Development of MetaXplore: An Interactive Tool for Targeted Metagenomic Analysis

Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.

Modulation of the rat intestinal microbiota in the course of Anisakis pegreffii infection

Background

Anisakis are globally distributed, marine parasitic nematodes that can cause human health problems, including symptoms such as vomiting, acute diarrhea, and allergic reactions. As parasitic nematodes that primarily affect the patient's digestive tract, intestinal helminths can interact directly with the host microbiota through physical contact, chemicals, or nutrient competition. It is widely accepted that the host microbiota plays a crucial role in the regulation of immunity.

Materials and methods

Nematodes collected from the abdominal cavity of marine fish were identified by molecular biology and live worms were artificially infected in rats. Infection was determined by indirect ELISA based on rat serum and worm extraction. Feces were collected for 16S rDNA-based analysis of microbiota diversity.

Results

Molecular biology identification based on ITS sequences identified the collected nematodes as A. pegreffii. The success of the artificial infection was determined by indirect ELISA based on serum and worm extraction from artificially infected rats. Microbiota diversity analysis showed that a total of 773 ASVs were generated, and PCoA showed that the infected group was differentiated from the control group. The control group contained five characterized genera (Prevotellaceae NK3B31 group, Turicibacter, Clostridium sensu stricto 1, Candidatus Stoquefichus, Lachnospira) and the infected group contained nine characterized genera (Rodentibacter, Christensenella, Dubosiella, Streptococcus, Anaeroplasma, Lactococcus, Papillibacter, Desulfovibrio, Roseburia). Based on the Wilcoxon test, four processes were found to be significant: bacterial secretion system, bacterial invasion of epithelial cells, bacterial chemotaxis, and ABC transporters.

Conclusion

This study is the first to analyze the diversity of the intestinal microbiota of rats infected with A. pegreffii and to determine the damage and regulation of metabolism and immunity caused by the infection in the rat gut. The findings provide a basis for further research on host-helminth-microbe correlationships.

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process

The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.

Autoantibody Diversity Is Augmented in Women with Breast Cancer and Is Related to the Stage of the Disease

Breast cancer (BC) is the most frequent malignant neoplasia and leading cause of cancer mortality for women. A timely diagnosis of BC is crucial to ensure the best chances of survival. Among the various screening tools for BC, antibodies directed towards self-antigens or tumor-associated antigens (autoantibodies) have emerged as an alternative to image-based screening modalities. However, little attention has been paid to the global diversity of autoantibodies. This work aimed to analyze the diversity of autoantibodies reactive to antigens expressed by the BC cell line T47D in the sera of Mexican women with BC, benign breast pathology (BBP), or without breast pathology (WBP). We found that the diversity of antibodies in the sera was higher in the BC and BBP groups than in the WBP group. Likewise, the diversity changed with the progression of BC. Our results show and measure the complexity of the antibody response in breast health and disease.

Meta-analysis reveals variations in microbial communities from diverse stony coral taxa at different geographical distances

Coral-associated microbial communities play a vital role in underpinning the health and resilience of reef ecosystems. Previous studies have demonstrated that the microbial communities of corals are affected by multiple factors, mainly focusing on host species and geolocation. However, up-to-date, insight into how the coral microbiota is structured by vast geographic distance with rich taxa is deficient. In the present study, the coral microbiota in six stony coral species collected from the coastal area of three countries, including United States of America (USA), Australia and Fiji, was used for analysis. It was found that the geographic influence on the coral microbiota was stronger than the coral host influence, even though both were significant. Interestingly, the contribution of the deterministic process to bacterial community composition increased as geographical distance grew. A total of 65 differentially abundant features of functions in coral microbial communities were identified to be associated with three geolocations. While in the same coastal area of USA, the similar relationship of coral microbiota was consistent with the phylogenetic relationship of coral hosts. In contrast to the phylum Proteobacteria, which was most abundant in other coral species in USA, Cyanobacteria was the most abundant phylum in Orbicella faveolata. The above findings may help to better understand the multiple natural driving forces shaping the coral microbial community to contribute to defining the healthy baseline of the coral microbiome.

