scholarly journals Metagenomics: A Novel Tool for Livestock and Poultry Improvement: A Review

2021 ◽  
Author(s):  
Sachin S. Pawar ◽  
Pallavi A. Mohanapure ◽  
Manoj P. Brahmane ◽  
Mukesh P. Bhendarkar ◽  
Avinash V. Nirmale ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Bioactive Molecules ◽  
Microbial Populations ◽  
Reference Database ◽  
Genetic Characteristics ◽  
Distinct Mechanism ◽  
Rapid Pace ◽  
Recent Addition ◽  
Biotechnological Processes ◽  
Adaptive Ability

A distinct mechanism of generating metagenome is metagenomics which includes sequencing the whole DNA extracted from an environmental sample, mapping it to a reference database followed by gene annotation. Advancement in sequence-based metagenomics has significantly reduced processing costs and has acquired a rapid pace. Metagenomics has been crucial in investigating “hidden” genetic characteristics and construction biotechnological processes through the discovery of novel genes, enzymes, pathways and bioactive molecules with entirely different or improved biochemical functions. Metagenomics is a fairly recent addition to the molecular toolbox and is the simplest, impartial way of challenging the adaptive ability of microbial populations. Metagenomics is beneficial in recognising the complex consortium of bacteria, protozoa, archaea, fungi, etc. and association amongst them resulting in higher feed utilization and productivity of animals. It allows formulating probiotics feed materials, as well as in immunomodulation in both livestock and poultry. This review emphasizes significant recent achievements in metagenomics, offers insights into the possibilities, modern-day challenges and its utility in livestock and poultry.

scholarly journals Crowded growth leads to the spontaneous evolution of semistable coexistence in laboratory yeast populations

2015 ◽  
Vol 112 (36) ◽  
pp. 11306-11311 ◽  
Author(s):  
Evgeni M. Frenkel ◽  
Michael J. McDonald ◽  
J. David Van Dyken ◽  
Katya Kosheleva ◽  
Gregory I. Lang ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Interference Competition ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Microbial Populations ◽  
Natural Environments ◽  
Distinct Mechanism ◽  
The Cost ◽  
Spontaneous Evolution

Identifying the mechanisms that create and maintain biodiversity is a central challenge in biology. Stable diversification of microbial populations often requires the evolution of differences in resource utilization. Alternatively, coexistence can be maintained by specialization to exploit spatial heterogeneity in the environment. Here, we report spontaneous diversification maintained by a related but distinct mechanism: crowding avoidance. During experimental evolution of laboratorySaccharomyces cerevisiaepopulations, we observed the repeated appearance of “adherent” (A) lineages able to grow as a dispersed film, in contrast to their crowded “bottom-dweller” (B) ancestors. These two types stably coexist because dispersal reduces interference competition for nutrients among kin, at the cost of a slower maximum growth rate. This tradeoff causes the frequencies of the two types to oscillate around equilibrium over the course of repeated cycles of growth, crowding, and dispersal. However, further coevolution of theAandBtypes can perturb and eventually destroy their coexistence over longer time scales. We introduce a simple mathematical model of this “semistable” coexistence, which explains the interplay between ecological and evolutionary dynamics. Because crowded growth generally limits nutrient access in biofilms, the mechanism we report here may be broadly important in maintaining diversity in these natural environments.

scholarly journals Genetic characteristics and prognosis of m6A RNAmethylation regulator in acute myeloid leukemia

2020 ◽  
Author(s):  
Jiasheng Xu ◽  
Kaili Liao ◽  
Zhonghua Fu ◽  
Zhenfang Xiong
Keyword(s):  
Myeloid Leukemia ◽  
Gene Annotation ◽  
Clinicopathological Characteristics ◽  
Risk Scores ◽  
Genetic Characteristics ◽  
Rna Methylation ◽  
Pathological Characteristics ◽  
Potential Value ◽  
M6a Rna Methylation ◽  
Acute Myeloid

Abstract Background: To identify the genetic characteristics of m6A RNA methylation regulators in AML and explore their potential value as prognostic markers.Methods: RNA-seq transcriptome data and clinical survival data of acute myeloid leukemia (AML) were downloaded from ICGC and TCGA, gene annotation files were downloaded from GENECODE (1). 13 widely reported m6A RNA alphas were obtained from the literature. The expression of m6A RNA methylation regulators were collected and analized using gene annotation files. The samples were subjected to consistent clustering to obtain two subgroups RM1 and RM2, and the pathological characteristics and survival between the two subgroups were analyzed. Comparative analysis and functional analysis of m6A RNA methylation regulators between subgroups were completed. The STRING database analyzed the interactions between m6A RNA methylation regulators, and Spearman analyzed the correlation of expression of m6A RNA methylation regulators. COX regression analysis and risk scores were used to predict prognosis and pathological characteristics, and risk scores calculated using features were used to predict the prognosis and clinicopathological characteristics of tumor patients.Results: According to the morphological characteristics of AML, the samples were divided into 8 categories (M0 Undifferentiated, M1, M2, M3, M4, M5, M6, M7), and among them, the expression profile and expression heat map of 13 m6A RNA methylation regulators were constructed. Using m6A RNA methylation regulator as a feature vector, consistent clustering of 151 samples yielded two subgroups RM1 and RM2. Among them, the expression of the regulator in RM1 was higher than RM2,and RM2 patients had a longer survival time than RM1. Gene set enrichment analysis found that functional processes such as endothelial-hematopoietic transformation through the Notch pathway were significantly enriched in RM1. The analysis of the KM curve indicates that when the expression of FTO or ALKBH5 or of ZC3H13 was low, the survival time of patients was significantly higher than that with high expression.Conclusion: m6A RNA methylase regulator is not only an independent prognostic marker of AML, but also can predict its clinicopathological characteristics, which has potential value for stratifying prognosis and improving treatment strategies.

