Ecological Genetics and Genomics最新文献

The heat shock matters with specific attention to the expression of Hsp60 under thermal stress in fish: A critical review

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-02-24 DOI: 10.1016/j.egg.2025.100337

Md Toasin Hossain Aunkor , Mohammad Mehedi Hasan Khan , Muhammad Anamul Kabir , Md Topu Raihan , Md Faruque Miah

Thermal stress caused by global climate change can create major challenges in the life of fish, as they are strongly affected by deviations in environmental temperatures. Heat shock proteins (HSPs) are generally synthesized when cells are subjected to temperatures above their normal requirements for survival. In particular, Hsp60 plays a vital role in managing this stress by assisting protein folding, preventing aggregation, and maintaining cellular integrity. This review primarily highlights the different effects of heat stress on the life of fish. However, special emphasis is placed on compiling and analyzing current knowledge of Hsp60 expression in various fish species under different temperatures. This paper also investigates the physiological impacts of thermal stress on various organs, such as the liver, heart, spleen, gills, kidney, brain, muscle, ovary, and testis to enhance the broader understanding of fish response to temperature fluctuations, with a focus on Hsp60 expression. In addition, the contribution of Hsp60 to embryonic development is also accentuated to some extent. Furthermore, the paper outlines several research gaps in the study of Hsp60 expression, which will be imperative for future efforts to improve our understanding of this essential chaperon in fish species.

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引用次数: 0

Tracing the trails: Insights into the genetic connectivity and potential origin of Nile tilapia populations in Tanzanian Saline Rift Valley Lakes 追踪踪迹：坦桑尼亚盐碱地裂谷湖中尼罗罗非鱼种群遗传连接性和潜在起源的见解

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-02-11 DOI: 10.1016/j.egg.2025.100336

Bonus M. Morandus , Justine D. Maganira , Cyrus Rumisha

Despite their elevated salinity levels, the East African Saline Rift Valley Lakes (SRVLs) are home to unique endemic fish species that support local communities. However, the non-native Nile tilapia (Oreochromis niloticus) has rapidly established itself in some of these lakes, threatening endemic fish populations. Yet, the genetic connectivity and potential origin of Nile tilapia populations in the SRVLs remain poorly understood. This study aimed to address this gap by analysing 203 mitochondrial cytochrome oxidase subunit I (COI) sequences (599 base pairs) from Nile tilapia collected across the SRVLs, fish farms, and three freshwater ecosystems in Tanzania. We identified five distinct haplotypes, three of which were shared among the SRVLs, local fish farms, and three freshwater ecosystems: Lake Victoria, the Pangani River, and Mindu Dam. Given the lack of apparent physical connectivity among most of these sites, these shared haplotypes suggest that human-mediated introductions and escape events from aquaculture are likely the main drivers of Nile tilapia's spread into the SRVLs, rather than natural gene flow. Furthermore, significant genetic differentiation was observed among some SRVL populations, suggesting multiple introductions from different source populations, or founder effects and genetic drift, particularly in smaller and newly established populations. Our findings highlight the need for stringent measures to prevent the further spread of Nile tilapia into other SRVLs. Additionally, effective management strategies are necessary in SRVLs where Nile tilapia has already been introduced to safeguard endemic fish stocks and mitigate unintended ecological impacts.