Diversity analysis of agronomic and nutritional traits of hybrid offspring of forage bermudagrass

Because of its excellent stress resistance and forage quality, the forage bermudagrass hybrid population had attracted the attention of scientific researchers in recent years. Studying its diversity could promote the breeding of desirable varieties. The variability in agronomic traits including fresh weight, dry weight, ash content, crude protein content, crude fat, phosphorus content, and relative feed value for 56 bermudagrass was investigated using Wrangler as an experimental reference. Grey correlation analysis and cluster analysis were employed to screen bermudagrass with high yield and superior quality. WCF-34 had the highest 2-year fresh weight (109,773.3 kg/ha), WCF-37 had the highest 2-year dry weight (31,951.6 kg/ha), WCF-24 had the lowest Ash content (7.46%), WCF-26 had the highest crude protein content (16.27%), WCF-27 had the highest curde fat content (3.58%), WCF-13 had the highest P content (0.45%), and WCF-42 had the highest relative feed value (95.32). Combining the results of grey relational analysis and cluster analysis, WCF-42, WCF-34, WCF-38, WCF-37, and WCF-40 were selected as high-quality bermudagrass. Through comprehensive analysis of the agronomic characters of bermudagrass, five bermudagrass were selected, the outcomes of this study would provide a theoretical basis for the breeding and genetic enhancement of bermudagrass.

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Introduction

The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).

Methods

In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.

Results and discussion

Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

Comparative Analyses of Soil Bacterial Colonies of Two Types of Chinese Ginger after a Major Flood Disaster

Ginger, an important cash crop, has been cultivated for thousands of years in China. However, comparative studies on soil bacterial communities of Chinese ginger varieties, especially after flooding, are lacking. Here, we comprehensively compared the bacterial communities of two types of ginger soils from four different locations. Surprisingly, the 100-year flood (20 July 2021, in Henan, China) did not significantly affect the soil bacterial composition compared with previous reports. In contrast, flooding may have brought in nutrients and promoted the propagation of eutrophic bacteria, and Alphaproteobacteria were the most abundant in the Zhangliang region (~25%). However, due to the most severe flooding and inundation, the Zhangliang region, also probably contaminated with polycyclic aromatic hydrocarbons and heavy metals, showed the lowest microbial diversity. Moreover, the geographical location influenced the microbial communities more than did the soil type or ginger variety. These findings help us understand the species and composition of bacteria and infection of ginger after flooding and soaking. Further, the interaction mechanisms underlying these emerging phenomena need to be further investigated. IMPORTANCE There are few comparative studies on the soil bacterial communities of Chinese ginger varieties after flooding. After a 100-year flood (20 July 2021, in Henan, China), we comprehensively compared the bacterial communities of two types of ginger soils from four different locations. Surprisingly, this flood did not significantly affect the soil bacterial composition compared with previous reports. In contrast, it was found that the flooding may have brought in nutrients and promoted the propagation of eutrophic bacteria for the Zhangliang region. However, the flooding had also brought in polycyclic aromatic hydrocarbon and heavy metal contamination. Moreover, we also verified that geographical location influenced the microbial communities more than did the soil type or ginger variety. These findings help us understand the species and composition of bacteria and infection of ginger after flooding and soaking.

Phenolic and anthocyanin content characterization related to genetic diversity analysis of Solanum tuberosum subsp. tuberosum Chilotanum Group in southern Chile

The potato (Solanum tuberosum L) is one of the four most important crops worldwide in production and consumption. It originated from South America along the Andes, where six hotspots of diversity known as subcenters of origin are described from Venezuela to Chiloe Island in Chile, and where the greatest diversity of potatoes in the world is found. Today, the use of ancestral genetic resources has gained significant relevance, recovering and producing foods with a greater nutrient content and beneficial to human health. Therefore, native potatoes possess a set of characteristics with great potential for use in potato breeding guided primarily to produce better feed, especially potatoes of the Chilotanum Group that are easily crossed with conventional varieties. The primary objective of this study was to evaluate 290 accessions of S. tuberosum subsp tuberosum belonging to the Chilotanum Group using a set of molecular markers and correlate them to its phenotypic traits for future use in breeding programs. For this purpose, 290 accessions were analysed through 22 specific microsatellites described previously, correlating them with flesh and skin colour, total phenolic content, and anthocyanin content. A division into groups considering all the 290 accessions resulted in two clusters using STRUCTURE analysis and seven different genetic clusters using UPGMA. The latter exhibited common phenotypic characteristics as well as anthocyanin content, strongly supporting a correlation between phenotypic traits and the genetic fingerprint. These results will enable breeders to focus on the development of potatoes with high polyphenol and anthocyanin content.

