珍珠鸟(Taeniopygia guttata)小染色体基因表达的密码子偏性

从NCBI数据库（http：／／www．ncbi．nlm．nih．gov／projects／mapview／map）下载珍珠鸟全部小染色体基因的cDNA序列,最终共有1586个基因的CDS序列纳入统计分析。密码子的偏性分析使用CodonW（1．4．2）完成,初步确定了UUC、UCC、UCG等27个密码子为珍珠鸟小染色体基因表达的“最优”密码子。对应分析表明,影响珍珠鸟小染色体基因密码子使用的主要因素分别为GC3s、CDS的GC含量基以及因的表达丰度。珍珠鸟小染色体基因的密码子用法受到了基因碱基组成的显著影响,其密码子的偏性是碱基组成及选择等因素综合作用的结果。本研究的目的是系统探究珍珠乌小染色体基因的密码子用法,探究鸟类基因表达的分子调控机制。     

Lactobacillus and Pediococcus species richness and relative abundance in the vagina of rhesus monkeys (Macaca mulatta)

Background The rhesus monkey is an important animal model to study human vaginal health to which lactic acid bacteria play a significant role. However, the vaginal lactic acid bacterial species richness and relative abundance in rhesus monkeys is largely unknown. Methods Vaginal swab samples were aseptically obtained from 200 reproductive‐aged female rhesus monkeys. Following Rogosa agar plating, single bacterial colonies representing different morphotypes were isolated and analyzed for whole‐cell protein profile, species‐specific polymerase chain reaction, and 16S rRNA gene sequence. Results A total of 510 Lactobacillus strains of 17 species and one Pediococcus acidilactici were identified. The most abundant species was Lactobacillus reuteri, which colonized the vaginas of 86% monkeys. Lactobacillus johnsonii was the second most abundant species, which colonized 36% of monkeys. The majority of monkeys were colonized by multiple Lactobacillus species. Conclusions The vaginas of rhesus monkeys are frequently colonized by multiple Lactobacillus species, dominated by L. reuteri.     

Response to begging calls by Zebra Finch parents: "first come, first served" rule may overcome a parental preference between chicks

In birds, parents may provide differential food provisioning among offspring according to their sex. Here, we test the hypothesis that events linked to the fine dynamics of begging behaviour could modulate parental preferences. After evaluating the preference related to chick sex for each parent of six Zebra Finch Taeniopygia guttata pairs, we studied the possible modifications of this preference when offspring begging was asynchronous. Our observations show that male parents follow a "first come, first served" rule, whereas females keep their initial choice. Although this study remains preliminary due to the sample size, it underlines the potential importance of investigating fine temporal features of begging behaviour to fully understand parents' provisioning strategies.     

Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea

The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample. Most sequences with more than 97% sequence similarity, a value often taken as indicative of species delimitation, were only found at a single location/depth; nevertheless, a few examples of cosmopolitan sequences were found in all samples. Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea.     

分子生物学技术在胃肠道微生态中应用研究进展

哺乳动物胃肠道中栖息着大量的微生物(主要为细菌),它们在营养、生理、免疫等方面对宿主起着有益作用。传统上,胃肠道菌群研究主要依靠培养技术。近来,一些基于16S rRNA(DNA)的分子生物学技术已被广泛应用于胃肠道菌群的研究,这些技术主要有16S rDNA克隆基因文库、16S rDNA指纹技术、定量PCR技术、荧光原位杂交技术及基因芯片技术等。对这些用于胃肠道微生态研究的分子生物学技术作一综述。     

The intestinal LABs

The complete gastrointestinal (GI) tract of humans is colonised soon after birth by a myriad of microbial species with a characteristic distribution depending on the location. GI-tract ecology has been experiencing a revival due to the development of molecular techniques, especially those based on 16S RNA (zRNA) genes. A richer ecosystem than previously imagined of novel species is being discovered that is significantly influenced by our host genotype. Special attention has been focused on the bifidobacteria and the lactic acid bacterial (LAB) populations, both those that are naturally present within this complex ecosystem and those that are ingested as probiotics in functional foods. Overall this interest stems from a increasing awareness of interplay between microflora, diet and the health of the host, and is further stimulated by an increasing incidence of gastrointestinal illnesses and atopy. Substantial documentation of benefits to host health has especially distinguished the LAB for multidisciplinary research aimed to determine the molecular mechanisms involved. Recent advances in molecular technologies, including high-throughput genomics-based approaches, can significantly advance our understanding of the microbe–diet–host interactions and offer valuable information for design and application of health-targeted microbes.     