scholarly journals Lactobacillus Plantarum LRCC5314 Includes a Gene for a Substance that Stimulates the Secretion of Serotonin

2021 ◽  
Author(s):  
Jiseon Jeong ◽  
Seokmin Yoon ◽  
Jong-Hwa Kim ◽  
Wonyong Kim
Keyword(s):  
Lactobacillus Plantarum ◽  
Biosynthetic Pathway ◽  
Gene Annotation ◽  
Industrial Applications ◽  
Elisa Test ◽  
Comparative Genomic ◽  
Genetic Characteristics ◽  
Stress Regulation ◽  
Physiological Properties ◽  
Genomic Analyses

Abstract Background: As the functions of probiotics within the same species may not be shared, it is important to analyze the genetic characteristics of strains to determine their safety and usefulness before industrial applications. Results: The complete genome of Lactobacillus plantarum LRCC5314 isolated from kimchi was acquired through PacBio sequencing to confirm probiotic functions and genetic characteristics. Phylogenetic and comparative genomic analyses were performed between L. plantarum LRCC5314 and L. plantarum ATCC 14917T, and the results showed that two strains were highly similar. However, there were some genetic differences. The characteristics of carbon source metabolism were also determined based on the KEGG database and physiological properties. L. plantarum LRCC5314 could metabolize hexoses through homofermentation, which produces only lactic acid. According to gene annotation, L. plantarum LRCC5314 could encode almost complete biosynthetic pathway to produce tryptophan, which can be used as a precursor of serotonin. The serotonin ELISA test using Caco-2 and HT-22 cells treated with a supernatant of the bacterial culture showed that more serotonin was produced by treated cells than by untreated cells.Conclusion: L. plantarum LRCC5314 could provide a source for serotonin production, and L. plantarum LRCC5314 could be used as a functional probiotic for stress regulation.

scholarly journals Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 360 ◽  
Author(s):  
Qiuxiang Zhang ◽  
Lili Zhang ◽  
Paul Ross ◽  
Jianxin Zhao ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Annotation ◽  
Evolutionary Relationship ◽  
Glycoside Hydrolases ◽  
Human Feces ◽  
Genetic Characteristics ◽  
Lactobacillus Crispatus ◽  
Carbohydrate Binding Modules ◽  
Significant Difference ◽  
Human Vagina

Lactobacillus crispatus colonizes the human feces, human vagina, and the crops and ceca of chicken. To explore the genetic characteristics and evolutionary relationships of L. crispatus isolated from different niches, we selected 37 strains isolated from the human vagina (n = 17), human feces (n = 11), and chicken feces (n = 9), and used comparative genomics to explore the genetic information of L. crispatus from the feces and vagina. No significant difference was found in the three sources of genomic features such as genome size, GC content, and number of protein coding sequences (CDS). However, in a phylogenetic tree constructed based on core genes, vagina-derived L. crispatus and feces-derived strains were each clustered separately. Therefore, the niche exerted an important impact on the evolution of L. crispatus. According to gene annotation, the L. crispatus derived from the vagina possessed a high abundance of genes related to acid tolerance, redox reactions, pullulanase, and carbohydrate-binding modules (CBMs). These genes helped L. crispatus to better adapt to the acidic environment of the vagina and obtain more nutrients, maintaining its dominance in the vagina in competition with other strains. In feces-derived bacteria, more genes encoding CRISPR/Cas system, glycoside hydrolases (GHs) family, and tetracycline/lincomycin resistance genes were found to adapt to the complex intestinal environment. This study highlights the evolutionary relationship of L. crispatus strains isolated from the vagina and feces, and the adaptation of L. crispatus to the host environment.

scholarly journals Marine ChitinolyticPseudoalteromonasRepresents an Untapped Reservoir of Bioactive Potential

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Sara Skøtt Paulsen ◽  
Mikael Lenz Strube ◽  
Pernille Kjersgaard Bech ◽  
Lone Gram ◽  
Eva C. Sonnenschein
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolism ◽  
Glycosyl Hydrolase ◽  
Natural Habitat ◽  
Bioactive Molecules ◽  
Chitin Degradation ◽  
Antibiotic Compounds ◽  
Rapid Pace ◽  
Bioactive Potential ◽  
Untapped Resource