Relationships between fungal diversity and fruit quality of Yuluxiang pear during low temperature storage

Postharvest decay is an urgent problem that affects the storage of pears. Low temperature storage is one of the most important methods to reduce the prevalence of fruit diseases during storage. In this study, the microbial diversity of postharvest Yuluxiang pear (Pyrus × michauxii "Yu Lu Xiang") fruits stored at low temperature for different lengths of times was analyzed. Illumina MiSeq high-throughput sequencing was used to analyze the composition and diversity of fungal communities. The results showed that the fungi within fruit were classified into 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera based on the 97% sequence similarity level. They belonged to 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera. The highest richness of fungi was obtained after 30 d of treatment. The β-diversity index showed that the fungal community composition of these fruit was significantly different at the beginning of storage compared with the different timepoints of samples at low temperature during storage. The comparison of fungal composition at the phylum level indicated that Ascomycota was dominant in the different timepoints of samples at low temperature, while Alternaria was the primary fungus at the genus level. A correlation analysis was used to further explore the correlation between fungi and fruit firmness, titratable acid, and solid soluble contents at low temperatures during storage. Aureobasidium and Didymella positively correlated with the soluble solids and hardness. Phoma positively correlated with the titratable acid, and Aspergillus positively correlated with titratable acid and hardness. This study can guide the industrial production of Yulu pear and also provide a theoretical basis to prevent and control diseases during the storage period of Yulu pear.

The cultivable endophytic fungal community of Scutellaria baicalensis: diversity and relevance to flavonoid production by the host

Scutellaria baicalensis (SB), a traditional Chinese medicinal plant, is widely used because of its important pharmacological activities. However, the endophytic fungi that promote flavonoid accumulation in SB remain unclear. Therefore, we analyzed the endophytic fungal community of SB and screened the endophytic fungi that might promote flavonoid synthesis in SB. ITS1/ITS4Blast was used to identify the endophytic fungi in SB. In total, 687 strains were identified in 57 genera. The dominant genus in the leaves and stems was Alternaria and that in the roots was Fusarium. Alternaria was the dominant genus in SB collected from all sites and in wild and cultivated SB. Alpha diversity indexes indicated more abundant endophytic fungi in samples from Chengde, the genuine producing area of SB, than in those from other sites. Beta diversity index analysis indicated that SB plants with closer geographical relationships showed more similar endophytic fungal community profiles. Spearman correlation analysis revealed that baicalin, wogonoside, wogonin, and oroxylin A contents were significantly correlated with the relative abundance of Alternaria. Overall, the results indicate the importance of geographical factors in influencing the endophytic fungal community of SB and suggest that the presence of Alternaria spp. might contribute to flavonoid synthesis in SB.

16S rRNA Gene Sequencing Reveals Specific Gut Microbes Common to Medicinal Insects

Insects have a long history of being used in medicine, with clear primary and secondary functions and less side effects, and the study and exploitation of medicinal insects have received increasing attention. Insects gut microbiota and their metabolites play an important role in protecting the hosts from other potentially harmful microbes, providing nutrients, promoting digestion and degradation, and regulating growth and metabolism of the hosts. However, there are still few studies linking the medicinal values of insects with their gut microbes. In this study, we focused on the specific gut microbiota common to medicinal insects, hoping to trace the potential connection between medicinal values and gut microbes of medicinal insects. Based on 16S rRNA gene sequencing data, we compared the gut microbiota of medicinal insects [Periplaneta americana, Protaetia (Liocola) brevitarsis (Lewis) and Musca domestica], in their medicinal stages, and non-medicinal insects (Hermetia illucens L., Tenebrio molitor, and Drosophila melanogaster), and found that the intestinal microbial richness of medicinal insects was higher, and there were significant differences in the microbial community structure between the two groups. We established a model using a random-forest method to preliminarily screen out several types of gut microbiota common to medicinal insects that may play medicinal values: Parabacteroides goldsteinii, Lactobacillus dextrinicus, Bifidobacterium longum subsp. infantis (B. infantis), and Vagococcus carniphilus. In particular, P. goldsteinii and B. infantis were most probably involved in the anti-inflammatory effects of medicinal insects. Our results revealed an association between medicinal insects and their gut microbes, providing new development directions and possibly potential tools for utilizing microbes to enhance the medicinal efficacy of medicinal insects.

Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing

Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses. The polymorphism information content (PIC) values of SNPs ranged from 0.1 to 0.4, with a large proportion of SNPs (8633 nos.; 79.7%) having a higher PIC in the range of 0.3-0.4. The genetic diversity analysis revealed the existence of a high level of variation in coconut accessions, with an average expected heterozygosity (H_e) value of 0.43. Unweighted neighbor-joining phylogenetic tree and Bayesian-based model population structure grouped coconut genotypes into four main clusters. The accessions are generally clustered based on their height (tall or dwarf), with a few accession clusterings based on geographical origins. Investigation of LD pattern in coconut indicated a relatively rapid LD decay with a short range (9 kb). The results obtained in this study will contribute to enhancing the capacity of coconut researchers to utilize genetic diversity for further genetic improvement. In addition, it would open up possibilities for performing genomic studies such as genome-wide association studies and genomic selection to accelerate the efficiency and speed of coconut genetic improvement.

[Genetic diversity and antibacterial activity of endophytic fungi from Zanthoxylum nitidum]

In order to reveal the distribution and population characteristics of endophytic fungi from Zanthoxylum nitidum and the antibacterial potential,this study performed molecular identification and analyzed the genetic diversity and antibacterial activity of endophytic fungi from Z. nitidum in Guangxi. Through culture and molecular identification,35 strains,belonging to 15 genera,12 families,10 orders,4 classes,and 2 phyla,were isolated from various tissues of Z. nitidum,of which Colletotrichum and Fusarium were the dominant genera,respectively accounting for 20% of total strains. The diversity of endophytic fungi was significantly different among roots,stems,and leaves,as manifested by the significantly higher Shannon index( H') in stems( 1. 678) than in roots( 0. 882 1) and leaves( 0. 515 4). The antimicrobial activity analysis showed that 14. 28% of endophytic fungi inhibited at least one indicator pathogen. Among them,Fusarium sp. ZN-34 and Fusarium sp. ZN-26 separately demonstrated the strongest inhibitory effect on Escherichia coli and Staphylococcus aureus. In general,Fusarium sp. ZN-26 and Phialemoniopsis plurioloculosa ZN-35 were advantageous in suppressing the two bacteria owing to the broad spectrum and strong efficacy. In summary,Z. nitidum in Guangxi boasts rich endophytic fungi with the majority showing strong antibacterial activity,which can be used as candidates for the extraction and separation of basic antibacterial substances and the development of natural antibacterial agents.

Effects of Iron and Zinc Biofortified Foods on Gut Microbiota In Vivo (Gallus gallus): A Systematic Review

Dietary iron and zinc deficiencies are a global health concern. Bacteria that colonize the gastrointestinal tract depend on minerals to maintain their activities; thus, recent evidence suggests that biofortified foods can modulate the host’s beneficial bacterial taxa. The current review analyzed the research data that linked between iron and zinc biofortified foods and gut microbiota modulation. The data analysis was based on the PRISMA guidelines and the data search was performed at PubMed, Web of Science, Science Direct, and Scopus databases for experimental studies published from January 2010 until December 2020. The five selected studies were conducted in an experimental in vivo model (Gallus gallus). The identified and discussed research showed positive effects of biofortified foods on the composition and function of the gut microbiota. Further, an increase in short chain fatty acids producing bacterial populations as Lactobacillus and Ruminococcus, and a decrease in potentially pathogenic bacteria as Streptococcus, Escherichia, and Enterobacter was identified due to the consumption of biofortified foods. In conclusion, biofortified foods may contribute to improved gut health without increasing the colonization of pathogenic bacteria. The dietary inclusion of approximately 50% of iron/zinc biofortified foods has a significant beneficial effect on the gut microbiota. Additional studies in humans and animal models are warranted to further establish the suggested effects on the intestinal microbiome. PROSPERO (CRD42020184221).

