Metagenomic dissection of the canine gut microbiota: insights into taxonomic,metabolic and nutritional features

Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.     

Metagenomic assessment of the Cebus apella gut microbiota

Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero‐tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in‐depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model.     

Characteristic gut microbiota and metabolic changes in patients with pulmonary tuberculosis

Intestinal flora provides an important contribution to the development of pulmonary tuberculosis (PTB). We performed a cross-sectional study in 52 healthy controls (HCs) and 83 patients with untreated active PTB to assess the differences in their microbiomic and metabolic profiles in faeces via V3-V4 16S rRNA gene sequencing and gas chromatography–mass spectrometry. Patients with PTB had considerable reductions in phylogenetic alpha diversity and the production of short-chain fatty acids, dysbiosis of the intestinal flora and alterations in the faecal metabolomics composition compared with HCs. Significant alterations in faecal metabolites were associated with changes in the relative abundance of specific genera. Our study describes the imbalance of the gut microbiota and altered faecal metabolomics profiles in patients with PTB; the results indicate that the gut microbiota and faecal metabolomic profiles can be used as potential preventive and therapeutic targets for PTB.     

Alterations in the gut microbiota of patients with acquired immune deficiency syndrome

Acquired immune deficiency syndrome (AIDS), caused by infection with human immunodeficiency virus (HIV), is associated with gastrointestinal disease, systemic immune activation and changes in the gut microbiota. Here, we aim to investigate the gut microbiota patterns of HIV‐infected individuals and HIV‐uninfected individuals in populations from South China. We enrolled 33 patients with HIV (14 participants treated with highly active antiretroviral therapy [HAART] for more than 3 months; the remaining 19 individuals had not received treatment) and 35 healthy controls (HC) for a cross‐sectional comparison of gut microbiota using stool samples. Gut microbial communities were profiled by sequencing the bacterial 16S rRNA genes. Dysbiosis was more common among patients with AIDS compared with healthy individuals. Dysbiosis was characterized by decreased α‐diversity, low mean counts of Bacteroidetes, Faecalibacterium, Prevotella, Bacteroides vulgatus, Dialister and Roseburia inulnivorans, and high mean counts of Proteobacteria, Enterococcus, Streptococcus, Lactobacillus, Lachnociostridium, Ruminococcus gnavus and Streptococcus vestibularis. Increased abundance of Bacilli was observed in homosexual patients. Proteobacteria were higher among heterosexual patients with HIV infections. Tenericutes were higher among patients with history of intravenous drug abuse. Restoration of gut microbiota diversity and a significant increase in abundance of Faecalibacterium, Blautia and Bacteroides were found in patients receiving HAART compared to those who did not receive. HIV infection‐associated dysbiosis is characterized by decreased levels of α‐diversity and Bacteroidetes, increased levels of Proteobacteria and the alterations of gut microbiota correlate with the route of HIV transmission. The imbalanced faecal microbiota of HIV infection is partially restored after therapy.     

Characterization of gut microbiota composition in HIV-infected patients with metabolic syndrome

Journal of Physiology and Biochemistry - The presence of metabolic syndrome (MS) per se or its separated components in HIV-infected patients contributes to an accelerated aging and increased...     

Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions

The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in‐depth characterization of gut bacterial diversity from field (native and invasive range) and lab‐reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab‐reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.     

包衣益生菌对功能性便秘患者肠道菌群的影响和临床疗效

观察包衣益生菌产品对功能性便秘患者的疗效及对患者肠道菌群的影响。

收集2022年1月到3月大连市第二人民医院消化内科就诊的功能性便秘患者10例,患者均服用包衣益生菌产品7 d,使用16S rDNA测序技术检测患者服用前后及停药后3 d和7 d的肠道菌群变化情况,评价患者便秘情况是否改善。

治疗后患者便秘相关生活质量（PAC-QOL）评分、便秘严重程度（CSI）评分均较治疗前显著降低（均P＜0.01）,粪便性状好转。停用3 d和7 d时,患者肠道菌群Ace和Chao1指数均较服用前升高（均P＜0.05）。服用后,在属水平上,患者肠道Klebsiella、Lactococcus、Bacteroides相对丰度上升,Blautia和Anaerostipes相对丰度下降;在种水平上,肠道Lactobacillus plantarum、Klebsiella quasipneumoniae、Enterococcus faecium和Megasphaera elsdenii相对丰度升高,Anaerostipes hadrus相对丰度降低。