{"title":"Tracing the trails: Insights into the genetic connectivity and potential origin of Nile tilapia populations in Tanzanian Saline Rift Valley Lakes","authors":"Bonus M. Morandus , Justine D. Maganira , Cyrus Rumisha","doi":"10.1016/j.egg.2025.100336","DOIUrl":"10.1016/j.egg.2025.100336","url":null,"abstract":"<div><div>Despite their elevated salinity levels, the East African Saline Rift Valley Lakes (SRVLs) are home to unique endemic fish species that support local communities. However, the non-native Nile tilapia (<em>Oreochromis niloticus</em>) has rapidly established itself in some of these lakes, threatening endemic fish populations. Yet, the genetic connectivity and potential origin of Nile tilapia populations in the SRVLs remain poorly understood. This study aimed to address this gap by analysing 203 mitochondrial cytochrome oxidase subunit I (COI) sequences (599 base pairs) from Nile tilapia collected across the SRVLs, fish farms, and three freshwater ecosystems in Tanzania. We identified five distinct haplotypes, three of which were shared among the SRVLs, local fish farms, and three freshwater ecosystems: Lake Victoria, the Pangani River, and Mindu Dam. Given the lack of apparent physical connectivity among most of these sites, these shared haplotypes suggest that human-mediated introductions and escape events from aquaculture are likely the main drivers of Nile tilapia's spread into the SRVLs, rather than natural gene flow. Furthermore, significant genetic differentiation was observed among some SRVL populations, suggesting multiple introductions from different source populations, or founder effects and genetic drift, particularly in smaller and newly established populations. Our findings highlight the need for stringent measures to prevent the further spread of Nile tilapia into other SRVLs. Additionally, effective management strategies are necessary in SRVLs where Nile tilapia has already been introduced to safeguard endemic fish stocks and mitigate unintended ecological impacts.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100336"},"PeriodicalIF":0.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143394575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Whole mitogenome analysis of endangered freshwater catfish Horabagrus nigricollaris

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-02-06 DOI: 10.1016/j.egg.2025.100335

V.J. Rejish Kumar , S. Chandhini , V.M. Arjunan , P.H. Anvar Ali

The genus Horabagrus comprised of two species of freshwater catfish endemic to peninsular India, H. brachysoma and H. nigricollaris. Compared to H. brachysoma, H. nigricollaris (black collared catfish) distribution is very much limited and the species is under the threat of extinction. In the present study we have sequenced and analysed the complete mitochondrial genome of H. nigricollaris. The mitochondrial genome is 16561 bp in length that consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes with a control region (D-loop). The overall base composition was A: 31.3 %, T: 25.4 %, G: 15.2 % and C: 28 %. Most frequently used codon was CUA which codes for the amino acid Leucine. Comparative analysis of H. nigricollaris mitogenome demonstrated a close similarity with its sister species H. brachysoma in composition, gene order and orientation. The mitogenome characterised in this study can form a primary genomic resource for further research on this endangered catfish.

引用次数: 0

Whole genome analysis of Planococcus chinensis MB653 isolated from an infected orthopaedic implant sample from Pakistan

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-02-04 DOI: 10.1016/j.egg.2025.100334

Sidra Abbas , Martin Welch , Azra Yasmin

This study presents the isolation and genomic analysis of the strain Planococcus chinensis MB653, which was obtained from an infected orthopaedic implant sample. Strain MB653 grew optimally at pH 7.0 and at 30–37 °C. The genome of MB653 was sequenced using Illumina sequencing, and the resulting contigs were annotated, with 46.5 % G + C content. The analysis revealed the presence of various virulence factors, including genes involved in protein secretion systems and secretion pathways. Additionally, the strain possessed genes related to flagella and pili, although it was not found to be motile. The whole genome sequence revealed that strain MB653 encoded a larger number of genes associated with antimicrobial resistance than its most other environmental counterpart. The genome analysis identified several antibiotic resistance genes and genes associated with resistance to different compounds. Genes conferring resistance to heavy metals such as cadmium (cadA, cadC), arsenic (arsABC, arsR) and quaternary ammonium compounds (qacC) were also identified. Furthermore, the study explored the secondary metabolite potential of MB653, revealing the presence of gene clusters associated with the production of antimicrobial peptides and terpenes. These findings suggest that MB653 possesses potential virulence factors and may produce secondary metabolites that contribute to its pathogenicity. Further research is needed to investigate the specific roles of these gene clusters and their implications for virulence.