Analysis of rice root bacterial microbiota of Nipponbare and IR24

The root-associated bacterial microbiota is closely related to life activities of land plants, and its composition is affected by geographic locations and plant genotypes. However, the influence of plant genotypes on root microbiota in rice grown in northern China remains to be explained. In this study, we performed 16S rRNA gene amplicon sequencing to generate bacterial community profiles of two representative rice cultivars, Nipponbare and IR24. They are planted in Changping and Shangzhuang farms in Beijing and have reached the reproductive stage. We compared their root microbiota in details by Random Forest machine learning algorithm and network analysis. We found that the diversity of rice root microbiota was significantly affected by geographic locations and rice genotypes. Nipponbare and IR24 showed distinct taxonomic composition of the root microbiota and the interactions between different bacteria. Moreover, the root bacteria could be used as biomarkers to distinguish Nipponbare from IR24 across regions. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota in Northern China and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection

Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population

This study is to investigate the subgingival bacterial diversity and community structure in the Uygur subjects with peri-implantitis.Totally 40 cases of gingival crevicular fluid were collected from Uygur subjects and divided into the Control group (healthy implants) and Case group (peri-implantitis), respectively. DNA was extracted, and the sequencing in the 16SrRNA V4-V5 region was conducted on the Illumina Miseq sequencing platform. The 16SrRNA gene clone library was constructed and analyzed.Totally 733,759 valid tags were obtained from these 40 samples. After comparing with the Silva-16S database by the Uparse software, 263 operational taxonomic unit were finally harvested (135 for the Control group and 128 for the Case group). The differential bacteria between these 2 groups at the phylum, class, order, family, and genus levels were Actinobacteria, Actinomycetes, Pasteurellales, Moraxellaceae, and Acinetobacter, respectively. The dominant genera with significantly different distribution between the Control and Case groups included Vibrio, Campylobacter, Granulicatella, Acinetobacter, Micrococcus, and Moraxella. The α diverstiy analysis based on the chao diversity index showed that there was significant difference in the microbiological diversity between these 2 groups. Principal coordinates analysis analysis indicated significant differences in the bacterial community structure between these 2 groups. Cluster analysis showed higher abundance of Micrococcus in the Case group, while higher abundance of Prevotella in the Control group.There are significant differences in the diversity of subgingival bacteria between the Uygur subjects with healthy implants and peri-implantitis. Moraxella, Micrococcus, and Acinetobacter might represent dominant bacteria genera causing peri-implantitis in the Uygur population.

Public Clonotypes and Convergent Recombination Characterize the Naïve CD8+ T-Cell Receptor Repertoire of Extremely Preterm Neonates

Respiratory support improvements have aided survival of premature neonates, but infection susceptibility remains a predominant problem. We previously reported that neonatal mice have a rapidly evolving T-cell receptor (TCR) repertoire that impairs CD8⁺ T cell immunity. To understand the impact of prematurity on the human CD8⁺ TCR repertoire, we performed next-generation sequencing of the complementarity-determining region 3 (CDR3) from the rearranged TCR variable beta (Vβ) in sorted, naïve CD8⁺ T cells from extremely preterm neonates (23–27 weeks gestation), term neonates (37–41 weeks gestation), children (16–56 months), and adults (25–50 years old). Strikingly, preterm neonates had an increased frequency of public clonotypes shared between unrelated individuals. Public clonotypes identified in preterm infants were encoded by germline gene sequences, and some of these clonotypes persisted into adulthood. The preterm neonatal naïve CD8⁺ TCR repertoire exhibited convergent recombination, characterized by different nucleotide sequences encoding the same amino acid CDR3 sequence. As determined by Pielou’s evenness and iChao1 metrics, extremely preterm neonates have less clonality, and a much lower bound for the number of unique TCR within an individual preterm neonate, which indicates a less rich and diverse repertoire, as compared to term neonates, children, and adults. This suggests that T cell selection in the preterm neonate may be less stringent or different. Our analysis is the first to compare the TCR repertoire of naïve CD8⁺ T cells between viable preterm neonates and term neonates. We find preterm neonates have a repertoire immaturity which potentially contributes to their increased infection susceptibility. A developmentally regulated, evenly distributed repertoire in preterm neonates may lead to the inclusion of public TCR CDR3β sequences that overlap between unrelated individuals in the preterm repertoire.

Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures

Undefined mesophilic mixed (DL-type) starter cultures are composed of predominantly Lactococcus lactis subspecies and 1-10% Leuconostoc spp. The composition of the Leuconostoc population in the starter culture ultimately affects the characteristics and the quality of the final product. The scientific basis for the taxonomy of dairy relevant leuconostocs can be traced back 50 years, and no documentation on the genomic diversity of leuconostocs in starter cultures exists. We present data on the Leuconostoc population in five DL-type starter cultures commonly used by the dairy industry. The analyses were performed using traditional cultivation methods, and further augmented by next-generation DNA sequencing methods. Bacterial counts for starter cultures cultivated on two different media, MRS and MPCA, revealed large differences in the relative abundance of leuconostocs. Most of the leuconostocs in two of the starter cultures were unable to grow on MRS, emphasizing the limitations of culture-based methods and the importance of careful media selection or use of culture independent methods. Pan-genomic analysis of 59 Leuconostoc genomes enabled differentiation into twelve robust lineages. The genomic analyses show that the dairy-associated leuconostocs are highly adapted to their environment, characterized by the acquisition of genotype traits, such as the ability to metabolize citrate. In particular, Leuconostoc mesenteroides subsp. cremoris display telltale signs of a degenerative evolution, likely resulting from a long period of growth in milk in association with lactococci. Great differences in the metabolic potential between Leuconostoc species and subspecies were revealed. Using targeted amplicon sequencing, the composition of the Leuconostoc population in the five commercial starter cultures was shown to be significantly different. Three of the cultures were dominated by Ln. mesenteroides subspecies cremoris. Leuconostoc pseudomesenteroides dominated in two of the cultures while Leuconostoc lactis, reported to be a major constituent in fermented dairy products, was only present in low amounts in one of the cultures. This is the first in-depth study of Leuconostoc genomics and diversity in dairy starter cultures. The results and the techniques presented may be of great value for the dairy industry.

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

The advent of next generation sequencing (NGS) has enabled investigations of the gut microbiome with unprecedented resolution and throughput. This has stimulated the development of sophisticated bioinformatics tools to analyze the massive amounts of data generated. Researchers therefore need a clear understanding of the key concepts required for the design, execution and interpretation of NGS experiments on microbiomes. We conducted a literature review and used our own data to determine which approaches work best. The two main approaches for analyzing the microbiome, 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses. Several methods for taxonomic classification of bacterial sequences are discussed. We present simulations to assess the number of sequences that are required to perform reliable appraisals of bacterial community structure. To the extent that fluctuations in the diversity of gut bacterial populations correlate with health and disease, we emphasize various techniques for the analysis of bacterial communities within samples (α-diversity) and between samples (β-diversity). Finally, we demonstrate techniques to infer the metabolic capabilities of a bacteria community from these 16S and shotgun data.

Introgression of a rare haplotype from Southeastern Africa to breed California blackeyes with larger seeds

Seed size distinguishes most crops from their wild relatives and is an important quality trait for the grain legume cowpea. In order to breed cowpea varieties with larger seeds we introgressed a rare haplotype associated with large seeds at the Css-1 locus from an African buff seed type cultivar, IT82E-18 (18.5 g/100 seeds), into a blackeye seed type cultivar, CB27 (22 g/100 seed). Four recombinant inbred lines derived from these two parents were chosen for marker-assisted breeding based on SNP genotyping with a goal of stacking large seed haplotypes into a CB27 background. Foreground and background selection were performed during two cycles of backcrossing based on genome-wide SNP markers. The average seed size of introgression lines homozygous for haplotypes associated with large seeds was 28.7g/100 seed and 24.8 g/100 seed for cycles 1 and 2, respectively. One cycle 1 introgression line with desirable seed quality was selfed for two generations to make families with very large seeds (28-35 g/100 seeds). Field-based performance trials helped identify breeding lines that not only have large seeds but are also desirable in terms of yield, maturity, and plant architecture when compared to industry standards. A principal component analysis was used to explore the relationships between the parents relative to a core set of landraces and improved varieties based on high-density SNP data. The geographic distribution of haplotypes at the Css-1 locus suggest the haplotype associated with large seeds is unique to accessions collected from Southeastern Africa. Therefore this quantitative trait locus has a strong potential to develop larger seeded varieties for other growing regions which is demonstrated in this work using a California pedigree.

The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis

T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.