SMRT sequencing and ddPCR reveal the complexity of developmental trajectories and temporal dynamics of gut bifidobacterial communities in infants

Infant intestinal microbiome is closely linked with health and risk of disease. Bifidobacterium are important components of the infant gut and are known to confer various health effects on the host. However, few studies have described the precise composition and dynamics of early infant gut bifidobacterial communities. Thus, this was a pilot study aiming to describe the developmental trajectories and temporal dynamics of bifidobacterial communities in infants before 6 months of age. A total of 28 fecal samples from 4 infants(GF, ZZ, QM, TN, respectively)were collected and analyzed after 5, 15, 30, 60, 90, 120, 150, and 180 days of birth by a bifidobacteria-target method(based on single-molecule real-time sequencing of partial bifidobacterial rpsK genes)in conjunction with droplet digital polymerase chain reaction(ddPCR). The infant fecal microbiota comprised a total of 11 bifidobacterial species, including 4 major species, i.e., B. dentium(37.35%), B. catenulatum(32.04%), B. breve(22.24%), and B. animalis(8.02%). The infant microbiota showed highly individualized developmental trajectories. The leading species for GF was B. catenulatum, with a relatively stable developmental trajectory. In ZZ, B. breve was enriched, and the developmental trajectory was rather fluctuating. The most abundant species for QM and TN was B. dentium. The developmental trajectory of B. dentium in QM showed a trend of gradual decrease, whereas an opposite trend was seen in samples of TN. The results of ddPCR confirmed large variations in quantities of bifidobacteria between infants and suggested discordances in temporal dynamics of bifidobacterial communities during the first half year of infancy. In conclusion, our results suggested that the early infant gut bifidobacterial microbiota was highly complex and temporal dynamics, with individualized developmental trajectories, which should be considered in future research of infant gut microbiota.

Complete genome of Cobetia marina JCM 21022T and phylogenomic analysis of the family Halomonadaceae

Cobetia marina is a model proteobacteria in researches on marine biofouling. Its taxonomic nomenclature has been revised many times over the past few decades. ~To better understand the role of the surface-associated lifestyle of C. marina and the phylogeny of the family Halomonadaceae, we sequenced the entire genome of C. marina JCM 21022 ~T using single molecule real-time sequencing technology(SMR^T) and performed comparative genomics and phylogenomics analyses. ~The circular chromosome was 4 176 300 bp with an average GC content of 62.44% and contained 3 611 predicted coding sequences, 72 t RNA genes, and 21 r RNA genes. ~The C. marina JCM 21022 ~T genome contained a set of crucial genes involved in surface colonization processes. ~The comparative genome analysis indicated the significant diff erences between C. marina JCM 21022 ~T and Cobetia amphilecti KMM 296(formerly named C. marina KMM 296) resulted from sequence insertions or deletions and chromosomal recombination. Despite these diff erences, pan and core genome analysis showed similar gene functions between the two strains. ~The phylogenomic study of the family Halomonadaceae is reported here for the first time. We found that the relationships were well resolved among every genera tested, including Chromohalobacter, Halomonas, Cobetia, Kushneria, Zymobacter, and Halotalea.

Effect of dietary interventions on the intestinal microbiota of Mongolian hosts

The gut microbiota of Mongolian hosts has distinctive characteristics due to their meat- and dairyoriented daily diets and unique genotype.The aim of the present study was to investigate the effect of switching from the typical high protein and fat Mongolian diets to carbohydrate-rich meals composed principally of wheat,rice and naked oats on the host gut microbiota within 3 weeks.Our study took the advantage of the long sequence reads produced by the Pac Bio single molecule real-time sequencing technology to enable the profiling of subjects' gut microbiota communities along the diet intervention to the species precision.We found that the bacterial richness and diversity decreased apparently along the diet intervention.During the diet intervention,the gut microbiota composition displayed no significant difference at phylum level(with major phyla of Firmicutes,Bacteroidetes,Tenericutes and Proteobacteria).The relative abundances of some genera such as Bacteroidetes,Faecalibacterium,Roseburia,Alistipes,Streptococcus,and Oscillospira were significantly altered after the diet switching started.Notably,significant changes were also observed in the proportions of the species Bacteroides dorei,Bacteroides fragilis,Bacteroides thetaiotaomicron,Ruminococcus albus,Ruminococcus faecis,Roseburia faecis and Eubacterium ventriosum.These results have demonstrated that diet and host gut microbiota is closely linked.