Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.
Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology* ; Escherichia coli/classification* ; Gastrointestinal Microbiome/genetics* ; Metagenomics ; East Asian People

: Bacteroides, as one of the most abundant and diverse genera in the human gut, is regarded as a window into the study of gut microbiota-host interactions. Currently, CRISPR/Cas-based gene editing systems targeting Bacteroides have been widely applied, while the large size of Cas nucleases limits their potential application scenarios (such as in situ gut Bacteroides editing based on phage delivery). Therefore, this study aims to develop a compact and highly efficient genetic editing tool in Bacteroides., We developed a miniaturized CRISPR/Cas gene editing system for human gut Bacteroides. First, the editing capabilities of different miniaturized CRISPR/Cas systems, including AsCas12f, CasΦ2, and ISDge10, were evaluated in Bacteroides fragilis. Subsequently, the editing capability of AsCas12f was assessed across various Bacteroides species, and the size of this system was further optimized. The results demonstrated that the CRISPR/AsCas12f genome editing system exhibited the highest editing efficiency in B. fragilis. The CRISPR/AsCas12f system achieved efficient genome editing in B. fragilis, Bacteroides thetaiotaomicron, and Phocaeicola vulgatus. Furthermore, with a repair template of 500 bp homologous arms, the editing efficiency remained as high as 94.7%. In conclusion, CRISPR/AsCas12f can serve as a chassis tool enzyme for the development of Bacteroides-based miniature gene editors and derivative technologies, laying a foundation for the further development of gene editing technology for Bacteroides.
CRISPR-Cas Systems/genetics* ; Gene Editing/methods* ; Bacteroides/genetics* ; Humans ; Gastrointestinal Microbiome/genetics* ; Bacteroides fragilis/genetics*

BACKGROUND/AIMS: Several clinical trials have revealed various advantages for probiotics in inflammatory bowel disease (IBD). The aim of this study was to further investigate the effects of probiotic yogurt consumption on gut microbiota in patients with this disease. METHODS: A total of 305 participants were divided into three groups; group A (IBD patients receiving probiotic yogurt; n=105), group B (IBD patients receiving placebo; n=105), and control group (healthy individuals receiving probiotic yogurt; n=95). Stool samples were collected both before and after 8 weeks of intervention; and population of Lactobacillus, Bifidobacterium and Bacteroides in the stool specimens was measured by Taqman real-time PCR method. ': By the end of the intervention, no significant variations in the mean weight and body mass index were observed between three groups (p>0.05). However, the mean numbers of Lactobacillus, Bifidobacterium, and Bacteroides in group A were significantly increased compared to group B (p<0.001, p<0.001, and p<0.01, respectively). There were also significant differences in the mean numbers of either of three bacteria between group A and the healthy control group; however, these differences between two groups were observed both at baseline and the end of the intervention. CONCLUSIONS: Consumption of probiotic yogurt by patients with IBD may help to improve intestinal function by increasing the number of probiotic bacteria in the intestine and colon. However, many more studies are required in order to prove the concept.
Adult ; Bacteroides/genetics ; Bifidobacterium/genetics ; DNA, Bacterial/analysis ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*drug therapy ; Intestines/microbiology ; Lactobacillus/genetics ; Male ; Middle Aged ; Placebo Effect ; Probiotics/*therapeutic use ; Real-Time Polymerase Chain Reaction

OBJECTIVETo investigate the effect of triggering receptor expressed on myeloid cells 1 (TREM-1) vshRNA vector on expression of inflammatory cytokines and survival rate in septic mice infected by Bacteroides fragilis.

METHODS(1) TREM-1 vshRNA vector was constructed. Bacteroides fragilis (2.5 x 10(9) CFU/mL, 0.5 mL) was intraperitoneally injected in each mouse, and septic model was reproduced after 12 hours. (2) One hundred and fifteen mice were divided into healthy control group (n = 3, HC), sepsis group (n = 28, S), TREM-1 vshRNA group (n = 28, T), TREM-1 vshRNA hd group (n = 28, Th), GFP group (n = 28, G) according to random number table. Mice in S, T, Th, G groups were firstly injected with isotonic saline, TREM-1 vshRNA 2 x 10(8) TU, TREM-1 vshRNA 1 x 10(8) TU, GFP siRNA through tail vein, and then sepsis was induced after 1 hour. Mice in HC group were injected with equal volume of isotonic saline through tail vein. Three mice in each group were sacrificed after 12 hours for determination of plasma level of TNF-alpha, IL-1 beta and IL-6, and level of TREM-1mRNA and its protein in hepatic tissue. The survival rate of other mice in each group was monitored for 72 hours. (3) In 125 mice sepsis was reproduced, among them 100 mice were injected with TREM-1 vshRNA 2 x 10(8) TU after 1, 2, 4, 6 hours through tail vein (25 mice at each time point), other 25 mice were injected with equal volume of isotonic saline as control. The survival rate of mice in each group was recorded 72 hours after injection.

RESULTS(1) Compared with those in S group, the plasma level of TNF-alpha, IL-1 beta and IL-6 lowered in T and Th groups (P < 0.05), especially in T group, while those in G group showed no obvious difference (P > 0.05). (2) Compared with those in G group, the level of TREM-1mRNA and its protein in hepatic tissue in T and Th groups decreased (P < 0.01), especially in T group. (3) The survival rate of mice in S and G group was 16%, which was obviously lower than that in T and Th groups (76%, 44%, respectively, P < 0.05 or P < 0.01). (4) The survival rate of mice at 1, 2, 4, 6 hours after injection was 72%, 56%, 40%, 16%, respectively, while all that except at 6 hour after injection were higher significantly than that of control (P < 0.05 or P < 0.01).

CONCLUSIONSThe intervention with TREM-1 vshRNA can effectively decrease hepatic level of TREM-1 in septic mice induced by Bacteroides fragilis, inhibit inflammatory response, and improve the survival rate.

Animals ; Bacteroides fragilis ; Disease Models, Animal ; Genetic Vectors ; Lentivirus ; Male ; Mice ; Mice, Inbred BALB C ; RNA, Messenger ; metabolism ; Receptors, Immunologic ; genetics ; Sepsis ; metabolism ; microbiology ; therapy ; Virosomes