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Journal, genetic engineering & biotechnology2026; 24(3); 100731; doi: 10.1016/j.jgeb.2026.100731

In silico genome mining and characterization of putative horse feces-derived bacterial phytases as potential monogastric animal feed additive candidates.

Abstract: Phytic acid exerts a significant antinutritional effect in poultry, swine, and fish, which can be mitigated by supplementing monogastric feeds with efficient microbial phytases. Accordingly, mining bacterial genomes for novel phytases represents a strategic computational approach to identifying candidates for improving monogastric animal nutrition. In this study, 162 bacterial genomes associated with horse feces were systematically mined using an in silico pipeline to identify and characterize putative phytases.A total of 69 non-redundant sequences were identified and classified as histidine acid phytase (HAPhy) or protein tyrosine phosphatase-like phytase (PTPLPhy). HAPhys were detected in the genomes of Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, and Cutibacterium equinum, whereas PTPLPhys were found in K. pneumoniae, Limosilactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium pseudolongum, and Prescottella equi. Principal component analysis identified glucose-1-phosphatase (CAJ1242485.1) and bifunctional acid phosphatase (NHR17779.1) as the HAPhy candidates exhibiting the most favorable predicted physicochemical properties for potential feed applications. Similarly, among the PTPLPhys, protein tyrosine phosphatase (UNQ40438.1) and a hypothetical protein (CAJ1246072.1) showed the most favorable computational profiles. Biosafety analysis identified potential virulence factors, indicating that sources should be screened prior to feed application. High-quality AlphaFold2 models were obtained for these phytases (90.9-97.2). Molecular docking analysis showed that NHR17779.1 exhibited the strongest binding to phytic acid, whereas CAJ1246072.1 demonstrated the weakest interaction. Overall, this study identifies the horse fecal microbiota as a diverse source of putative phytases that may serve as promising targets for genetic and protein engineering; however, further in vitro and in vivo studies are essential to validate the enzymatic activity and industrial efficacy of these computational candidates.
Copyright © 2024. Published by Elsevier Inc.
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Publication Date: 2026-06-23 PubMed ID: 42749412PubMed Central: PMC13316621DOI: 10.1016/j.jgeb.2026.100731Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Horse feces-associated bacterial genomes were analyzed using computational methods to identify and characterize potential phytase enzymes that could be used as animal feed additives to improve nutrient absorption in monogastric animals like poultry, swine, and fish.

Background and Objective

  • Phytic acid is an antinutritional compound found in many plant-based feeds that negatively affects nutrient availability in monogastric animals.
  • Phytase enzymes break down phytic acid, improving feed value and animal growth.
  • There is interest in discovering novel microbial phytases with better properties for use as feed additives.
  • This study aimed to mine bacterial genomes derived from horse feces using computational methods (“in silico”) to identify new putative phytases with suitable properties for feed applications.

Methods

  • 162 bacterial genomes isolated from horse feces were analyzed systematically through a bioinformatics pipeline.
  • Identified phytase-related sequences were classified into two main classes: histidine acid phytases (HAPhy) and protein tyrosine phosphatase-like phytases (PTPLPhy).
  • Gene and protein sequences were characterized computationally for physicochemical properties, enzymatic classification, and potential biosafety risks.
  • Principal component analysis (PCA) was used to select candidates with desirable features for feed additive use.
  • Structural models were predicted using AlphaFold2 to assess protein folding quality.
  • Molecular docking simulations were performed to estimate binding affinities of phytases to phytic acid substrate.

Key Results

  • 69 non-redundant phytase sequences were identified, belonging either to the HAPhy or PTPLPhy classes.
  • HAPhy candidates were found in genomes of Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, and Cutibacterium equinum.
  • PTPLPhy sequences were identified in K. pneumoniae, Limosilactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium pseudolongum, and Prescottella equi.
  • PCA pinpointed glucose-1-phosphatase (CAJ1242485.1) and bifunctional acid phosphatase (NHR17779.1) as the top HAPhy candidates.
  • Protein tyrosine phosphatase (UNQ40438.1) and a hypothetical protein (CAJ1246072.1) were selected as leading PTPLPhy candidates.
  • Biosafety assessment revealed some candidates had potential virulence factors, highlighting the need for safety screening before practical use.
  • AlphaFold2 structural predictions yielded high-quality models (confidence scores between 90.9 and 97.2), supporting structural integrity.
  • Molecular docking showed the bifunctional acid phosphatase (NHR17779.1) had the strongest predicted binding affinity to phytic acid, indicating high substrate interaction potential.
  • The hypothetical protein (CAJ1246072.1) showed the weakest binding, suggesting less likelihood of efficient phytase activity.

Conclusions and Implications

  • The horse fecal microbiota represents a rich and diverse source of novel phytase enzymes.
  • Several identified phytase candidates demonstrate promising computational properties and structural stability for potential use as monogastric feed additives.
  • Safety concerns require thorough screening of bacterial sources to avoid introducing virulence factors into animal feeds.
  • High-quality computational models and docking analyses support the viability of these candidates but do not confirm functional activity.
  • Further laboratory experiments, including enzyme activity assays and animal feeding trials, are essential to validate the usefulness of these phytases in industrial and agricultural settings.
  • The study provides a framework for the in silico discovery pipeline to accelerate enzyme bioprospecting for animal nutrition improvements.

Cite This Article

APA
Urgessa OE, Gemeda MT, Dinka H, Abdi FG, Tafess K. (2026). In silico genome mining and characterization of putative horse feces-derived bacterial phytases as potential monogastric animal feed additive candidates. J Genet Eng Biotechnol, 24(3), 100731. https://doi.org/10.1016/j.jgeb.2026.100731

Publication

Journal, genetic engineering & biotechnology
ISSN: 2090-5920
NlmUniqueID: 101317150
Country: Netherlands
Language: English
Volume: 24
Issue: 3
Pages: 100731
PII: 100731

Researcher Affiliations

Urgessa, Olyad Erba
  • School of Biological Sciences and Biotechnology, College of Natural and Computational Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia; Department of Applied Biology, College of Applied Natural Sciences, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.
Gemeda, Mesfin Tafesse
  • Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology, P.O. Box 16417, Addis Ababa, Ethiopia.
Dinka, Hunduma
  • Department of Applied Biology, College of Applied Natural Sciences, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.
Abdi, Firayad Girma
  • School of Biological Sciences and Biotechnology, College of Natural and Computational Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.
Tafess, Ketema
  • Department of Applied Biology, College of Applied Natural Sciences, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia; Institute of Pharmaceutical Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia. Electronic address: ttafess@gmail.com.

Conflict of Interest Statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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