The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

Comparison of culture-dependent and culture-independent techniques in the detection of lactic acid bacteria biodiversity and dynamics throughout the ripening process: The case of Turkish artisanal Tulum cheese produced in the Anamur region

Our objective was to analyze the diversity of the microbiota over 180 d of ripening of eight batches of artisanal goatskin Tulum cheeses by culture-dependent and culture-independent (PCR-DGGE) methods. V3 region of the bacterial 16S rRNA gene was amplified with the PCR after direct DNA isolation from the cheese samples. Nine different species and five genera were determined by culturing, while 11 species were identified in the PCR-DGGE technique. This diversity revealed the uniqueness of artisanal cheese varieties. The dominant genera in all the cheese samples were composed of Enterococcus species. The culture-dependent method revealed five genera (Enterococcus,Bacillus,Lactococcus,Lactobacillus, Sphingomonas) while three genera (Enterococcus, Streptococcus, Lactococcus) were detected in the culture-independent method. It was concluded that combining the two methods is important for characterizing the whole microbiota of the Tulum cheese varieties produced in the Anamur region.

Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

Evidence of bacterial DNA presence in chorionic villi and amniotic fluid in the first and second trimester of pregnancy

The sterile-womb dogma in uncomplicated pregnancy has been lively debated. Data regarding the in utero microbiome environment are based mainly on studies performed at the time of delivery. Aim: To determine whether human placenta and amniotic fluid are populated by a bacterial microbiota in the first and second trimesters of pregnancy. Materials & methods: We analyzed by next-generation sequencing method 24 and 29 samples from chorionic villus sampling (CVS) and amniocentesis (AC), respectively. The V3 region of the 16S rRNA gene was sequenced. Results: 37.5% of CVS and 14% of AC samples showed the presence of bacterial DNA. Conclusion: Our study suggests that bacterial DNA can be identified in the placenta and amniotic fluid during early prenatal life.

Effect of dietary inulin in the gut microbiota of whiteleg shrimp Penaeus vannamei

The effect of dietary inulin on the intestinal bacterial communities of Penaeus vannamei by 16S metagenomic analysis was assessed. PCR amplified the V3 region of the bacterial 16S rDNA. Sequencing reads were generated using the 2×150 (300 cycles) for the base-read length chemistry of the Illumina MiniSeq platform. The software Shaman and MicrobiomeAnalyst were used to analyze the sequences. The phylum Proteobacteria and the genus Vibrio were among the most abundant taxonomic ranks for control and inulin treatment. The relative abundance of the phylum Bacteroidetes and genus Ruegeria was lower in inulin treatment concerning the control condition. Alpha and beta indices did not show significant differences between inulin treatment and control conditions. For all samples, most of the bacterial organisms showed the presence of carbohydrate and amino acid metabolism-related genes, and to a lesser extent, of energy, lipid, and cofactors and vitamin metabolism-related genes. The principal metabolic functions were glycine, serine, threonine, glyoxylate and dicarboxylate, purine, pyrimidine, pyruvate, and quorum sensing. The interaction network analysis showed fewer interactions in the inulin treatment concerning control condition. Proteobacteria, Bacteroidetes, Vibrio, and Ruegeria predominated in all samples, and inulin did not change the net microbial diversity in the intestine of P. vannamei. Streptomyces, Roseobacter, and Ruegeria showed negative interactions with Vibrio, suggesting their use as probiotics. This study sheds light on the inulin supplement on the essential role of microbiota in the shrimp.

Neutralization Characteristics HIV-1 CRF01_AE Env Clones from Infections in China

Owing to the increasing prevalence of HIV-1 CRF_01AE, it is necessary to understand the neutralization properties of CRF_01AE and to develop broadly neutralizing monoclonal antibodies (bnmAbs) that can neutralize this virus. The full-length Env gene was cloned from HIV-1 CRF01_AE-infected plasma specimens collected in China and used to establish pseudoviruses. Neutralization phenotypes of the pseudoviruses were characterized with bnmAbs. The neutralizing activities of 11 bnmAbs VRC01, VRC03, IgG1b12 and 3BNC117 (targeting the CD4 binding site); PG9 (targeting the V1V2 region); 2G12 (sugar chain specific), PGT135 and 10-1074 (targeting the V3 region); 2F5, 4E10 and 10E8 (targeting the membrane proximal external region), against 36 pseudoviruses were analyzed, demonstrating varying efficacies. In general, VRC01, 10E8 and 3BNC117 showed strong neutralizing activity, neutralizing more than 75% of the pseudoviruses; followed by PG9 and 4E10, showing moderate neutralizing activity with neutralization of 50%–60% of the pseudoviruses; whereas the efficacies of the remaining bnmAbs were poor, neutralizing less than 15% of pseudoviruses tested. Env variants of CRF_01AE also showed significant differences in resistance to neutralization. CRF_01AE Env variants pose a serious challenge for the development of bnmAbs and vaccines, and these characterized HIV-1 CRF_01AE pseudoviruses could be used for neutralization studies and evaluation of vaccines or anti-HIV-1 products in China.

