees started to rest in the evening. The behaviors were recorded every 1 min. The results showed that on weekdays, feeding time and resting time of the experimental chimpanzees were almost the same as those of wild chimpanzees. However, for the nonexperimental chimpanzees, feeding time was significantly shorter and resting time was longer than those of the wild chimpanzees. In contrast, no difference was found in feeding time or resting time of the two groups of captive chimpanzees on weekends. The results suggested that the cognitive experiments worked as an efficient method for food‐based enrichment. Am. J. Primatol. 73:1231–1238, 2011. © 2011 Wiley Periodicals, Inc.     

口服益生菌对根治性放疗宫颈癌患者放疗相关性腹泻及肠道菌群的影响

评价口服益生菌预防根治性放疗宫颈癌患者放疗相关性腹泻（RE）的有效性,并探讨益生菌对根治性放疗宫颈癌患者肠道菌群的影响。

选取2020年1月—2022年12月于广西医科大学附属肿瘤医院妇瘤科行根治性放化疗宫颈癌患者46例,随机分为口服益生菌组（OP组）和非口服益生菌组（NOP组）,每组各23例。采集两组放疗前后粪便标本,通过16S rDNA测序检测肠道菌群,分析肠道菌群多样性和组间的菌群差异。

OP组RE发生率为8.7%,NOP组RE发生率高达47.8%,两组差异具有统计学意义（P=0.009）。口服益生菌能够增加放疗病人肠道菌群丰富度,但不能逆转肠道菌群α−多样性下降（P=0.012）。放疗前后肠道菌群β−多样性差异不显著（P＞0.05）。物种丰度分析显示放疗后肠道菌群在门、科、属、种水平的组成均发生改变;特别是腹泻患者与非腹泻患者比较：放疗前惰性乳杆菌相对丰度较高,但在放疗后惰性乳杆菌相对丰度较低。

宫颈癌患者根治性放疗期间口服益生菌可有效预防放疗相关性腹泻的发生。放疗影响肠道菌群的组成,特别是显著降低肠道厌氧菌的相对丰度。

     

Response of fecal cortisol to stress in captive chimpanzees (Pan troglodytes)

This study examined whether fecal cortisol could be used as an index of stress responses. The stress responsiveness of fecal cortisol was tested with a stressor known to stimulate adrenal activity, the stress of anesthesia. Daily fecal and urine samples were collected from four captive chimpanzees (Pan troglodytes) before and after anesthetizations with Telazol^®/Ketasat^®. Tests of assay validity indicated that cortisol was measurable in chimpanzee fecal extracts. Fecal cortisol concentrations were significantly elevated 2 days after anesthetization, with elevations in seven of the eight treatments. The posttreatment peak was significantly greater than baseline values in three of the four subjects. Both fecal concentrations and proportionate increases in response to stress were significantly correlated with the corresponding values in urinary cortisol, confirming the stressfulness of these procedures and the stress responsiveness of fecal cortisol. These findings provide evidence for the application of fecal cortisol as a noninvasive index of physiologic stress in nonhuman primates. Am. J. Primatol. 44:57–69, 1998. © 1998 Wiley-Liss, Inc.     

Molecular Phylogenetic Analysis of Archaea and Bacteria in Wind Cave,South Dakota