包衣益生菌产品对功能性便秘有一定的改善作用,能够增加患者肠道菌群的丰度,使肠道菌群结构更加接近健康人群。

     

便秘型肠易激综合征患者肠道菌群变化特点及双歧杆菌四联活菌片的疗效观察

研究便秘型肠易激综合征（IBS-C）患者肠道菌群变化特点,并进一步分析双歧杆菌四联活菌片对其的干预效果。

选取2020年2月至2021年11月于我院消化内科就诊的162例IBS-C患者为研究组;选择同期113例健康体检者作为对照组。采用16S rDNA高通量测序法检测受试者肠道菌群的构成,分析菌群多样性,比较双歧杆菌四联活菌片干预前后IBS-C患者肠道菌群变化特点及便秘症状相关指标变化情况。

研究组患者肠道菌群Ace指数（P=0.001）、Chao指数（P＜0.001）、Shannon指数（P=0.020）、Sobs指数（P＜0.001）均显著低于对照组。在门水平上,研究组患者肠道厚壁菌门和变形菌门的丰度均显著高于对照组,而拟杆菌门丰度均显著低于对照组。双歧杆菌四联活菌片干预后,患者肠道厚壁菌门和变形菌门丰度均显著下降,拟杆菌门丰度显著提高。在属水平上,研究组患者肠道乳杆菌属和双歧杆菌属丰度均显著低于对照组。双歧杆菌四联活菌片干预后,患者肠道乳杆菌属、双歧杆菌属、粪杆菌属丰度均显著上升。干预后IBS-C患者的便秘症状积分（P＜0.001）、GIQLI评分（P＜0.001）、WC评分（P＜0.001）、PAC-QOL评分（P=0.005）均较干预前差异显著,排便次数也显著增加（P＜0.001）。

IBS-C患者肠道菌群显著紊乱,双歧杆菌四联活菌片能在一定程度上调节患者肠道菌群失衡,同时能够改善胃肠道功能,缓解便秘。

     

人工饲养恒河猴幼猴不同肠段微生物宏基因组学研究

目的以恒河猴幼猴为模型,采用16S rRNA宏基因组方法探讨十二指肠、盲肠、直肠的菌群组成。方法收集4例健康幼猴十二指肠、盲肠、直肠样本,提取细菌总DNA,采用新一代高通量测序技术对16S rRNA基因的V3-V4高变区测序,分析比较菌群结构及多样性。结果 (1)门水平各肠段微生物优势菌群主要为硬壁菌门、变形菌门及拟杆菌门,在各肠段中的占比总和超过88%;(2)属水平,十二指肠中以芽胞杆菌属等为优势菌属,盲肠中以螺杆菌属、颤杆菌属、孢杆菌属等为优势菌属,直肠中以乳酸菌属、链球菌属、颤杆菌属等为优势菌属;(3)各肠段微生物功能差异较大,十二指肠主要承担营养物质的消化吸收,盲肠主要承担细胞及遗传物质的合成,直肠主要承担调节机体免疫力、抗感染等功能。结论各肠段菌群组成差异较大;各肠段细菌功能差异较大,且与其生理功能有一定关联;在肠道菌群研究中,应充分考虑粪便样品微生物的组成是否能够完全代表肠道微生物的组成。     

规定饮食条件下不同性别和年龄恒河猴的肠道菌群差异探讨

探讨规范统一的饮食在不受饮食因素干扰前提下不同性别和年龄恒河猴肠道菌群的差异。

将38只恒河猴按性别和年龄分为6组,规定饮食喂养3个月,收集粪便标本,应用16S rRNA测序和生物信息学分析探讨不同性别和年龄恒河猴肠道菌群的差异。

雄性和雌性恒河猴肠道菌群多样性无显著差异,但雌性群体中Epsilonproteobacteria和Helicobacter macacae的丰度显著增加。成年和老年恒河猴肠道菌群的多样性均显著高于幼年,Rikenellaceae、Christensenellaceae和Prevotella的丰度在老年群体中显著增加。

恒河猴的肠道菌群受性别和年龄的影响,尤其是与代谢和精神疾病相关的Rikenellaceae、Christensenellaceae和Prevotella在老龄恒河猴肠道菌群丰度更高。这些特定肠道菌群在不同性别和不同生命阶段调节机体生理或行为过程中的功能有待进一步研究。

     