Multiple Mechanisms of HIV-1 resistance to PGT135 in Chinese Subtype B’ Slow Progressor

ABSTRACTIn our study, we describe a slow progressor CBJC515 from whom we constructed pseudoviruses expressing autologous Env. We surprisingly found all the pseudoviruses were resistant to PGT135. By making site-directed mutations and chimeric Env constructs, we found the early 05 strains escaped from PGT135 by losing the N332 glycan site, while the later 06 and 08 strains may escape with the retention of key epitopes through the change of V1/V4/C2 region or by N398/N611 glycan, which was selected as unique N-glycosylation site of CBJC515 compared with CBJC437 whose viruses were also harboring key epitopes but sensitive to PGT135. These findings provide insights into how HIV-1 can escape from N332-directed broadly neutralizing antibody (bNAb) responses without changing the epitope itself, and these ways may be useful to prolong the exposures of bNAb epitopes and contribute to bNAb development. Furthermore, our chimeric experiments also allowed us to explore the co-evolution and retention of functionality among regions. We confirmed that the V1V2 region has a wide range of effectiveness in interfering with the function of envelope protein and the V3 region can promote protein function recovery and buffer the harmful polymorphisms in the other regions contributing to the Env antigenic diversity. These results may provide some clues for the design of vaccines against HIV-1 strains.IMPORTANCEOur findings of mechanisms escaping from PGT135 verified the extensive role of long V1 region in mediating escape from V3-bNAbs. In addition, we also found multiple additional ways suggested that extreme variation may be needed by HIV-1 to escape from PGT135 without changing the epitope itself. Although the V3-glycan bNAb responses are among the most promising vaccine targets, as they are commonly elicited during infection, our findings indicated there may be additional difficulties to be taken into account in immunogen design, such as the consideration of other regions and some glycosylation sites affecting the mask of key epitopes, as well as the selection pressure that may be required by other bNAbs. Our chimeric experiment also highlighted the key role of V3 region in contributing to the maintenance of Env diversity by buffering deleterious polymorphisms, which may be helpful for vaccine design.

Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China

Endophytic bacteria may be important for plant health and other ecologically relevant functions of cotton. However, the endophytic bacterial community structure and diversity in cotton is still poorly characterized. We investigated the community structure of endophytic bacteria in cotton roots growing in Xinjiang, China, using the Illumina amplicon sequencing. A total of 60.84 M effective sequences of 16S rRNA gene V3 region were obtained from cotton samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in cotton, that is, 81-338 OTUs in a cotton sample, at 3% cutoff level and sequencing depth of 50000 sequences. We identified 23 classes from the resulting 2,723,384 sequences. Gammaproteobacteria were the dominant class in all cottons, followed by Alphaproteobacteria, Actinobacteria and Bacilli. A marked difference in the diversity of endophytic bacteria in cotton for different growth periods was evident. The greatest number of OTUs was detected during seedling (654 OTUs) and budding (381 OTUs). Endophytic bacteria diversity was reduced during flowering (350 OTUs) and boll-opening (351 OTUs). 217 OTUs were common to all four periods. There were more tags of Pantoea in Shihezi than other locations. While there were more tags of Erwinia in Hami than other locations. The dynamics of endophytic bacteria communities were influenced by plant growth stage. These results show the complexity of the bacterial populations present in inner tissues of cotton.

The influence of race on cervical length in pregnant women in Brazil

ObjectivesShort cervical length is a predictor of preterm birth. We evaluated if there were racial differences in variables associated with cervical length in pregnant Brazilian women.MethodsCervical length was determined by vaginal ultrasound in 414 women at 21 weeks gestation. All women were seen at the same clinic and analyzed by the same investigators. Women found to have a short cervix (≤25 mm) received vaginal progesterone throughout gestation. Composition of the vaginal microbiome was determined by analysis of the V1–V3 region of the gene coding for bacterial 16S ribosomal RNA. Demographic, clinical and outcome variables were determined by chart review. Subjects were 53.4% White, 37.2% mixed race and 9.4% Black. Results: Pregnancy, medical history and education level were similar in all groups. Mean cervical length was shorter in Black women (28.4 mm) than in White (32.4 mm) or mixed race (32.8 mm) women (p≤0.016) as was the percentage of women with a short cervix (23.1, 12.2, 7.8% in Black, White, mixed race respectively) (p≤0.026). Mean cervical length increased with maternal age in White (p=0.001) and mixed race (p=0.045) women but not Black women. There were no differences in bacterial dominance in the vaginal microbiota between groups. Most women with a short cervix delivered at term.ConclusionsWe conclude that Black women in Brazil have a shorter cervical length than White or mixed race women independent of maternal age, pregnancy and demographic history or composition of the vaginal microbiome.