The diversity of bacteria and archaea was characterized from sediments collected from Wind Cave located in Wind Cave National Park in the Black Hills of South Dakota. Wind Cave is a limestone dissolution cave with strata that started forming over 300 million years ago, making it one of the oldest in the world. Previous work suggested that the cave was largely a detritus based system ultimately dependent upon allochthonous energy and carbon from photosynthesis of the overlying vegetation, and algae growing near lights along the tour routes. In this work, we used a molecular phylogenetic approach to characterize the microbial structure and infer a corresponding ecosystem function where appropriate. Four bacterial divisions and subdivisions were found in the culture collection, which represented 14 phylotypes, whereas 12 divisions and subdivisions were identified in the clonal analysis comprising 49 phylotypes. The predominant groups were the γ-Proteobacteria and Acidobacteria. Although a few of the clones resembled sequences from other cave and subterranean systems, no cave-specific bacterial community was evident in this work. Archaeal phylotypes (20 Crenarchaeota and 2 Euryarchaeota) were detected, with a large proportion of the Crenarchaeota resembling sequences from a South African gold mine. One archaeal cluster in particular appears to be specific to the subterranean environment. Most of the microbial sequences were not related to known chemolithoautotrophs, therefore we conclude that this particular community is likely detritus based where allochthonous energy and carbon are transported into the cave by infiltrating waters.     

单级自养脱氮系统中厌氧氨氧化菌的分子生物学鉴定

对具有厌氧氨氧化作用的细菌进行更深入的分析有助于了解该菌在生物脱氮过程的应用。对稳定运行、氨氮转化率及总氮去除率分别达到90%及80%左右的单级自养脱氮系统的底部取活性污泥,采用分子生物学方法提取活性污泥细菌总DNA,利用特异引物Pla46rc/Amx820对单级自养脱氮系统中的厌氧氨氧化菌16S rDNA基因进行PCR扩增。扩增产物经克隆、测序及BLAST分析,结果表明该单级自养脱氮系统中存在的厌氧氨氧化菌与Candidatus Kueneniastuttgartiensis和Candidatus Brocadia anammoxidans的16S rDNA序列同源性达99%,进化分析证明与Candidatus Kuenenia stuttgartiensis进化上较为接近。     

滑桃树不同器官伴生细菌多样性的分子特征

应用不依赖于培养的16S rRNA基因技术,揭示滑桃树根皮、茎皮以及种子伴生细菌的种类多样性,为建立伴生细菌的宏基因组文库奠定基础。基于我们新近发表的植物伴生菌富集方法,建立富集和未富集样品的全长16S rRNA基因文库,随机挑取至少100个克隆进行酶切分型并测序,根据16S rDNA的部分序列推测其所属伴生菌的种类。结果表明,所检测的细菌克隆大部分属于γ-Proteobacteria,有少量来源于α-Proteobacteria或放线菌（Actinobacteria）,也包括不可培养或分类地位不明确的细菌。经过富集,16S rRNA基因文库中细菌克隆的比例和序列多样性显著增加,根皮的伴生细菌种类最为丰富,其次是成熟种子和茎皮;幼嫩种子16S rDNA文库的细菌克隆比例较小（1．18％）,说明幼嫩种子的伴生菌最少。     

Nutritional significance of the selective ingestion of Albizia zygia gum exudate by wild chimpanzees in Bossou, Guinea

The selective ingestion of plant gum exudates by chimpanzees has been frequently observed at various study sites. At Bossou, Guinea, chimpanzees also frequently ingest Albizia zygia gum exudate. A functional explanation for this behavior is lacking, so we evaluated its possible contribution of energy in the form of short-chain fatty acids (SCFA) as well as minerals. An in vitro fermentation study of A. zygia gum using the fecal bacteria of a Bossou chimpanzee showed that carboxylic acids were produced with a 6-hr lag phase up to 44 mmol/l by 18 hr of incubation. Acetate was the most abundant acid produced, followed by lactate and propionate. The energy supplied from the fermentation of a piece of gum exudate (20-30 g) was negligible in comparison with the estimated daily energy requirements of chimpanzees in the wild. However, A. zygia gum exudate (20-30 g) can supply sufficient amounts of calcium, manganese, magnesium, and potassium to fulfill the daily requirements for these minerals in chimpanzees.     

