Assessment of Microbial Genomes Isolated from Ancient City Stratonikeia in Western Anatolia and Speculations on Human Activities and Environmental Interactions
Ancient DNA and metagenomic studies provide valuable insights into microbial evolution, host–microbe interactions, and the ecology of ancient microbial communities; however, data from urban archaeological contexts remain limited. This study investigated microbial DNA preserved in paired petrous bone and adjacent sediment samples recovered from the Bath–Gymnasium complex of Stratonikeia, a Hellenistic–Roman city in western Anatolia, to characterize microbial diversity and functional gene profiles in an archaeological context. DNA was extracted under contamination-controlled conditions and analysed using high-throughput shotgun metagenomic sequencing. Bioinformatic analyses included taxonomic profiling, microbial diversity assessment, differential abundance analysis, and characterization of virulence-associated and antimicrobial resistance-related genes. The RH1MK1 (Tepidarium) samples exhibited greater microbial diversity and a higher relative abundance of bacterial taxa with recognized pathogenic potential, including Escherichia coli, Shigella flexneri, Vibrio cholerae, and Clostridioides difficile, compared with the SRH1PPG (Palaestra) samples. Virulence-associated genes, including Shiga toxin-, cholera toxin-, and type III secretion system-related sequences, together with antimicrobial resistance-associated genes, were more abundant in RH1MK1, consistent with differences in depositional and microenvironmental conditions between the two archaeological contexts. Comparative analyses revealed both shared and site-specific microbial profiles relative to other Anatolian archaeological sites. These findings demonstrate the potential of shotgun metagenomics for investigating preserved microbial DNA in archaeological materials while emphasizing that the detected microbial taxa and functional genes should be interpreted within their archaeological and depositional context rather than as direct evidence of ancient infectious diseases or epidemic events.
Riverine sediments serve as critical reservoirs of microbial diversity and functional genes, reflecting both natural ecological processes and anthropogenic impacts. In the present study, we employed a shotgun metagenomic approach to investigate microbial community composition, antimicrobial resistance (AMR) genes, and virulence factors in sediments collected from three environmentally distinct locations of the Yamuna River near Agra, India, representing BSA, TGY, and YEA. The sediment DNA was subjected to high-throughput Illumina sequencing, followed by quality control, assembly, and open reading frame prediction. Taxonomic classification and diversity analyses were performed using MEGAN6 and R-based statistical tools, while AMR genes were identified from predicted metagenomic proteins using the Resistance Gene Identifier (RGI) against the CARD database, with high-confidence perfect and strict hits retained; ARGs were interpreted independently of species-level host assignment. Virulence factors were assessed through presence–absence profiling of functionally relevant gene categories. The results revealed pronounced spatial heterogeneity in microbial communities, with increasing taxonomic diversity, functional complexity, and evenness from BSA to TGY and YEA. TGY and YEA composite samples showed greater observed representation of high-confidence AMR gene predictions spanning multiple drug classes and resistance mechanisms, alongside a diverse repertoire of virulence-associated genes linked to motility, adhesion, and secretion systems. In contrast, the BSA site harbored a comparatively simpler resistome and virulome. Overall, this study highlights Yamuna River sediments as important reservoirs of resistance and virulence determinants and underscores the need for long-term genomic surveillance to inform risk assessment, pollution control, and sustainable river management strategies.
A. K. Rout, P. Tripathy, S. Dey et al.· Frontiers in Microbiology· 0 citations
Bacteria employ diverse mechanisms to cope with environmental stress, yet how sediment-associated microbial communities adjust to contamination—particularly heavy metals—in tropical port ecosystems remains insufficiently characterized. This study characterized the bacterial community profile based on amplicon sequencing and predicted the functional potential for heavy-metal resistance in surface sediments from Tanjung Emas Port, Semarang (TEPS), an area chronically exposed to wastewater pollutants and metal contamination from intensive anthropogenic activities. Amplicon-based metabarcoding targeting the 16S rRNA V3–V4 region was applied. Sequence processing using Cutadapt and DADA2 yielded 38,742–42,064 high-quality Amplicon Sequence Variants (ASVs) per sample. Functional potentials were inferred using PICRUSt2, and downstream analyses were conducted in RStudio. The community was dominated by the phylum Pseudomonadota (31–39%), class Gammaproteobacteria (27–35%), order Steroidobacterales (8–10%), family Woeseiaceae (8–10%), and genus Woeseia (13–16%), reflecting adaptation to organic-rich, pollutant-impacted conditions including Cu and Pb contamination. Alpha and beta-diversity analyses revealed significant differences among sampling locations (p<0.05). Predictive functional profiling indicated a high potential for putative heavy-metal resistance genes (HMRGs) associated with Cu and Pb resistance, highlighting the ecological resilience and bioremediation potential of the indigenous bacterial community.