高原红细胞增多症患者肠道菌群变化研究

目的探究高原红细胞增多症患者肠道菌群变化及相关意义。方法招募西藏那曲地区血红蛋白(hemoglobin, HB)含量高于210 g/L的高原红细胞增多症患者12人,对照组(170 g/LHB210 g/L)42人,采集粪便、血液等样本。从中选取高原红细胞增多症患者9人,对照组16人粪便样本提取DNA,进行16S rRNA测序分析。结果高原红细胞增多症患者的血红蛋白水平以及红细胞比容显著高于对照组。红细胞增多症患者的肠道菌群整体结构改变不明显,多样性没有显著差异。红细胞增多症患者的粪便菌群出现厚壁菌门中梭状芽胞杆菌BB60属、纺锤链杆菌属、厌氧棒杆菌属、霍氏真杆菌,变形菌门中假单胞菌属,拟杆菌门中副拟杆菌属丰度的显著增高。这些菌属改变经KEGG预测分析显示与代谢紊乱相关。斯皮尔曼分析显示多种菌群改变与血红蛋白水平以及红细胞比容正相关。结论高原红细胞增多症患者肠道菌群出现紊乱,菌群变化与代谢紊乱和红细胞增多相关。     

老年结直肠癌患者肠道菌群变化与机体免疫炎症营养相关性

目的探讨老年结直肠癌患者肠道菌群变化与机体免疫、炎症、营养指标的相关性,为结直肠癌的防治提供参考。方法纳入2016年1月至2018年6月在我院接受治疗的老年结直肠癌患者30例和同期健康查体的老年人群30例,收集粪便标本,采用FloraCheck~(TM)高通量测序技术对粪便样本中所有细菌的16S rRNA V3-V4区进行DNA测序,序列通过MiSeq 16S宏基因组APP及QIIME软件,分析两组人群间属水平上显著差异性菌群。比较两组人群炎性指标(TNF-α、IL-6、IL-1、IL-12)、营养指标(总蛋白、白蛋白、前白蛋白、转铁蛋白)和免疫指标(CD3~+、CD4~+、CD8~+、NK)的差异。分析老年结直肠癌患者肠道菌群变化与营养、炎症、免疫的内在联系。结果老年结直肠癌组和老年健康组人群免疫指标CD3~+、CD4~+、CD8~+、NK和CD4~+/CD8~+比较差异无统计学意义;炎性指标老年结直肠癌组TNF-α含量较对照组明显增高(t=3.769,P=0.001),两组人群IL-1、IL-6、IL-12比较差异无统计学意义;营养指标老年结直肠癌组白蛋白、前白蛋白较对照组明显下降(t=-4.107,P=0.001;t=-4.366,P=0.001),两组人群总蛋白、转铁蛋白比较差异无统计学意义。老年结直肠癌组肠道差异性菌属变化,包括Eubacterium、Ruminococcaceae_UCG-002、Peptostreptococcus、Porphyromonas和部分炎症指标、营养指标、免疫指标有明显相关性。结论老年结直肠癌患者肠道菌群结构和功能异常,可能是导致患者机体免疫损伤、炎症反应、营养不佳的主要原因之一。有针对性地对肠道菌群结构进行优化,改善肠道菌群对宿主的影响,是一种帮助老年结直肠癌患者促进健康的策略。     

High-resolution analysis of gut environment and bacterial microbiota reveals functional compartmentation of the gut in wood-feeding higher termites (Nasutitermes spp.)

Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H(2), O(2), pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H(2) to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.     

慢性萎缩性胃炎患者肠道菌群特征

探讨不同炎症程度慢性萎缩性胃炎（CAG）患者肠道菌群特征,为该类患者的治疗提供参考。

对36例健康人（健康对照组）和8例轻度炎症（轻度炎症组）、26例中度炎症（中度炎症组）、8例重度炎症（重度炎症组）的CAG患者的粪便样本进行16S rRNA基因高通量测序（V4—V5区）,采用Sobs、Shannon、Simpson、Ace、Chao指数评估4组对象肠道菌群的物种丰富度与多样性;采用PLS-DA分析评估4组对象肠道微生物群落结构;采用LDA与LEfSe分析确定4组对象相对丰度存在显著差异的肠道菌群;采用PICRUSt预测CAG患者显著富集肠道菌属的代谢通路信息。