Proximity and estrous synchrony in Mahale chimpanzees

Since McClintock [Nature 229:244-255, 1971] first reported menstrual synchrony in women, a number of studies have reported similar phenomena. Many researchers have suggested that one of the proximate factors leading to synchrony is spatial proximity among females (e.g., close friends or roommates). However, most studies on menstrual synchrony have been conducted in limited spaces, and it remains to be determined whether controlled environments, such as those used in experiments, actually exist in the wild. In this study, we analyzed the relationship between proximity and estrous synchrony using data from wild female chimpanzees at Mahale, Tanzania. In the cycling females, we observed two pairs that spent a large amount of time together. We compared the estrous synchrony indices (ESIs) between these two pairs and the other females. Our results showed that the ESIs of the high-proximity pairs did not differ from those of other pairs. .     

Tracing microbiota changes in yamahai-moto,the traditional Japanese sake starter

Sake is made from steamed rice, malted rice, and water. Sake production begins with the preparation of a small-scale starter (moto); the quality of moto significantly influences the flavor and richness of sake. In the traditional starter, yamahai-moto, the growth of naturally occurring lactic acid bacteria represses the putrefactive micro-organisms, whereas in the modern starter, sokujo-moto, this is achieved by adding lactic acid. In this study, the successive change in bacterial flora of yamahai-moto was analyzed by pyrosequencing 16S ribosomal RNA genes. Lactobacillus was dominant throughout the process (93–98%). Nitrate-reducing bacteria that have been generally assumed to be the first colonizers of yamahai-moto were scarcely found in the early stage, but Lactobacillus acidipiscis dominated. Lactobacillus sakei drastically increased in the middle stage. This is the first report, though one case study, to show how the early stage microbiota in Japanese yamahai-moto is varyingly controlled without nitrate-reducing bacteria using next-generation sequencing.     

Isolation and characterization of bacteriocin‐producing bacteria from the intestinal microbiota of elderly Irish subjects

Aims

To isolate and characterize bacteriocins produced by predominant species of lactic acid bacteria from faeces of elderly subjects.

Methods and Results

Screening over 70 000 colonies, from faecal samples collected from 266 subjects, using the indicator organisms Lactobacillus bulgaricus LMG 6901 and Listeria innocua DPC 3572, identified 55 antimicrobial‐producing bacteria. Genomic fingerprinting following ApaI digestion revealed 15 distinct strains. The antimicrobial activities associated with 13 of the 15 strains were sensitive to protease treatment. The predominant antimicrobial‐producing species were identified as Lactobacillus salivarius, Lactobacillus gasseri, Lactobacillus acidophilus, Lactobacillus crispatus and Enterococcus spp. A number of previously characterized bacteriocins, including ABP‐118 and salivaricin B (from Lact. salivarius), enterocin B (Enterococcus faecium), lactacin B (Lact. acidophilus), gassericin T and a variant of gassericin A (Lact. gasseri), were identified. Interestingly, two antimicrobial‐producing species, not generally associated with intestinally derived microorganisms were also isolated: Lactococcus lactis producing nisin Z and Streptococcus mutans producing mutacin II.

Conclusion

These data suggest that bacteriocin production by intestinal isolates against our chosen targets under the screening conditions used was not frequent (0·08%).

Significance and Impact of the Study

The results presented are important due to growing evidence indicating bacteriocin production as a potential probiotic trait by virtue of strain dominance and/or pathogen inhibition in the mammalian intestine.     

Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP

Fecal microbiota in six elderly individuals were characterized by the 16S rDNA libraries and terminal restriction fragment length polymorphism (T-RFLP) analysis. Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets from total genomic DNA extracted from feces of three elderly individuals. These clones were partially sequenced (about 500 bp). T-RFLP analysis was performed using 16S rDNA amplified from six subjects. The lengths of the terminal restriction fragment (T-RF) were analyzed after digestion by HhaI and MspI. Among 240 clones obtained, approximately 46% belonged to 27 known species. About 54% of the other clones were 56 novel "phylotypes" (at least 98% homology of clone sequence). These libraries included 83 species or phylotypes. In addition, about 13% (30 phylotypes) of these phylotypes were newly discovered in these libraries. A large number of species that are not yet known exist in the feces of elderly individuals. 16S rDNA libraries and T-RFLP analysis revealed that the majority of bacteria were Bacteroides and relatives, Clostridium rRNA cluster IV, IX, Clostridium rRNA subcluster XIVa, and "Gammaproteobacteria". The proportion of Clostridium rRNA subcluster XIVa was lower than in healthy adults. In addition, although Ruminococcus obeum and its closely related phylotypes were detected in high frequency in healthy young subjects, hardly any were detected in our elderly individuals. "Gammaproteobacteria" were detected at high frequency.     

