Microbiome Analysis Exploring Taxonomic Diversity in Kasaragod Dwarf and Holstein Crossbred Cattle

The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.

Virulence of Icelandic Pyrenophora teres f. teres populations and resistance of Icelandic spring barley lines

The causal agent of the barley net blotch disease, Pyrenophora teres, is known for its high level of diversity due to sexual reproduction. Different pathotypes, defined by a virulence combination, even within the same fields are frequently found and virulence between locations can vary considerably. Evaluation of virulence patterns of a pathogen population is essential for breeding resistant cultivars suitable for specific locations. To identify virulence patterns in Icelandic Pyrenophora teres f. teres (Ptt) isolates, twenty single spore isolates of Ptt were collected from seven locations in Iceland and analysed with AFLP markers. Principle Coordinate Analysis (PCoA) revealed Icelandic Ptt isolates clustering away from reference isolates from Austria, Finland, Sweden, Switzerland, UK, and USA. Hierarchical clustering grouped the Icelandic isolates into three distinct groups. Furthermore, the virulence of these twenty isolates was tested on 16 barley differential lines and revealed high variation in their virulence. Twenty-one barley cultivars commonly used in Iceland showed high susceptibility towards inoculation with Icelandic Ptt isolates.

Fecal Microbiota Analysis Exploring Taxonomic Diversity of Hindgut Microbial Communities in Kasaragod Dwarf and Holstein Friesian Cattle

The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf (K-Dwarf) cattle, a non-descriptive native cattle variety of Kerala, are noted for their unique qualities, like short stature, low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. This study hypothesizes that K-Dwarf cow relies on their unique hindgut microbes to ferment the low quality feeds into the efficient animal product. To compare and contrast this unique microbiota and their relationship between the host, we performed microbial profiling of the two genetically distinct cattle-type viz., K-Dwarf, and Holstein utilizing 16S rRNA high-throughput sequencing. Principle Coordinate Analysis using weighted and unweighted UniFrac distance matrices showed significantly distinct clustering of K-Dwarf microbial community compared to Holstein, implying the distinct microbial architecture that K-Dwarf harbors. The dissimilarities observed between the two cattle types were further revealed from the signature taxa identified in each cattle type following Random Forest analysis. In addition, the study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in K-Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in K-Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of K-Dwarf cattle gut microbiome profiling. Further molecular characterization is solicited to better understand the microbial role in the conversion of low-quality feeds into more efficient animal products, a well-defined characteristic of indigenous cattle.

Comparison of the Intestinal Microbiome of Italian Patients with Multiple Sclerosis and Their Household Relatives

Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system, caused by a combination of genetic and environmental factors. In recent years, a role in MS pathogenesis was assigned to the gut microbiota. However, different signatures of gut dysbiosis have been shown to depend on environmental factors, like diet and lifestyle. In this study, we compared the gut microbiome in MS patients and their household healthy relatives sharing lifestyle and environmental factors. Faecal metagenomic DNA was extracted and the V3–V4 regions of the conserved bacterial 16S ribosomal RNA gene were amplified and sequenced. While overall bacterial communities were similar, specific families differed between healthy and MS subjects. We observed an increase in Ruminococcaceae, Christensenellaceae, Desulfovibrionaceae, Clostridiales, and Family XIII in MS patients, while Bacteroidaceae, Tannerellaceae, Veillonellaceae, and Burkholderiaceae were more abundant in healthy controls. In addition, principle coordinate analysis showed that the gut microbiome of all MS patients formed a cluster being less diverse than the household relatives and that gut microbiota of MS patients with EDSS 4.5–7 formed a distinct cluster in respect to their controls. Overall, our study is consistent with the hypothesis that MS patients have gut microbial dysbiosis and evidenced the importance of environmental factors in shaping the gut microbiome.

Analysis of genetic diversity among different Rose (Rosa) genotypes using morphological and molecular markers (ISSR)

Rose is a woody perennial of the genus Rosa within the family Rosaceae. In this study, phylogenetic relationship among seven different genotypes of Rose (Rosa) was determined using ISSR primers and morphological parameters. DNA was isolated using CTAB method with 0.5% of CTAB concentration. Out of 50 ISSR primers, 16 primers gave reproducible banding pattern with all the seven genotypes of Rose while others failed to produce polymorphism. A total of 108 bands were obtained with an average polymorphism of 54.69% and an average of 9.06 bands per primer. The average similarity was found to be 0.69 among all the seven genotypes using Jaccard’s similarity coefficient. On basis of polymorphism cluster analysis divided them into two major groups separating one genotype (light pink) from rest of the six genotypes and principle coordinate analysis confirmed the results. A parallel correlation was found between the morphological parameter (flower diameter) and the results of ISSR analysis as both of them divided the seven genotypes into two main groups.

Genetic Diversity, Identification and Utilization of Novel Genetic Resources for Resistance to Meloidogyne incognita in Mulberry (Morus spp.)