ABSTRACTChitin is the most abundant polymer in the marine environment and a nutrient-rich surface for adhering marine bacteria. We have previously shown that chitin can induce the production of antibiotic compounds inVibrionaceae, suggesting that the discovery of novel bioactive molecules from bacteria can be facilitated by mimicking their natural habitat. The purpose of this study was to determine the glycosyl hydrolase (GH) profiles of strains of the genusPseudoalteromonasto enable selection of presumed growth substrates and explore possible links to secondary metabolism. Genomic analyses were conducted on 62 pigmented and 95 nonpigmented strains. Analysis of the total GH profiles and multidimensional scaling suggested that the degradation of chitin is a significant trait of pigmented strains, whereas nonpigmented strains seem to be driven toward the degradation of alga-derived carbohydrates. The genomes of all pigmented strains and 40 nonpigmented strains encoded at least one conserved chitin degradation cluster, and chitinolytic activity was phenotypically confirmed. Additionally, the genomes of all pigmented and a few nonpigmented strains encoded chitinases of the rare GH family 19. Pigmented strains devote up to 15% of their genome to secondary metabolism, while for nonpigmented species it was 3% at most. Thus, pigmentedPseudoalteromonasstrains have a bioactive potential similar to that of well-known antibiotic producers of theActinobacteriaphylum. Growth on chitin did not measurably enhance the antibacterial activity of the strains; however, we demonstrated a remarkable co-occurrence of chitin degradation and the potential for secondary metabolite production in pigmentedPseudoalteromonasstrains. This indicates that chitin and its colonizers of thePseudoalteromonasgenus represent a so far underexplored niche for novel enzymes and bioactive compounds.IMPORTANCEInfectious bacteria are developing and spreading resistance to conventional treatments at a rapid pace. To provide novel potent antimicrobials, we must develop new bioprospecting strategies. Here, we combinedin silicoand phenotypic approaches to explore the bioactive potential of the marine bacterial genusPseudoalteromonas. We found that pigmented strains in particular represent an untapped resource of secondary metabolites and that they also harbor an elaborate chitinolytic machinery. Furthermore, our analysis showed that chitin is likely a preferred substrate for pigmented species, in contrast to nonpigmented species. Potentially, chitin could facilitate the production of new secondary metabolites in pigmentedPseudoalteromonasstrains.

Omics Technologies for Profiling Toxin Diversity and Evolution in Snake Venom: Impacts on the Discovery of Therapeutic and Diagnostic Agents

2020 ◽  
Vol 8 (1) ◽  
pp. 91-116 ◽  
Author(s):  
Cassandra M. Modahl ◽  
Rajeev Kungur Brahma ◽  
Cho Yeow Koh ◽  
Narumi Shioi ◽  
R. Manjunatha Kini
Keyword(s):  
Snake Venom ◽  
Posttranslational Modifications ◽  
Bioactive Molecules ◽  
Venom Protein ◽  
Biological Targets ◽  
Functional Sites ◽  
Protein Superfamilies ◽  
Rich Diversity ◽  
Diagnostic Agents ◽  
Rapid Pace

Snake venoms are primarily composed of proteins and peptides, and these toxins have developed high selectivity to their biological targets. This makes venoms interesting for exploration into protein evolution and structure–function relationships. A single venom protein superfamily can exhibit a variety of pharmacological effects; these variations in activity originate from differences in functional sites, domains, posttranslational modifications, and the formations of toxin complexes. In this review, we discuss examples of how the major venom protein superfamilies have diversified, as well as how newer technologies in the omics fields, such as genomics, transcriptomics, and proteomics, can be used to characterize both known and unknown toxins.Because toxins are bioactive molecules with a rich diversity of activities, they can be useful as therapeutic and diagnostic agents, and successful examples of toxin applications in these areas are also reviewed. With the current rapid pace of technology, snake venom research and its applications will only continue to expand.

Distinct mechanism of helicobacter pylori-mediated NF-κB activation between gastric cancer cells, MKN45 and monocystic cells, THP-1

2001 ◽  
Vol 120 (5) ◽  
pp. A82-A82 ◽  
Author(s):  
S MAEDA ◽  
Y MITSUNO ◽  
Y HIRATA ◽  
M AKANUMA ◽  
H YOSHIDA ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Cancer Cells ◽  
Gastric Cancer Cells ◽  
Distinct Mechanism

TBE in Croatia

2020 ◽  
Keyword(s):  
Tick Species ◽  
Limited Data ◽  
Notifiable Disease ◽  
Genetic Characteristics ◽  
Central European ◽  
Tick Borne Encephalitis ◽  
Tbe Virus ◽  
Endemic Areas ◽  
European Subtype

Even though tick-borne encephalitis (TBE) has been a notifiable disease in Croatia since 2007, there are no or only limited data available on the occurring tick species in the endemic areas, on the prevalence of TBE virus (TBEV) in ticks, its distribution in Croatia, and its genetic characteristics. Reporting of human cases also is very scarce. The Central European subtype of virus (TBEV-EU) appears to be present in Croatia

Sign in / Sign up

Export Citation Format

Share Document