Comparison of DNA extraction methods for human gut microbial community profiling

The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome.     

Species diversity and relative abundance of lactic acid bacteria in the milk of rhesus monkeys (Macaca mulatta)

Background Mother’s milk is a source of bacteria that influences the development of the infant commensal gut microbiota. To date, the species diversity and relative abundance of lactic acid bacteria in the milk of non‐human primates have not been described. Methods Milk samples were aseptically obtained from 54 female rhesus monkeys (Macaca mulatta) at peak lactation. Following GM17 and MRS agar plating, single bacterial colonies were isolated based on difference in morphotypes, then grouped based on whole‐cell protein profiles on SDS–PAGE. Bacterial DNA was isolated and the sequence the 16S rRNA gene was analyzed. Results A total of 106 strains of 19 distinct bacterial species, belonging to five genera, Bacillus, Enterococcus, Lactobacillus, Pediococcus, and Streptococcus, were identified. Conclusions Maternal gut and oral commensal bacteria may be translocated to the mammary gland during lactation and present in milk. This pathway can be an important source of commensal bacteria to the infant gut and oral cavity.     

Optimization and characterization of extracellular cellulase produced by Bacillus pumilus MGB05 isolated from midgut of muga silkworm (Antheraea assamensis Helfer)

Mature larvae of Antheraea assamensis were collected from different locations of Assam to isolate the cellulolytic gut microflora. Altogether sixty cellulase degrading bacteria were isolated on agar plates containing microcrystalline cellulose as the sole carbon source. Among them, ten isolates showed hydrolyzing zone on agar plates containing carboxy methyl cellulose (CMC) after staining with Congo-red. Isolate MGB05 exhibited the highest CMCase activity (0.262?U/mL) at 72?h of incubation under submerged condition. FPase and β-glucosidase activity were 0.012?U/mL and 3.71?U/mL respectively. It showed maximum FPase (0.022?U/mL) activity on the 3rd day of incubation in the media containing wheat bran as a carbon source. β-glucosidase production was also found to be highest with wheat bran (20.03?U/mL) at 48?h of incubation. The optimum pH and temperature of FPase activity of MGB05 were found at 6.0 and 50?°C respectively while for β-glucosidase activity, it was maximum at pH?6.0 under 50?°C. In addition, metal ion Mg⁺⁺ and Ca⁺⁺ enhanced FPase activity up to 110.92% (0.026?U/mL) and 105.31% (0.025?U/mL) respectively. In-vitro antimicrobial bioassay of the most potent cellulolytic bacteria (MGB05) also showed high antimicrobial activity against Escherichia coli (2.9?cm) and Pseudomonas aeruginosa (3.0?cm). The isolate MGB05 has been identified based on 16S rDNA homology as Bacillus pumilus MGB05 with accession KP298708.2. Results encompass the prospective beneficial role of gut-microflora on digestion and disease resistance, which might be a potential probiotic component to enhance silk productivity.     

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life

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16S rRNA测序技术在肠道微生物中的应用研究进展

16S rRNA测序是高通量测序依赖的肠道微生物研究方法之一,该方法可以对肠道微生物中的所有菌种进行精确定量,因此正逐渐成为研究肠道微生物菌种丰度变化的主流。肠道微生物16S rRNA测序的应用过程中有两个问题至关重要,一是如何根据需要选择测序方案;二是面对高通量测序得到的海量数据,如何进行生物信息学分析,以得到具有生物学意义的结果。从测序平台、测序片段、测序数据量的选择3个方面讨论了如何选择测序方案,并从序列聚类与注释、群落结构分析、关键分类单位的筛选与功能分析等方面对目前常用的生物信息学分析手段进行综述。     

The effect of Codonopis bulleynana Forest ex Diels on chronically constipated mice

To verify the laxative effect of Codonopsis bulleyana and its effect on intestinal microbiota, a long-term constipation model was established using 3.0?mg/kg loperamide hydrochloride, after which, the long-term constipation model was administered by 0.2?g/ml high-dose Codonopsis bulleyana water extract. The therapeutic effects were observed by measuring defecation amount and feces moisture content. The composition of intestinal microbiota was detected and analyzed using16S rDNA sequencing technology. The results showed that Codonopsis bulleyana water extract can increase stool quantity and promote intestinal tract movement in constipated mice. Obvious changes were shown in intestinal microbiota of chronically constipated mice treated with Codonopsis bulleyana water extract as the proportion of beneficial bacteria increased in the model treated by Codonopsis bulleyana. Codonopsis bulleyana water extract alleviates constipation symptoms caused by loperamide hydrochloride and improves the intestinal microbiota in constipated mice.