E. Purnomo, H. Kusumaningrum, A. Budiharjo et al.· Biointerface Research in App...· 0 citations
Soda lakes represent some of the most extreme aquatic ecosystems on Earth, yet their microbial diversity and functional potential remain poorly characterized, particularly in East Africa. This study presents the first shotgun metagenomic analysis of bacterial communities inhabiting both water and sediment of Small Momela Lake, a soda lake in northern Tanzania. Samples were sequenced using Illumina NovaSeq and analyzed with MetaPhlAn4 and HUMAnN3 to resolve taxonomic composition, diversity patterns and predicted metabolic functions. Results showed 27 distinct species within Pseudomonadota, Bacteroidota, Firmicutes, Cyanobacteria and Verrucomicrobia dominated by sulfur-cycling Thioalkalivibrio denitrificans and uncultured Candidatus lineages. Notably, based on currently available literature multiple taxa were detected for the first time in soda lake environments globally, within Africa and East Africa, expanding the known biogeography of extremophiles. Functional profiling revealed a strong enrichment of nucleotide and amino acid biosynthesis pathways, alongside marker genes linked to pH homeostasis, osmotic stress tolerance, sulfur metabolism and carbon fixation. These features suggest pronounced metabolic flexibility supporting microbial persistence under extreme alkaline and saline conditions. These findings underscore Small Momela Lake as a critical reservoir of novel, functional bacterial resources with promising applications in biotechnology and bioprospecting.
A. A. Siima, Sadikiel E. Kaale, F. Mpenda et al.· Discover Life· 0 citations
Antarctic soils harbor highly specialized bacterial communities that perform essential functions in the functioning of polar ecosystems; however, the composition and structure of these communities remain poorly understood in many areas of Antarctica. The objective of this study was to characterize the diversity and structure of bacterial communities present in soils from four islands in the South Shetland Archipelago (Torre, Barrientos, Greenwich, and Dee) using 16S rRNA gene amplicon sequencing. Total genomic DNA was extracted from composite soil samples, followed by amplification of the 16S rRNA gene and sequencing on the Illumina MiSeq platform. Taxonomic classification allowed the sequences to be assigned from the domain level down to the species level, achieving classification rates between 98.47% and 99.39% at the domain level and between 57.39% and 65.88% at the species level. The bacterial communities were dominated by the phyla Bacillota, Pseudomonadota, Actinomycetota, and Bacteroidota, although variations in relative abundance patterns were observed among the composite samples analyzed. Alpha diversity indices revealed high taxonomic complexity, with greater species richness on Dee Island and greater evenness in Greenwich, highlighting differences in the diversity patterns observed among the composite samples analyzed. Taken together, these results expand our understanding of bacterial biodiversity in Antarctic soils and provide a baseline for future research in microbial ecology, biogeography, and the exploration of the biotechnological potential of microorganisms adapted to extreme environments.
María Fernanda Pincay Cantos, Juan J. Garrido, Gabriela María Vergara-Grandes et al.· Bacteria· 0 citations
The El Tatio geothermal field is identified as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration and expands current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems.
Bernardita Valenzuela, Ignacio Navarrete-Diaz, Mayra Cayo et al.· International Journal of Mol...· 0 citations
A comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome is provided and microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake are identified.
M. Macey, Velislava Ilieva, B. Stephens et al.· Environmental Microbiome· 0 citations
