Metagenomic surveillance and comparative genomic analysis of Chlamydia psittaci in patients with pneumonia.

Chlamydia psittaci, a strictly intracellular bacterium, is an underestimated etiologic agent leading to infections in a broad range of animals and mild illness or pneumonia in humans. In this study, the metagenomes of bronchoalveolar lavage fluids from the patients with pneumonia were sequenced and highly abundant C. psittaci was found. The target-enriched metagenomic reads were recruited to reconstruct draft genomes with more than 99% completeness. Two C. psittaci strains from novel sequence types were detected and these were closely related to the animal-borne isolates derived from the lineages of ST43 and ST28, indicating the zoonotic transmissions of C. psittaci would benefit its prevalence worldwide. Comparative genomic analysis combined with public isolate genomes revealed that the pan-genome of C. psittaci possessed a more stable gene repertoire than those of other extracellular bacteria, with ~90% of the genes per genome being conserved core genes. Furthermore, the evidence for significantly positive selection was identified in 20 virulence-associated gene products, particularly bacterial membrane-embedded proteins and type three secretion machines, which may play important roles in the pathogen-host interactions. This survey uncovered novel strains of C. psittaci causing pneumonia and the evolutionary analysis characterized prominent gene candidates involved in bacterial adaptation to immune pressures. The metagenomic approach is of significance to the surveillance of difficult-to-culture intracellular pathogens and the research into molecular epidemiology and evolutionary biology of C. psittaci.

Characterization of CRISPR-Cas systems in Bifidobacterium breve.

The clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system is an important adaptive immune system for bacteria to resist foreign DNA infection, which has been widely used in genotyping and gene editing. To provide a theoretical basis for the application of the CRISPR-Cas system in Bifidobacterium breve, the occurrence and diversity of CRISPR-Cas systems were analysed in 150 B. breve strains. Specifically, 47 % (71/150) of B. breve genomes possessed the CRISPR-Cas system, and type I-C CRISPR-Cas system was the most widely distributed among those strains. The spacer sequences present in B. breve can be used as a genotyping marker. Additionally, the phage assembly-related proteins were important targets of the type I-C CRISPR-Cas system in B. breve, and the protospacer adjacent motif sequences were further characterized in B. breve type I-C system as 5'-TTC-3'. All these results might provide a molecular basis for the development of endogenous genome editing tools in B. breve.

[Effect of acupuncture for regulating spleen and stomach on aspirin resistance in patients with type 2 diabetes mellitus: a randomized controlled trial].

OBJECTIVE: To observe the effect of acupuncture for regulating spleen and stomach on aspirin resistance in patients with type 2 diabetes mellitus (T2DM) and explore the effect mechanism. METHODS: A total of 68 T2DM patients complicated with aspirin resistance were randomized into an observation group and a control group, 34 cases in each one. On the base of the conventional treatment for diabetes, aspirin enteric-coated tablets were prescribed for oral administration, 100 mg each time, once daily in the control group. In the observation group, on the basis of the treatment as the control group, acupuncture was used for regulating spleen and stomach at Zhongwan (CV 12), Zusanli (ST 36), Yinlingquan (SP 9), Hegu (LI 4), etc., once daily. The treatment for 1 week was as one course and 4 courses of treatment were required totally in two groups. Before and After treatment, the indexes of platelet function (platelet aggregation rate [PAG] and salicylic acid concentration), the indexes of vascular endothelial function (6-keone prostaglandin F1α[6-keto-PGF1α], thromin B2 [TXB2] and cyclooxysynthase-2 [COX-2]), blood glucose (fasting plasma glucose [FPG], 2 h plasma glucose [2h PG] and glycosylated hemoglobin [HbA1c]), insulin resistance index (HOMA-IR), blood lipid indexes (total cholesterol [TC], triacylglycerol [TG], high-density lipoprotein cholesterol [HDL-C] and low-density lipoprotein cholesterol [LDL-C]) and the total score of TCM symptoms were observed in the patients of two groups. Clinical therapeutic effect and safety was compared in the patients between the two groups after treatment and the recurrence rate of cardiocerebrovascular events was followed up 6 months after treatment. RESULTS: After treatment, PAG, salicylic acid concentration, TXB2, COX-2, FPG, 2h PG, HbA1c, HOMA-IR, LDL-C, TC, TG and the total scores of TCM symptoms were all reduced as compared with those before treatment in the two groups (P<0.01, P<0.05), and 6-keto-PGF1αand HDL-C were increased as compared with those before treatment in the two groups (P<0.01, P<0.05). In comparison with the control group, the aforementioned indexes in the observation group were all improved significantly (P<0.01). The total effective rate was 91.2% (31/34) in the observation group, higher than 70.6% (24/34) in the control group (P<0.05). In follow up visit, the recurrence rate of cardiocerebrovascular events was 14.7% (5/34) in the observation group, lower than 29.4% (10/34) in the control group (P<0.05). The therapies were safe and had no obvious adverse reactions in both two groups. CONCLUSION: Acupuncture for regulating spleen and stomach combined with aspirin enteric-coated tablets relieve insulin resistance and reduces blood glucose and lipid as well as the recurrence rate of cardiocerebrovascular events in the patients with T2DM, which is probably related to the regulation of insulin resistance and the improvement of vascular endothelial function. This combined therapy achieves the better effect on aspirin resistance as compared with simple aspirin enteric-coated tablets.

Comparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus.

Lactobacillus acidophilus is a common kind of lactic acid bacteria usually found in the human gastrointestinal tract, oral cavity, vagina, and various fermented foods. At present, many studies have focused on the probiotic function and industrial application of L. acidophilus. Additionally, dozens of L. acidophilus strains have been genome sequenced, but there has been no research to compare them at the genomic level. In this study, 46 strains of L. acidophilus were performed comparative analyses to explore their genetic diversity. The results showed that all the L. acidophilus strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition of bacteriocin operon, CRISPR-Cas systems and prophages mainly. Additionally, L. acidophilus was a pan-genome open species with a difference in carbohydrates utilization, antibiotic resistance, EPS operon, surface layer protein operon and other functional gene composition. This work provides a better understanding of L. acidophilus from a genetic perspective, and offers a frame for the biotechnological potentiality of this species.

Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons.

Bifidobacterium longum is one of the most widely distributed and abundant Bifidobacterium in the human intestine, and has been proven to have a variety of physiological functions. In this study, 80 strains of B. longum isolated from human subjects were classified into subspecies by ANI and phylogenetic analyses, and the functional genes were compared. The results showed that there were significant differences in carbohydrate metabolism between the two subspecies, which determined their preference for human milk oligosaccharides or plant-derived carbohydrates. The predicted exopolysaccharide (EPS) gene clusters had large variability within species but without difference at the subspecies level. Four subtype CRISPR-Cas systems presented in B. longum, while the subtypes I-U and II-C only existed in B. longum subsp. longum. The bacteriocin operons in B. longum subsp. infantis were more widely distributed compared with B. longum subsp. longum. In conclusion, this study revealed the similarities and differences between B. longum subsp. infantis and B. longum subsp. longum, which could provide a theoretical basis for further exploring the probiotic characteristics of B. longum.

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa.

BACKGROUND: Lactobacillus gasseri as a probiotic has history of safe consumption is prevalent in infants and adults gut microbiota to maintain gut homeostasis. RESULTS: In this study, to explore the genomic diversity and mine potential probiotic characteristics of L. gasseri, 92 strains of L. gasseri were isolated from Chinese human feces and identified based on 16 s rDNA sequencing, after draft genomes sequencing, further average nucleotide identity (ANI) value and phylogenetic analysis reclassified them as L. paragasseri (n = 79) and L. gasseri (n = 13), respectively. Their pan/core-genomes were determined, revealing that L. paragasseri had an open pan-genome. Comparative analysis was carried out to identify genetic features, and the results indicated that 39 strains of L. paragasseri harboured Type II-A CRISPR-Cas system while 12 strains of L. gasseri contained Type I-E and II-A CRISPR-Cas systems. Bacteriocin operons and the number of carbohydrate-active enzymes were significantly different between the two species. CONCLUSIONS: This is the first time to study pan/core-genome of L. gasseri and L. paragasseri, and compare their genetic diversity, and all the results provided better understating on genetics of the two species.