Mulberry (Morus spp.) is an important crop in the sericulture industry as the leaves constitute the primary feed for the silkworm. The availability of diverse genetic sources of resistance to root- knot nematode (RKN; Meloidogyne spp.) are very scanty and therefore, a set of 415 varied exotic and indigenous germplasm accessions were screened under glasshouse conditions. Twenty one accessions were identified as highly resistant and 48 were resistant, the highest numbers of highly resistant/resistant accessions were found in Morus alba. Further, thirty accessions based on rooting ability were evaluated for field resistance at four different locations with infested soil. Finally, eight germplasm accessions; BR-8, Karanjtoli-1, Hosur-C8, Nagalur Estate, Tippu, Calabresa, Thai Pecah and SRDC-3 were identified as potential genetic sources in RKN resistance breeding programs or as resistant rootstock for the establishment of mulberry gardens. Sixteen SSR markers analyzed among the 77 resistant and susceptible accessions, generated 55 alleles, ranging from 2 to 5 with an average of 3.43 alleles per locus. Principle coordinate analysis grouped the accessions on the basis of RKN susceptible and resistant to a greater extent. The RKN susceptible accessions exhibited higher variability as compared to resistant accessions and they were more dispersed. Analysis of molecular variance showed that maximum molecular variance (78%) within the population and 22% between populations. Results of this study indicate that SSR markers are reliable for assessing genetic variability among the RKN resistant and susceptible mulberry accessions.

Abstract P241: Intermittent Fasting Lowers Blood Pressure In A Rat Model Of Hypertension By Modulating The Gut Microbiota

Studies have demonstrated that disruption of the gut microbiota, termed gut dysbiosis, plays a causal role in the development of hypertension (HT) in animal models and patients. Recent studies revealed that intermittent fasting alters the gut microbiota and the production of microbial metabolites. Thus, we hypothesized that every-other-day-fasting (EODF) would prevent elevations of blood pressure (BP) in spontaneously hypertensive stroke prone rat (SHRSP) by maintaining a healthy gut microbiota. Five-week old SHRSP rats and normotensive Wistar Kyoto (WKY) rats were randomized to be fed ad lib or on EODF for 10 weeks. BP was measured weekly, and cecal content and plasma were collected at the end of the study. To examine the roles of gut microbiota and microbial metabolites in hypertension, we performed whole-genome shotgun sequencing on cecal samples and non-targeted metabolomics on cecal contents and plasma. To examine the direct effects of the EODF altered microbiota on BP regulation and eliminate the confounding variable of fasting, pooled cecal contents of SHRSP and WKY animals fed ad lib or EODF were given to germ free (GF) rats by oral gavage. We found that ten-weeks EODF was able to prevent elevations of systolic BP (SBP) in SHRSP compared to ad lib fed SHRSP (~220 vs. ~170mmHg; n=6-8, p<0.05), and that germ free rats transplanted with SHRSP ad lib microbiota had a significantly higher SBP as compared to those transplanted with SHRSP EODF microbiota (~152 vs. ~140 mmHg; n=6-7, p<0.01), indicating that microbiota and their metabolites are accountable for the effects of EODF. Principle coordinate analysis showed that EODF significantly altered the overall composition of both WKY and SHRSP microbiota (WKY p<0.01, SHRSP p<0.009). Multi-omics analysis indicates distinct microbiome and metabolome in SHRSP compared to WKY, and significant alterations to each induced by EODF. These findings suggest that EODF is able to prevent hypertension in SHRSP, and this involves altering the gut microbiota and metabolome.

Genetic Diversity and Pedigree Analysis of Muscadine Grape Using SSR Markers

Muscadine grape (Vitis rotundifolia) is the first native North American grape to be domesticated. During the past century, breeding programs have created a large collection of muscadine cultivars. Muscadine cultivars are usually identified by evaluating morphological traits and checking breeding records, which can be ambiguous and unauthentic. During this study, simple sequence repeat (SSR) markers were used to generate DNA fingerprinting profiles to identify muscadine cultivars and verify their reported pedigrees. Eighty-nine Vitis accessions were genotyped using 20 SSRs from 13 linkage groups. From these, 81 unique subgenus Muscadinia accessions were identified, and a core set of five SSR markers was able to distinguish all of them. Eighteen misidentifications were found, and five previously unknown accessions were matched with cultivars in the dataset. The profiles of 12 cultivars were not consistent with their reported parentage–progeny relationships. Genetic diversity was analyzed at four levels: all V. rotundifolia cultivars (N = 67); current cultivars (N = 39); historical cultivars (N = 28); and wild V. rotundifolia accessions (N = 9). There was substantial genetic diversity in both wild and historically cultivated muscadines. The principle coordinate analysis (PCoA) showed clear separation among subgenus Vitis cultivars, wild muscadine accessions, and cultivated muscadines, with PCoA1 and PCoA2 explaining 11.0% and 9.3% of the total variation, respectively.

Characterization of Tanzanian Avocado Using Morphological Traits

Two-hundred and twenty-six old avocado trees (Persea americana Mill) derived from seeds were selected from eight districts of the Mbeya, Njombe and Songwe regions in Tanzania. The tree, leaf, fruit and seed characteristics were studied using the descriptors for avocado (Persea spp.) from the International Plant Genetic Resources Institute. Cross tabulation and Chi-square tests were conducted in order to assess the distribution of traits between districts and altitude ranges. Principle coordinate analysis (PCoA) and hierarchical cluster analysis (HCA) were used to assess variation of traits within and among districts. Various morphological features were observed among the samples which point to the existence of the Mexican, Guatemalan and West Indian avocado races in Tanzania. The biplot from PCoA revealed extensive variation between the sampled trees at the district level but no clear groupings of the samples based on geographic location. Likewise, dendrograms ensuing from the neighbor–joining and Wards methods displayed that the avocado samples from the same district and even region differed considerably. This morphological trait variation suggests high diversity that may help in planning germplasm management and conservation, as well as breeding strategies in the future.

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

Background Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation. Methodology We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusion This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).