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引用次数: 0

Molecular identification and phylogenetics analysis of southern Indian Amaranthus L. using chloroplast barcodes

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-22 DOI: 10.1016/j.egg.2025.100329

Pinke Cherian , Stalin Nithaniyal , Prabhu Srinivasan

The genus Amaranthus L. is an underutilized short-lived perennial herb belonging to the Amaranthaceae. Some nutritive-rich species are used as food crops, pseudocereal, and vegetables and are farmed worldwide. Species-level identification of congeners is often complex due to transitional forms and overlapping diagnostic features. Therefore, the current study employed molecular identification and differentiation of five Amaranthus species such as Amaranthus caudatus, A. dubius, A. spinosus, A. tricolor, and A. viridis, using Ribulose 1,5 Biphosphate Carboxylase (rbcL) and Maturase K (matK) chloroplast barcode markers. The DNA extraction and PCR amplification were 100 % successful, and the bidirectional DNA sequencing recovered 607 bp and 820 bp target sequences for rbcL and matK, respectively. Primary validation of DNA sequences of each species using the BLAST algorithm showed the highest similarity between 99.8 % and 100 % with the expected species. The results of nucleotide composition indicated that matK had more variable and parsimony informative sites than the rbcL DNA barcode. The phylogenetic relationship was studied by assembling DNA barcodes for twelve Amaranthus species. The Bayesian likelihood analysis using a concatenated dataset of the rbcL + matK tree revealed two major clades. Clade one comprises seven species, and five other species in two sub-clades formed in the clade two. All the species of Amaranthus resolved as a distinct monophyletic clade, with Celosia argentea as the basal clade. This study provides the foundation for applying DNA barcoding in delineating complex congeners and understanding the genetic relationships. In addition, DNA barcodes obtained from this study could be helpful for stakeholders, consumers, and regulatory agencies to authenticate Amaranthus species traded as functional foods, medicine, and ornamental plants.

{"title":"Molecular identification and phylogenetics analysis of southern Indian Amaranthus L. using chloroplast barcodes","authors":"Pinke Cherian , Stalin Nithaniyal , Prabhu Srinivasan","doi":"10.1016/j.egg.2025.100329","DOIUrl":"10.1016/j.egg.2025.100329","url":null,"abstract":"<div><div>The genus <em>Amaranthus</em> L. is an underutilized short-lived perennial herb belonging to the Amaranthaceae. Some nutritive-rich species are used as food crops, pseudocereal, and vegetables and are farmed worldwide. Species-level identification of congeners is often complex due to transitional forms and overlapping diagnostic features. Therefore, the current study employed molecular identification and differentiation of five <em>Amaranthus</em> species such as <em>A</em><em>maranthus</em> <em>caudatus</em>, <em>A. dubius</em>, <em>A. spinosus</em>, <em>A. tricolor</em>, and <em>A. viridis</em>, using Ribulose 1,5 Biphosphate Carboxylase (<em>rbcL</em>) and Maturase K (<em>matK</em>) chloroplast barcode markers. The DNA extraction and PCR amplification were 100 % successful, and the bidirectional DNA sequencing recovered 607 bp and 820 bp target sequences for <em>rbcL</em> and <em>matK,</em> respectively<em>.</em> Primary validation of DNA sequences of each species using the BLAST algorithm showed the highest similarity between 99.8 % and 100 % with the expected species. The results of nucleotide composition indicated that <em>matK</em> had more variable and parsimony informative sites than the <em>rbcL</em> DNA barcode<em>.</em> The phylogenetic relationship was studied by assembling DNA barcodes for twelve <em>Amaranthus</em> species<em>.</em> The Bayesian likelihood analysis using a concatenated dataset of the <em>rbcL</em> + <em>matK</em> tree revealed two major clades. Clade one comprises seven species, and five other species in two sub-clades formed in the clade two<em>.</em> All the species of <em>Amaranthus</em> resolved as a distinct monophyletic clade, with <em>C</em><em>elosia argentea</em> as the basal clade. This study provides the foundation for applying DNA barcoding in delineating complex congeners and understanding the genetic relationships. In addition, DNA barcodes obtained from this study could be helpful for stakeholders, consumers, and regulatory agencies to authenticate Amaranthus species traded as functional foods, medicine, and ornamental plants.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100329"},"PeriodicalIF":0.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Utilization of Start Codon Targeted (SCoT) markers for the evaluation of population structure and genetic variability in Persicaria glabra (Willd.) M. Gomez