A longitudinal study of urinary dipstick parameters in wild chimpanzees (Pan troglodytes verus) in Côte d'Ivoire

We performed 796 dip‐stick tests on urine from 100 wild West African chimpanzees (Pan troglodytes verus) from 4 habituated groups in the tropical rain forest of Taï National Park, Cote d'Ivoire, to establish reference values for health monitoring. Specific gravity was also measured on 359 urine samples from 62 chimpanzees. The effect of age, sex, group, month, estrus, pregnancy, meat consumption, and acute respiratory disease on pH, leucocytes, protein, blood, hemoglobin, and glucose was examined using ordinal logistic regression. The presence of nitrite, ketones, bilirubin, and urobilinogen in urine was also recorded. Outbreak of acute respiratory disease did not influence any of the urinary parameters. Thirty‐seven percent of the samples had a pH <7 and the whole range of pH was found through the year, in all age groups, and in both sexes. Meat consumption lowered the urinary pH. Our results show that all pH levels must be considered normal for the West African chimpanzee subspecies P. troglodytes verus living in the rainforest. We also found a cluster of glucose‐positive samples at a specific point in time which was not attributed to diabetes mellitus. These findings highlight that there are differences in normal physiological parameters among wild chimpanzees living in different habitats. Am. J. Primatol. 72:689–698, 2010. © 2010 Wiley‐Liss, Inc.     

Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss)

The aim of this study was to evaluate different molecular tools based on the 16S rRNA gene, internal transcribed spacer, and the rpo B gene to examine the bacterial populations present in juvenile rainbow trout intestines. DNA was extracted from both pooled intestinal samples and bacterial strains. Genes were PCR-amplified and analysed using both temporal temperature gradient gel electrophoresis (TTGE) and restriction fragment length polymorphism methods. Because of the high cultivability of the samples, representative bacterial strains were retrieved and we compared the profiles obtained from isolated bacteria with the profile of total bacteria from intestinal contents. Direct analysis based on rpo B-TTGE revealed a simple bacterial composition with two to four bands per sample, while the 16S rRNA gene-TTGE showed multiple bands and comigration for a few species. Sequencing of the 16S rRNA gene- and rpo B-TTGE bands revealed that the intestinal microbiota was dominated by Lactococcus lactis, Citrobacter gillenii, Kluyvera intermedia, Obesumbacterium proteus , and Shewanella marinus . In contrast to 16S rRNA gene-TTGE, rpo B-TTGE profiles derived from bacterial strains produced one band per species. Because the single-copy state of rpo B leads to a single band in TTGE, the rpo B gene is a promising molecular marker for investigating the bacterial community of the rainbow trout intestinal microbiota.     

Diurnal patterns of urinary steroid excretion in wild chimpanzees

Urinary testosterone and cortisol concentrations were quantified in a large number of samples (>500) collected from wild male chimpanzees (n=11) over the course of 1 year. For both steroids, urinary concentrations were higher and more variable in the morning than in the afternoon. Urinary creatinine levels showed no such diurnal pattern. These patterns are consistent with studies of steroid excretion in humans and gorillas. This study emphasizes the importance of considering time of day as a confounding variable in field studies of primate endocrine function. It also suggests that if a small number of samples are to be used to characterize an individual's basal steroid levels, afternoon samples may be preferable because they show less intra-individual variability.