A metagenomic perspective on the microbial prokaryotic genome census

Science Advances, Journal Year: 2025, Volume and Issue: 11(3)

Published: Jan. 17, 2025

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) >1.5 million microbial genomes in public databases, including metagenome-assembled (MAGs) uncultivated microbes. As compared to vast uncovered by metagenomic sequences, cultivated taxa account for a modest portion overall diversity, 9.73% bacteria and 6.55% archaea, while MAGs contribute 48.54% 57.05%, respectively. Therefore, substantial fraction bacterial (41.73%) archaeal PD (36.39%) still lacks any genomic representation. This unrepresented manifests primarily at lower taxonomic ranks, exemplified 134,966 species identified 18,087 samples. Our study exposes hotspots freshwater, marine subsurface, sediment, soil, other environments, whereas human samples yielded minimal novelty within context existing datasets. These results offer roadmap future genome recovery efforts, delineating uncaptured underexplored environments underscoring necessity renewed isolation sequencing.

Language: Английский

---

Ribotyping Staphylococcus epidermidis Using Probabilistic Sequence Analysis and Levenshtein Distance Algorithm

Current Microbiology, Journal Year: 2025, Volume and Issue: 82(2)

Published: Jan. 10, 2025

Staphylococcus epidermidis (S. epidermidis) live in different human locations and natural environments. For ribotyping S. sub-species, 2507 PCR-amplified reads of 16S rRNA genes a public dataset were used for probabilistic sequence analysis. A probability logo (sequence pLogo) as reference was constructed. Through implementation Levenshtein Distance algorithm, two 20-base pairs (bp) motifs, commonly present reads, identified. The top 38 isolates, which carried nucleotide domains that made sequences but have high similarity scores to 20-bp found from 11 human, 8 animal, 9 plant 10 environmental samples, indicating these motifs broadly diverse isolates. Thirty-one genes, currently not the dataset, utilized verify feasibility using sub-species. S1, S3, S2, isolates on scalp domain with similarities motif pLogo. phylogenetic tree showed S2 S3 single common ancestor. Two newly identified here, thus, provided residues epidermidis.

Language: Английский

---

Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus

The ISME Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

Language: Английский

---

Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2025, Volume and Issue: 75(1)

Published: Jan. 28, 2025

Three bacterial strains, designated FZUC8N2.13 T , FBOR7N2.3 and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic phylogenomic analysis places them within the genus Flavobacterium . Strains FZUR7N2.5 share 100% of similarity 16S rRNA gene sequence, both are most closely related to cellulosilyticum AR-3-4 with which they 97.5% similarity. Strain forms a lineage lacustre IMCC36792 97.7% The closest neighbours these three strains flevense DSM 1076 ‘ undicola ’ BBQ-18 commune PK15 average nucleotide identity digital DNA–DNA hybridization values between members below threshold 95% 70%, respectively. stain Gram-negative, rod-shaped form yellow colonies. Optimum growth occurs at 25 °C pH 7. genomic G+C contents 33.4 mol% for strain 33.2 FZUR7N2.5. major isoprenoid quinone is menaquinone 6. fatty acids summed feature 3 (C 16 : 1 ω7c and/or C ω6c) (22.6–31.1%), iso-C 15 0 (13.6–16.2 %) anteiso-C (8.7–10.5%). polar lipids consist two aminolipids, aminophospholipids one glycolipid. phylogenetic, phylogenomic, phenotypic chemotaxonomic data indicate that described species should be classified as novel species, we propose names zubiriense (=UCCCB 179 =CECT 30977 ) magnesitis 178 30976 216=CECT 31036).

Language: Английский

---

Microbial ecosystems and ecological driving forces in the deepest ocean sediments

Cell, Journal Year: 2025, Volume and Issue: 188(5), P. 1363 - 1377.e9

Published: March 1, 2025

Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in Mariana Trench, Yap and Philippine Basin for Trench Environment Ecology Research (MEER) project. Metagenomic 16S rRNA gene amplicon sequencing generated 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism larger genomes. These findings indicated that environmental factors drive novelty advancing our understanding mechanisms governing microbial ecosystems such an extreme environment.

