Effects of captivity,diet, and relocation on the gut bacterial communities of white‐footed mice

Microbes can have important impacts on their host's survival. Captive breeding programs for endangered species include periods of captivity that can ultimately have an impact on reintroduction success. No study to date has investigated the impacts of captive diet on the gut microbiota during the relocation process of generalist species. This study simulated a captive breeding program with white‐footed mice (Peromyscus leucopus) to describe the variability in gut microbial community structure and composition during captivity and relocation in their natural habitat, and compared it to wild individuals. Mice born in captivity were fed two different diets, a control with dry standardized pellets and a treatment with nonprocessed components that reflect a version of their wild diet that could be provided in captivity. The mice from the two groups were then relocated to their natural habitat. Relocated mice that had the treatment diet had more phylotypes in common with the wild‐host microbiota than mice under the control diet or mice kept in captivity. These results have broad implications for our understanding of microbial community dynamics and the effects of captivity on reintroduced animals, including the potential impact on the survival of endangered species. This study demonstrates that ex situ conservation actions should consider a more holistic perspective of an animal's biology including its microbes.     

培养基灭菌方式对细菌分离效率的影响

自然界蕴含大量未/难培养微生物,分离这些微生物对理论研究和资源开发具有重要意义。本研究使用高压灭菌和过滤除菌方式制备培养基,采用稀释涂布方法,从红树林灰泥样品中分离获得123株细菌,通过16S rRNA基因序列分析对其进行鉴定,进而探究培养基灭菌方式对细菌分离效果的影响。结果表明：过滤除菌培养基生长的单菌落数目（339±82）个显著多于高压灭菌培养基生长的单菌落数目（179±65）个;两种培养基分离细菌的群落结构在门、科和属分类水平上总体相似,但优势类群的数目和少数类群存在差异;过滤除菌培养基分离细菌的Shannon Wiener’s指数、均匀度、新种率、基因多样性均高于高压灭菌培养基,而其与近缘模式菌株相似度的平均值和中位数则低于高压灭菌培养基。因此,过滤除菌培养基分离获得细菌的多样性、均匀性和新颖性均高于高压灭菌培养基。本研究首次探究培养基灭菌方式对细菌分离效果的影响,具有更高分离效率的过滤除菌培养基为未/难培养微生物菌株资源获取提供了借鉴。     

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo,Tibet Autonomous Region

The soil bacterial communities have been widely investigated. However, there has been little study of the bacteria in Qinghai-Tibet Plateau, especially about the culturable bacteria in highland barley cultivation soil. Here, a total of 830 individual strains were obtained at 4°C and 25°C from a highland barley cultivation soil in Qamdo, Tibet Autonomous Region, using fifteen kinds of media. Seventy-seven species were obtained, which belonged to 42 genera and four phyla; the predominant phylum was Actinobacteria (68.82%), followed by Proteobacteria (15.59%), Firmicutes (14.29%), and Bacteroidetes (1.30%). The predominant genus was Streptomyces (22.08%, 17 species), followed by Bacillus (6.49%, five species), Micromonospora (5.19%, four species), Microbacterium (5.19%, four species), and Kribbella (3.90%, three species). The most diverse isolates belonged to a high G+C Gram-positive group; in particular, the Streptomyces genus is a dominant genus in the high G+C Gram-positive group. There were 62 species and 33 genera bacteria isolated at 25°C (80.52%), 23 species, and 18 genera bacteria isolated at 4°C (29.87%). Meanwhile, only eight species and six genera bacteria could be isolated at 25°C and 4°C. Of the 77 species, six isolates related to six genera might be novel taxa. The results showed abundant bacterial species diversity in the soil sample from the Qamdo, Tibet Autonomous Region.     

Effects of Different Ambient Temperatures on Caecal Microbial Composition in Broilers

Short-term or acute temperature stress affect the immune responses and alters the gut microbiota of broilers, but the influences of long-term temperature stress on stress biomarkers and the intestinal microbiota remains largely unknown. Therefore, we examined the effect of three long-term ambient temperatures (high (HC), medium (MC), and low (LC) temperature groups) on the gene expression of broilers’ heat shock proteins (Hsps) and inflammation – related genes, as well as the caecal microbial composition. The results revealed that Hsp70 and Hsp90 levels in HC group significantly increased, and levels of Hsp70, Hsp90, IL-6, TNF-α, and NFKB1 in LC group were significantly higher than in MC group (p < 0.05). In comparison with the MC group, the proportion of Firmicutes increased in HC and LC groups, while that of Bacteroidetes decreased in LC group at phylum level (p < 0.05). At genus level, the proportion of Escherichia/Shigella, Phascolarctobacterium, Parabacteroides,and Enterococcus increased in HC group; the fraction of Faecalibacterium was higher in LC group; and the percentage of Barnesiella and Alistipes decreased in both HC and LC groups (p < 0.05). Functional analysis based on communities’ phylogenetic investigation revealed that the pathways involved in environmental information processing and metabolism were enriched in the HC group. Those involved in cellular processes and signaling, metabolism, and gene regulation were enriched in LC group. Hence, we conclude that the long-term temperature stress can greatly alter the intestinal microbial communities in broilers and may further affect the host’s immunity and health.     