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-21 DOI: 10.1016/j.egg.2025.100333

K. Arsha, B. Vishnu, E.A. Siril

Persicaria glabra (Willd.) M. Gomez; family Polygonaceae, an important medicinal herb and a wetland indicator species. The germplasm of this species is highly depleted due to habitat destructions coupled with overexploitation. The present research work was undertaken to evaluate the genetic variability and population structure of available germplasm across Kerala, South India. A total of 29 accessions of P. glabra (PG), were collected from various agroclimatic zones. During genetic diversity studies, Start Codon Targeted (SCoT) markers bring out 190 amplicons with selected individuals and 79 % of the bands were polymorphic. SCoT 9 has the highest resolving power (8.28) and thereby ensures better discrimination of accessions at the molecular level. The below median value for polymorphism information content (PIC) represented a moderate range of allelic variations at the individual level. Similarly, a modest extent of heterozygous alleles was present within the population as evident from the marginal value for Nei's gene diversity. However, the lowest value for Shannon's information index of 0.37 revealed the presence of genetically diverse individuals within the collection. The dendrogram created by the unweighted neighbor-joining method distributed all accessions into its three main clusters, and the grouping was not concordant with their habitats. Population structure analysis revealed the probability of two assumed subpopulations within the germplasm. Eventually, P. glabra accessions showed distinct population structure and genetic makeup. The significant level of genetic variability among the P. glabra accessions can be used for germplasm management, conservation, and selection of superior genotypes for breeding.

{"title":"Utilization of Start Codon Targeted (SCoT) markers for the evaluation of population structure and genetic variability in Persicaria glabra (Willd.) M. Gomez","authors":"K. Arsha, B. Vishnu, E.A. Siril","doi":"10.1016/j.egg.2025.100333","DOIUrl":"10.1016/j.egg.2025.100333","url":null,"abstract":"<div><div><em>Persicaria glabra</em> (Willd.) M. Gomez; family Polygonaceae, an important medicinal herb and a wetland indicator species. The germplasm of this species is highly depleted due to habitat destructions coupled with overexploitation. The present research work was undertaken to evaluate the genetic variability and population structure of available germplasm across Kerala, South India. A total of 29 accessions of <em>P. glabra</em> (PG), were collected from various agroclimatic zones. During genetic diversity studies, Start Codon Targeted (SCoT) markers bring out 190 amplicons with selected individuals and 79 % of the bands were polymorphic. SCoT 9 has the highest resolving power (8.28) and thereby ensures better discrimination of accessions at the molecular level. The below median value for polymorphism information content (PIC) represented a moderate range of allelic variations at the individual level. Similarly, a modest extent of heterozygous alleles was present within the population as evident from the marginal value for Nei's gene diversity. However, the lowest value for Shannon's information index of 0.37 revealed the presence of genetically diverse individuals within the collection. The dendrogram created by the unweighted neighbor-joining method distributed all accessions into its three main clusters, and the grouping was not concordant with their habitats. Population structure analysis revealed the probability of two assumed subpopulations within the germplasm. Eventually, <em>P. glabra</em> accessions showed distinct population structure and genetic makeup. The significant level of genetic variability among the <em>P. glabra</em> accessions can be used for germplasm management, conservation, and selection of superior genotypes for breeding.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100333"},"PeriodicalIF":0.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Agronomic evaluation of cowpea (Vigna unguiculata L.) lines for varietal development in the Brekum West municipality of Ghana

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-19 DOI: 10.1016/j.egg.2025.100332