与健康对照组相比,轻、中、重度炎症组患者肠道菌群Sobs、Ace、Chao、Simpson指数有降低趋势,但差异均无统计学意义（均P＞0.05）。Ruminococcus_gnavus_group、norank_f_Ruminococcaceae、Erysipelatoclostridium、Actinomyces在轻度炎症组中显著富集,Flavonifractor、Sellimonas在中度炎症组中显著富集,Eubacterium_rectale_group、Erysipelotrichaceae_UCG-003、Tyzzerella_3、Coprococcus_1、Candidatus_Soleaferrea在重度炎症组中显著富集。此外,Lachnospiraceae_UCG-004、Eubacterium_nodatum_group的丰度在健康对照组、轻度炎症组、中度炎症组、重度炎症组中呈递增趋势;Anaerostipes、Ruminiclostridium_9、Halomonas、Pelagibacterium的丰度在健康对照组、轻度炎症组、中度炎症组、重度炎症组中呈递减趋势,但差异均无统计学意义（均P＞0.05）。PICRUSt分析结果显示4组对象肠道菌群代谢通路相似,但是代谢通路的丰度不同,其中重度炎症组患者肠道菌群代谢功能潜力高于健康对照组、轻度炎症组和中度炎症组。

CAG患者肠道菌群变化的总体特征为产丁酸盐的菌属丰度减少,促炎菌属的丰度增加。促炎菌属可能通过附着于肠道上皮导致黏膜屏障受损和肠道通透性增加,影响宿主免疫反应,引起炎症。

     

Drastic changes in fecal and mucosa-associated microbiota in adult patients with short bowel syndrome

Short bowel syndrome (SBS) is observed in Humans after a large resection of gut. Since the remnant colon and its associated microbiota play a major role in the outcome of patients with SBS, we studied the overall qualitative and quantitative microbiota composition of SBS adult patients compared to controls. The population was composed of 11 SBS type II patients (with a jejuno-colonic anastomosis) and 8 controls without intestinal pathology. SBS patients had 38 ± 30 cm remnant small bowel length and 66 ± 19% of residual colon. The repartition of proteins, lipids, carbohydrates and fibres was expressed as % of total oral intake in patients and controls. The microbiota was profiled from stool and biopsy samples with temporal temperature gradient gel electrophoresis and quantitative PCR. We show here that microbiota of SBS patients is unbalanced with a high prevalence of Lactobacillus along with a sub-dominant presence and poor diversity of Clostridium leptum, Clostridium coccoides and Bacteroidetes. In addition, Lactobacillus mucosae was detected within the fecal and mucosa-associated microbiota of SBS patients, whereas it remained undetectable in controls. Thus, in SBS the microbial composition was deeply altered in fecal and mucosal samples, with a shift between dominant and sub-dominant microbial groups and the prevalence of L. mucosae.     

血液恶性肿瘤患者肠道菌群分析

目的 将血液恶性肿瘤患者肠道菌群与健康个体进行比较,观察血液肿瘤患者肠道菌群结构的变化,探讨肠道菌群与血液恶性肿瘤发生发展的联系。方法 收集血液恶性肿瘤患者与健康志愿者粪便样品,提取样品中菌群总DNA,然后通过变性凝胶梯度电泳（DGGE）技术分析肠道菌群多样性和差异性。结果 血液恶性肿瘤组与健康组肠道菌群的DGGE指纹图谱有明显差异。与正常组相比,患者组肠道大肠埃希菌呈现过度增长趋势,有益菌柔嫩梭菌减少或缺失,某些患者肠道内一些细菌呈现特异性增长,如粪肠球菌、硫磺肠球菌、约氏不动杆菌等。结论 与健康对照组相比,血液恶性肿瘤患者肠道菌群结构与多样性发生改变,这可能为血液恶性肿瘤早期抗感染提供实验依据。     

Comparative analysis of the gut microbiota in distinct statin response patients in East China

Statin response shows great interindividual variations. Recently, emerging studies have shown that gut microbiota is linked to therapeutic responses to drugs, including statins. However, the association between the gut bacteria composition and statin response is still unclear. In this study, gut microbiota of 202 hyperlipidemic patients with statin sensitive (SS) response and statin resistant (SR) response in East China were investigated by high throughput sequencing to compare the gut bacteria composition and biodiversity in distinct statin response patients. Higher biodiversity was detected in Group SS than Group SR. Specifically, group SS showed significantly increased proportion of genera Lactobacillus (P = 0.001), Eubacterium (P = 0.004), Faecalibacterium (P = 0.005), and Bifidobacterium (P = 0.002) and decreased proportion of genus Clostridium (P = 0.001) compared to Group SR. The results indicated that higher gut biodiversity was associated with statin sensitive response. The increased genera Lactobacillus, Eubacterium, Faecalibacterium, Bifidobacterium, and decreased genus Clostridium in patient gut microbiota may predict patient's statin response, and hence may guide statin dosage adjustments.