Early social contact alters the community structure and functions of the faecal microbiome in suckling-growing piglets

Social contact during suckling, in an enriched social environment, can reduce the aggressive behaviours of piglets during regrouping at weaning, and improve their production performance and welfare. The aim of this study was to determine the possible impact of suckling social contact on gut microbes. We performed 16S rRNA sequencing to measure the faecal microbial structure and function in piglets experiencing social contact. Eighteen-litter piglets were allocated to two treatments: an early continuous social contact (CSC) group where piglets from adjacent pens shared a mutual pen starting at 14 days postpartum and a control (CON) group where piglets had no contact with individuals from adjacent pens during the suckling period. The piglets were regrouped at 36 days of age. The litter weights at 35 and 63 days of age were measured. Faecal samples were randomly collected at 16, 35, 42, and 63 days of age and faecal DNA was determined. The results showed that the litter weight of piglets in the CSC group was significantly decreased at 63 days compared with the CON group. Continuous social contact also significantly decreased the microbial richness at 16 and 35 days of age (P < 0.05). Firmicutes was the most abundant bacterial phylum in both groups at all detected time-points and the abundance increased with social contact. At the genus level, Lactobacillus was the most abundant bacterium after weaning and the abundance increased in the piglets with social contact. Compared with the faecal microbiota of control piglets, a total of 22 genera at 16 days, 20 genera at 35 days, 12 genera at 42 days, and 27 genera at 63 days in the faeces of CSC piglets were observed to be significantly different in abundance (linear discriminant analysis score > 3, P < 0.05). Furthermore, functional analysis of the microbial composition showed that the changes induced by early CSC mainly altered the relative abundance of metabolic and related pathways. The social contact notably had an effect on the abundance of microbial pathways for amino acid and carbohydrate metabolism. In conclusion, CSC changed the microbial composition in the faeces of piglets, which might have a negative effect on nutrient metabolism for the suckling-growing piglets. Our study provided new insight into the influence of social contact on the suckling-growing piglets.     

Bacterial communities in the rumen and feces of lactating Holstein dairy cows are not affected when fed reduced-fat dried distillers’ grains with solubles

Reduced-fat dried distillers’ grains with solubles (RF-DDGSs) are co-products of ethanol production and contain less fat than traditional distillers’ grains. The fat in corn is ~91% unsaturated, and it is toxic to rumen microorganisms so it could influence the composition of the rumen microbiome. It has been demonstrated that RF-DDGS is a suitable ration ingredient to support the high-producing dairy cow, and this feedstuff is a promising alternative protein source for lactating dairy cows. The current study aims to better understand the effect of RF-DDGS on the rumen and fecal bacterial composition in lactating dairy cows. Thirty-six multiparous (two or three), mid-lactation Holstein cows (BW = 680 ± 11 kg; 106 ± 27 DIM) were randomly assigned to two groups which were fed a control diet made up of corn, corn silage, and alfalfa hay supplemented with expeller soybean meal or with added RF-DDGS (20% of the DM) containing approximately 6.0% fat. Whole rumen contents (rumen fluid and digesta; esophageal tubing method) and feces (free-catch method) were collected on day 35 of the experimental period, after the 14-d acclimation period. Rumen contents and feces from each cow were used for DNA extraction. The bacterial community composition in rumen and fecal samples was assessed via the 16S rRNA gene by using the Illumina MiSeq sequencing platform. Bacteroidetes, Actinobacteria, and Firmicutes were the most abundant phyla in rumen contents. The fecal microbiota was dominated by the phyla Firmicutes and Bacteroidetes, as well as Actinobacteria and Chloroflexi. RF-DGGS increased bacterial richness, evenness, and Shannon diversity in both rumen and fecal samples and was associated with several taxa that had different abundance in treatment versus control comparisons. The RF-DGGS, however, did not significantly alter the bacterial community in the rumen or feces. In general, these findings demonstrated that dietary inclusion of RF-DDGS did not impose any serious short-term (within 30 days) health or production consequences, as would be expected. With this study, we present further evidence that inclusion of 20% (DM basis) RF-DDGS in the diet of lactating dairy cows can be done without consequence on the microbiome of the rumen.     