John Abugri Amenga , Esther Fobi Donkor , Kwabena Atakora , Samuel Novor

Cowpea (Vigna unguiculata (L.) is a vital legume with high nutritional and economic value, well-adapted to drought, heat, and biotic stresses. Limited data on the growth and yield of Ghanaian cowpea lines prompted the evaluation of 15 lines in Berekum West for varietal development. The study was conducted across three locations (Nyekyemam, Mantukwa, and Prosu) in the Berekum West municipality in the Bono Region of Ghana during the major and minor seasons of 2021. The experiment followed a randomized complete block design (RCBD) with three replications. Data were analyzed using GenStat Statistical Software 12th Edition. AMMI stability analysis was also used to assess the stability of the cowpea lines across the environments. The analysis revealed significant differences among the growth and yield parameters. Genotype Yok-Kpitio Red performed best across the three environments with mean yield values of 392.00, 370.1, and 380.6 kg/ha, while the least performing genotype was UCC Early. Stability analysis identified Yok-Kpitio Red as the top-performing genotype with the lowest Genotype Rank value of 1. Yok-Kpitio White was the most stable genotype with the lowest AMMI Stability Value (ASV) and Rank AMMI Stability Value (RASV). Kum-Zoya had the highest Yield Stability Index (YSI) value, showing a good balance between high yield and stability. Farmers should prioritize cultivating Yok-Kpitio Red for its adaptability, robustness, and reliable yields during different farming seasons.

{"title":"Agronomic evaluation of cowpea (Vigna unguiculata L.) lines for varietal development in the Brekum West municipality of Ghana","authors":"John Abugri Amenga , Esther Fobi Donkor , Kwabena Atakora , Samuel Novor","doi":"10.1016/j.egg.2025.100332","DOIUrl":"10.1016/j.egg.2025.100332","url":null,"abstract":"<div><div>Cowpea (<em>Vigna unguiculata</em> (L.) is a vital legume with high nutritional and economic value, well-adapted to drought, heat, and biotic stresses. Limited data on the growth and yield of Ghanaian cowpea lines prompted the evaluation of 15 lines in Berekum West for varietal development. The study was conducted across three locations (Nyekyemam, Mantukwa, and Prosu) in the Berekum West municipality in the Bono Region of Ghana during the major and minor seasons of 2021. The experiment followed a randomized complete block design (RCBD) with three replications. Data were analyzed using GenStat Statistical Software 12th Edition. AMMI stability analysis was also used to assess the stability of the cowpea lines across the environments. The analysis revealed significant differences among the growth and yield parameters. Genotype Yok-Kpitio Red performed best across the three environments with mean yield values of 392.00, 370.1, and 380.6 kg/ha, while the least performing genotype was UCC Early. Stability analysis identified Yok-Kpitio Red as the top-performing genotype with the lowest Genotype Rank value of 1. Yok-Kpitio White was the most stable genotype with the lowest AMMI Stability Value (ASV) and Rank AMMI Stability Value (RASV). Kum-Zoya had the highest Yield Stability Index (YSI) value, showing a good balance between high yield and stability. Farmers should prioritize cultivating Yok-Kpitio Red for its adaptability, robustness, and reliable yields during different farming seasons.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100332"},"PeriodicalIF":0.0,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing bacterial diversity in Myristica swamps: A metagenomic perspective from the Southern Western Ghats

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-17 DOI: 10.1016/j.egg.2025.100330

Darshitha S, Pathissery John Sarlin, Megha M

The Western Ghats, a UNESCO World Heritage site, is home to the freshwater Myristica swamps, which thrive in acidic, waterlogged conditions in Karnataka, Kerala, and Tamil Nadu. Myristica trees, essential for maintaining the ecosystem, are vital for its integrity. A study comparing bacterial diversity in sediment samples from Myristica swamp patches (Pezhummoodu (S1) and Verukuzhypacha (S2) in the Punnala Model Forest Station, and Manthadam (S3) in the Ambanar Model Forest Station) in the Southern Western Ghats of Kerala, using a metagenomic approach and Illumina MiSeq sequencing revealed that Proteobacteria were the predominant phyla, followed by Firmicutes, Bacteroidetes, and Actinobacteria in both S1 and S2. Unclassified bacterial phyla were present in all samples. A Venn diagram revealed 43 genera unique to S1 and 194 unique to S2, with none found exclusively in S3. Pseudomonas is the dominant genera in S3, constituting 50.9 %. The study highlights significant bacterial communities in the myristica swamp soil and underscores the importance of microbial exploration in these environments. This is the first-ever metagenomic analysis of bacterial diversity in Myristica swamps, enhancing our understanding of the complex interactions that sustain these unique wetland habitats. The complex microbial network, comprising Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, promotes soil multi-nutrient cycling, pollutants breakdown, water quality, and nutrient availability. This knowledge has the potential to inform conservation strategies and facilitate the protection and restoration of Myristica swamps by maintaining their delicate microbial ecosystems.

