Evidence map›Paper›PMID 39786631›Full record

ArticleApplied biochemistry and biotechnology2025

Genomic, Molecular Networking-Based Metabolomic, and Bioactivity Profiling of Actinobacteria from Undisturbed Caves in Pakistan.

Shahid Nawaz, Leigh Skala, Muhammad Amin, Fernanda Iruegas-Bocardo, Arash Samadi, K H Ahammad Uz Zaman, Jeff H Chang, Imran Sajid, Taifo Mahmud

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Applied biochemistry and biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Shahid NawazInstitute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, 54590, Pakistan.
Leigh SkalaDepartment of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA.
Muhammad AminDepartment of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA.
Fernanda Iruegas-BocardoDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
Arash SamadiDepartment of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA.
K H Ahammad Uz ZamanDepartment of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA.
Jeff H ChangDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
Imran SajidInstitute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, 54590, Pakistan. imran.mmg@pu.edu.pk.ORCID http://orcid.org/0000-0002-4781-1455
Taifo MahmudDepartment of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA. taifo.mahmud@oregonstate.edu.ORCID http://orcid.org/0000-0001-9639-526X

Funding

Research Training in Natural Product Complementary and Integrative Health - Diversity Supplement to T32 Predoctoral Training GrantT32AT010131 · NCCIH · OREGON STATE UNIVERSITY · PI TAIFO MAHMUD, RICHARD B VAN BREEMEN · 2020 to 2026
$1.8M
Higher Education Commision, Pakistan IRSIP GrantHigher Education Commision, Pakistan NRPU-2121NCCIH NIH HHS T32 AT010131U.S. Department of Agriculture 2021-67013-33571
6 · The paper itself

Abstract

Caves are a unique ecosystem that harbor diverse microorganisms, and provide a challenging environment to the dwelling microbial communities, which may boost gene expression and can lead to the production of inimitable bioactive natural products. In this study, we obtained 59 actinobacteria from four different caves located in Bahadurkhel, District Karak, Pakistan. On the basis of taxonomic characteristics, 30 isolates were selected and screened for secondary metabolites production and bioactivity profiling. The extracts of all the isolates exhibited promising antibacterial activity against several pathogenic bacteria, with the best outcome seen in the extract of isolate SNK 21. The metabolomic analysis of the extracts by LC-MS/MS-based molecular networking and whole genome sequencing (WGS) followed by antiSMASH analysis revealed the presence of diverse secondary metabolites and biosynthetic gene clusters (BGCs) in SNK 21. Purification of compounds by manual chromatography, HPLC, and characterization by NMR, HR-MS, led to the identification of the active compounds, actinomycin D and its isomer. In addition, metabolomic analysis and genome mining of morphologically distinct isolates, SNK 202 and SNK 329, also showed diverse secondary metabolites and BGCs, underscoring the potential of actinobacteria from undisturbed caves in Pakistan as a new source of bioactive compounds.

Indexed as

ActinobacteriaAnti-Bacterial AgentsCavesGenome, BacterialGenomicsMetabolomicsPakistanAnti-Bacterial AgentsActinobacteriaActinomycinBiosynthetic gene clustersCavesGenome miningMolecular networking

Identifiers

PMID39786631
PMCPMC12658799

What Socratic holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.