Senescence‐associated β‐galactosidase reveals the abundance of senescent CD8+ T cells in aging humans

Aging leads to a progressive functional decline of the immune system, rendering the elderly increasingly susceptible to disease and infection. The degree to which immune cell senescence contributes to this decline remains unclear, however, since markers that label immune cells with classical features of cellular senescence accurately and comprehensively have not been identified. Using a second‐generation fluorogenic substrate for β‐galactosidase and multi‐parameter flow cytometry, we demonstrate here that peripheral blood mononuclear cells (PBMCs) isolated from healthy humans increasingly display cells with high senescence‐associated β‐galactosidase (SA‐βGal) activity with advancing donor age. The greatest age‐associated increases were observed in CD8+ T‐cell populations, in which the fraction of cells with high SA‐βGal activity reached average levels of 64% in donors in their 60s. CD8+ T cells with high SA‐βGal activity, but not those with low SA‐βGal activity, were found to exhibit features of telomere dysfunction‐induced senescence and p16‐mediated senescence, were impaired in their ability to proliferate, developed in various T‐cell differentiation states, and had a gene expression signature consistent with the senescence state previously observed in human fibroblasts. Based on these results, we propose that senescent CD8+ T cells with classical features of cellular senescence accumulate to levels that are significantly higher than previously reported and additionally provide a simple yet robust method for the isolation and characterization of senescent CD8+ T cells with predictive potential for biological age.     

小鼠阴道菌群紊乱模型的建立

目的建立小鼠阴道菌群紊乱模型,为调整阴道菌群紊乱的药物研发提供模型参考。方法采用雌激素化的C57BL/6小鼠经阴道以不同处理方式(链霉素50μg/只,加德纳菌50μL/只,链霉素50μg/只+抗链霉素加德纳菌50μL/只,每种处理方式各70只/组)诱导小鼠阴道菌群紊乱模型,采用细菌16S rDNA高通量测序考察造模后第1、第2、第3、第5、第7、第9、第11天内加德纳菌在阴道内的定植情况,以及阴道细菌结构和细菌生物多样性,并通过显微镜观察阴道组织的病理改变,比较3种造模方法的差异。另采用阳性药物(定君生,成分为德氏乳杆菌)对模型进行验证。结果采用链霉素联合抗链霉素加德纳菌能诱导形成典型的阴道菌群紊乱模型,造模后可见加德纳菌在阴道内的定植增多,优势菌以铜绿假单胞菌为主,且阴道细菌生物多样性增加,阴道组织可见明显的炎症浸润和上皮细胞坏死等病理改变。定君生能显著减少加德纳菌在阴道内的定植,减少阴道内的细菌生物多样性,并能显著改善阴道组织病理变化。结论采用链霉素联合抗链霉素加德纳菌诱导的小鼠阴道菌群紊乱模型方法更佳,模型的细菌学和组织病理学改变,以及对药物的反应性与临床有一定相似,具有临床应用价值。     

IgA肾病患者与健康人肠道菌群的比较

目的通过16S rRNA高通量基因测序方法对IgA肾病患者与健康人的肠道菌群进行比较。方法纳入生活于同一地区的40例IgA肾病患者与10例健康人,收集研究对象的新鲜粪便样本,提取粪便细菌总DNA,通过PCR扩增后上机测序,然后进行可操作分类单元聚类、物种分类分析及Alpha多样性分析、Beta多样性分析,最后比较两组之间的肠道菌群差异。结果与健康人相比,IgA肾病患者肠道菌群丰富度指数(Ace、Chao1)下降(u=2.308,P=0.033;u=2.259,P=0.039),多样性指数(Shannon、Simpson)升高(u=5.370,P0.001;u=4.601,P=0.007);相对丰度方面,IgA肾病患者的厚壁菌门、拟杆菌门、放线菌门细菌数量增加(t=2.301,P=0.037;t=6.729,P=0.005;t=5.285,P=0.006),而变形菌门细菌数量减少(t=4.138,P=0.009);拟杆菌属、链球菌属细菌数量增加(t=9.037,P=0.003;t=6.001,P=0.008),而unidentified_Enterobacteriaceae数量减少(t=2.198,P=0.033)。PCoA图提示两组肠道菌群有显著差异。LDA差异贡献分析发现两组之间共有15个物种存在显著差异,其中造成显著差异影响力最大的5个物种依次是γ-变形菌纲、unidentified_Enterobacteriaceae、肠杆菌科、肠杆菌目、变形菌门(t=9.930,P=0.002;t=2.198,P=0.033;t=2.604,P=0.015;t=2.393,P=0.021;t=4.138,P=0.009),它们刚好落在同一个进化树上,在IgA肾病组的相对丰度显著降低。结论 IgA肾病患者存在肠道菌群失调,显著减少的肠杆菌科的未知属可能是IgA肾病的特征菌,其对机体免疫的影响及在IgA肾病发生发展中的作用尚不清楚,进一步研究可能为IgA肾病的防治提供新的靶点。