Language: Английский

---

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2025, Volume and Issue: 75(3)

Published: March 10, 2025

We present the description of new species, Rhodococcus parequi , found during phylogenomic investigations a global collection strains identified as ( Prescottella ) equi . Strain PAM 2766 T was isolated from horse-breeding farm soil in Normandy, France, and indistinguishable R. based on usual identification tests. Whole-genome phylogenetic analyses located same sublineage together with agglutinans defluvii soli subtropicus spongiicola xishaensis is most closely related to, but sufficiently distinct from, DSM 20307 to be considered separate species. The average nt identity (ANI) aa (AAI) values are 88.60% 92.35, respectively, well below species cutoff. draft genome ~5.3 Mb size 68.98% G+C mol content. strictly aerobic non-motile produces smooth, creamy buff-coloured colonies very similar those It phenotypically differs latter by ability grow at 5 °C, strongly positive urease test 24 h specificities carbon nitrogen source utilization profile determined phenotype microarray screens. Our data indicate that belongs novel for which name sp. nov. proposed. avirulent macrophage infection assays assumed non-pathogenic. type strain (=CETC 30995 =NCTC 14987 ).

Language: Английский

---

Synergistic effects of biochar and plants can reduce greenhouse gas emissions from salt affected soil

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 14, 2025

Applying biochar and using cover crops are two potential approaches to reduce greenhouse gas (GHG) emissions. However, the effectiveness of these methods, individually or in combination, salt-affected soils remains unclear. Thus, objective was determine impact barley (Hordeum vulgare) on N2O CO2 emissions from soil. During 28-day replicated study, GHG were measured near-continuously number nirK, nirS, qnorB, nosZ gene copies 12 28 days after planting (DAP). Biochar accelerated emergence reduced N2O–N CO2–C by 68% 44% 8 14 DAP, respectively. Barley 30.4% between at DAP it nirK copies, that encodes for nitrite reductase 40.9% increased nitrous oxide 193%. The attributed reduction soil respiration, whereas changes leading efficiency N2. Overall, combining with resulted greatest (85%) compared alone.

Language: Английский

---

Research Status and Prospect of Amphibian Symbiotic Microbiota

Animals, Journal Year: 2025, Volume and Issue: 15(7), P. 934 - 934

Published: March 25, 2025

Amphibians are the most severely threatened vertebrate group in terms of biodiversity. The microbiota that coexist a mutualistic relationship with amphibians play crucial role shaping their health status, reproductive efficiency, and environmental adaptability. Understanding between is vital for elucidating causes amphibian diseases developing effective prevention control techniques, which turn significant enhancing effectiveness diversity conservation. main findings this article as follows: Firstly, it provides an overview systematic assessment analysis methods regarding importance symbiotic microbiota, detailing primary research techniques currently employed. Secondly, discusses impacts biological factors on characteristics microbial communities, including dimensions such altitude, temperature fluctuations, host dietary habits. Finally, future directions examined, five recommendations presented: (1) Establish comprehensive sample library database to create solid foundation scientific research. (2) Explore coevolutionary paths clarify dynamic evolutionary patterns principles interactions. (3) Strengthen specific areas amphibians, especially communities oral cavity cloaca. (4) Enhance Gymnophiona. (5) international cooperation build cross-border platforms jointly promote rapid development global microbiology. This summarizes current progress interaction (not necessarily mutualistic). It conservation biodiversity from perspective forward-looking directions. aims provide rich background information understanding complexity system, while also having value

Language: Английский

---

Decoding whole genome of an industrially important thermophilic bacterium Anoxybacteroides rupiense

Gene Reports, Journal Year: 2025, Volume and Issue: unknown, P. 102207 - 102207

Published: March 1, 2025

Language: Английский

---

Strategies for Actinobacteria Isolation, Cultivation, and Metabolite Production that Are Biologically Important

ACS Omega, Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Language: Английский

---