{"title":"Assessing bacterial diversity in Myristica swamps: A metagenomic perspective from the Southern Western Ghats","authors":"Darshitha S, Pathissery John Sarlin, Megha M","doi":"10.1016/j.egg.2025.100330","DOIUrl":"10.1016/j.egg.2025.100330","url":null,"abstract":"<div><div>The Western Ghats, a UNESCO World Heritage site, is home to the freshwater Myristica swamps, which thrive in acidic, waterlogged conditions in Karnataka, Kerala, and Tamil Nadu. Myristica trees, essential for maintaining the ecosystem, are vital for its integrity. A study comparing bacterial diversity in sediment samples from Myristica swamp patches (Pezhummoodu (S1) and Verukuzhypacha (S2) in the Punnala Model Forest Station, and Manthadam (S3) in the Ambanar Model Forest Station) in the Southern Western Ghats of Kerala, using a metagenomic approach and Illumina MiSeq sequencing revealed that Proteobacteria were the predominant phyla, followed by <em>Firmicutes</em>, <em>Bacteroidetes</em>, and <em>Actinobacteria</em> in both S1 and S2. Unclassified bacterial phyla were present in all samples. A Venn diagram revealed 43 genera unique to S1 and 194 unique to S2, with none found exclusively in S3. <em>Pseudomonas</em> is the dominant genera in S3, constituting 50.9 %. The study highlights significant bacterial communities in the myristica swamp soil and underscores the importance of microbial exploration in these environments. This is the first-ever metagenomic analysis of bacterial diversity in Myristica swamps, enhancing our understanding of the complex interactions that sustain these unique wetland habitats. The complex microbial network, comprising Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, promotes soil multi-nutrient cycling, pollutants breakdown, water quality, and nutrient availability. This knowledge has the potential to inform conservation strategies and facilitate the protection and restoration of Myristica swamps by maintaining their delicate microbial ecosystems.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100330"},"PeriodicalIF":0.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic adaptations of methicillin-resistant Staphylococcus aureus in healthcare environments

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-13 DOI: 10.1016/j.egg.2025.100331

Vishnu Priya Panneerselvam, Leela Kagithakara Vajravelu, Jayaprakash Thulukanam, Rahul Harikumar Lathakumari, Poornima Baskar Vimala, Dakshina M. Nair

Methicillin-resistant Staphylococcus aureus (MRSA) exemplifies genomic adaptation to selective pressures in high-stress environments, such as healthcare facilities. This study investigates the genomic divergence and adaptive mechanisms of MRSA strains isolated over three years (2021–2023) in a leading healthcare facility in southern India. A total of 36,127 patient samples were analyzed, yielding 1825 Staphylococcus aureus isolates, of which 364 (19.94 %) were identified as MRSA through phenotypic testing for oxacillin and cefoxitin resistance.

Molecular characterization using polymerase chain reaction confirmed the presence of mecA in 98 % of MRSA isolates and icaA and icaD in 87 %, indicating their critical role in methicillin resistance and biofilm formation. MRSA prevalence increased significantly over the study period, peaking at 27.08 % in 2023. Exudate samples accounted for 77.47 % of MRSA isolates, highlighting the role of biofilm-mediated persistence in wound infections. The Surgery department reported the highest burden, with 29.9 % of MRSA infections.

Antibiotic resistance was highest for cefoxitin (99.05 %), penicillin (96.27 %), and levofloxacin (87.47 %), while vancomycin and linezolid remained effective, with sensitivity rates of 99.33 %. These findings illustrate MRSA's genomic adaptations, showcasing its evolutionary resilience under anthropogenic pressures. By integrating molecular insights, this study provides critical insights into resistance evolution, biofilm-mediated persistence, and species diversification in high-stress ecosystems. Such findings highlight the importance of linking ecological genomics to strategies for mitigating antimicrobial resistance, addressing an urgent global health challenge.

{"title":"Genomic adaptations of methicillin-resistant Staphylococcus aureus in healthcare environments","authors":"Vishnu Priya Panneerselvam, Leela Kagithakara Vajravelu, Jayaprakash Thulukanam, Rahul Harikumar Lathakumari, Poornima Baskar Vimala, Dakshina M. Nair","doi":"10.1016/j.egg.2025.100331","DOIUrl":"10.1016/j.egg.2025.100331","url":null,"abstract":"<div><div>Methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) exemplifies genomic adaptation to selective pressures in high-stress environments, such as healthcare facilities. This study investigates the genomic divergence and adaptive mechanisms of MRSA strains isolated over three years (2021–2023) in a leading healthcare facility in southern India. A total of 36,127 patient samples were analyzed, yielding 1825 <em>Staphylococcus aureus</em> isolates, of which 364 (19.94 %) were identified as MRSA through phenotypic testing for oxacillin and cefoxitin resistance.</div><div>Molecular characterization using polymerase chain reaction confirmed the presence of <em>mecA</em> in 98 % of MRSA isolates and <em>icaA</em> and <em>icaD</em> in 87 %, indicating their critical role in methicillin resistance and biofilm formation. MRSA prevalence increased significantly over the study period, peaking at 27.08 % in 2023. Exudate samples accounted for 77.47 % of MRSA isolates, highlighting the role of biofilm-mediated persistence in wound infections. The Surgery department reported the highest burden, with 29.9 % of MRSA infections.</div><div>Antibiotic resistance was highest for cefoxitin (99.05 %), penicillin (96.27 %), and levofloxacin (87.47 %), while vancomycin and linezolid remained effective, with sensitivity rates of 99.33 %. These findings illustrate MRSA's genomic adaptations, showcasing its evolutionary resilience under anthropogenic pressures. By integrating molecular insights, this study provides critical insights into resistance evolution, biofilm-mediated persistence, and species diversification in high-stress ecosystems. Such findings highlight the importance of linking ecological genomics to strategies for mitigating antimicrobial resistance, addressing an urgent global health challenge.</div></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"34 ","pages":"Article 100331"},"PeriodicalIF":0.0,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143133911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Human gut microbiome determining athletes’ performance: An insight from genomic analysis

Q3 Agricultural and Biological Sciences

Ecological Genetics and Genomics

Pub Date : 2025-01-09 DOI: 10.1016/j.egg.2025.100327

Shih Chung Cheng , Chieh Chang , Yen-Cheng Chen , Takashi Gojobori , Ping-Kun Chiu

The Olympic Games are widely regarded as the pinnacle of global sports competition, where victories and medal counts symbolize a nation's strength and prestige. With growing attention on the Olympics and increasing interest in exercise, nutrition, and athletes as a population closely tied to gut microbiota, this article seeks to examine the relationship between athletes' gut microbiota and the optimization of athletic performance. Our goal is to provide a comprehensive overview and scientific evidence to guide training and dietary strategies for athletes, enhancing both their performance and health. Particular focus is placed on the effects of different types of sports, athletic disciplines, and fitness training programs on gut microbiota. It is well established that the gut microbiome plays a crucial role in digestion and nutrient absorption, providing energy to the host. Microbial fermentation produces key metabolites for athletes, such as short-chain fatty acids (SCFAs), lactate, and branched-chain fatty acids, which are essential for optimal performance. Through sports genomic analyses plus practice of Zone Diet, tailored solutions can be developed to boost the performance of athletes across various disciplines. This review highlights the differences in gut microbiota between elite and amateur athletes, the influence of diverse training regimens on microbial composition, and the role of dietary intake in shaping gut health. By exploring the intricate connections between exercise, diet, and gut microbiota, this research aims to contribute to advancements in sports science, nutrition, and public health, ultimately enhancing both athletic performance and general well-being.

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引用次数: 0