Open-access Revealing the Intestinal Microbiota of Collared Peccaries (Pecari tajacu Linnaeus, 1758): Connections Between Wildlife and One Health

Abstract

This study aimed to expand the understanding of the intestinal microbiota of collared peccaries (Pecari tajacu), using matrix-assisted laser desorption/ionization - time of flight mass spectrometry (MALDI-TOF MS) technique for bacterial identification. Rectal swabs from 70 peccaries kept in a breeding center at the Federal University of Piauí were collected for the isolation of Gram-negative bacteria, using Hektoen Enteric agar (HE) and MacConkey agar (MAC). In total, 114 colonies were evaluated by the MALDI-TOF technique, which revealed the presence of six bacterial orders, with emphasis on Enterobacterales (42.11 %), followed by Pseudomonadales (23.68%) and Lysobacterales (15.79%). Research on the microbiota of collared peccaries is scarce and reveals little diversity of species. However, in this study, it was possible to identify a greater variety of bacteria, including microorganisms considered pathogenic and zoonotic. To our knowledge, this is the first study to apply MALDI-TOF technique to assess the diversity of the microbiota of collared peccaries, demonstrating its effectiveness in the accurate identification of the microbiota in wild animals and highlighting its relevance for microbiological and animal health surveillance.

Keywords:
Enterobacterales; Mass Spectrometry; Lysobacterales; Pseudomonadales; Zoonoses.

HIGHLIGHTS

First study using MALDI-TOF to profile microbiota in collared peccaries.

Identified pathogenic and zoonotic bacteria in healthy captive peccaries.

Five bacterial families were reported for the first time in tayassuids.

Findings reinforce One Health relevance of wildlife microbiota monitoring.

GRAPHICAL ABSTRACT

INTRODUCTION

The relationship between intestinal microbiota and host health, whether human or animal, plays a crucial role in maintaining physiological homeostasis and well-being. This interaction is fundamental in processes such as gastrointestinal health, immune system modulation, and its correlation with chronic non-communicable diseases like obesity and diabetes. These benefits have instigated a growing interest in the detailed characterisation of these microbial communities [1,2].

However, when it comes to wildlife, detailed microbiota typification remains underexplored. The intestinal microbiome of wild animals may serve as a reservoir for zoonotic pathogens, and the lack of specific knowledge about microbial composition limits our understanding of complex microorganisms-hosts interactions in ecosystems [3,4]. This information is critical for assessing the health of wild populations, developing health management protocols, and planning their reintroduction into natural environments [5].

Traditional microbiology techniques, despite their progress, face significant limitations when applied to wildlife microbiota due to the complexity and diversity of these environments, which challenge the speed and accuracy required for microorganism identification [6]. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a promising approach, offering significant advantages over conventional techniques by providing rapid and accurate microorganism identification [7].

Within the plurality and importance of wild fauna, the collared peccaries (Pecari tajacu LINNAEUS, 1758) stand out as promising candidates for deepening our understanding of the microbiota of wild animals. These mammals are widely distributed in various biomes across the American continent, demonstrating its important role in maintaining ecosystems [8,9].

With the purpose to fill a gap in the understanding of wildlife microbiota, this study aimed to characterize Gram-negative microorganisms in the intestinal microbiota of collared peccaries, using routine microbiological procedures, combined with the support of MALDI-TOF technology as a tool for a more precise and comprehensive identification of the bacterial species that inhabit this niche.

MATERIAL AND METHODS

The collections were carried out in accordance with the ethical principles of animal experimentation and approved by the Ethics Committee for the Use of Animals of the Federal University of Piauí. (CEUA/UFPI - Register N° 680/21), of the Chico Mendes Institute for Biodiversity Conservation / Biodiversity Authorization and Information System (ICMBio/SISBIO - Register Nº 78643-1), and the bacterial strains were registered in the National System for the Management of Genetic Heritage and Associated Traditional Knowledge (SISGEN - Register N° A247A57).

Rectal swabs were collected from all 70 clinically healthy collared peccaries maintained ex situ at the Center for the Study, Production and Preservation of Wild Animals (NEPPAS/UFPI), independent of age group and sex, and all without any clinical history of disease. Each animal was sampled only once and considered an independent experimental unit. Therefore, the study encompassed the entire population available in the facility at the time of sampling, providing a comprehensive representation of the intestinal microbiota of peccaries maintained under these captive conditions.

Although maintained in a controlled environment, the enclosures were designed to simulate the animals’ natural habitat. The area comprises five stalls and three paddocks, which allow the division of the herds into smaller groups, facilitating management and enabling individualized care when necessary. This structure promotes animal welfare by preserving natural behavioral and social patterns typical of the species.

For sampling, the animals were initially physically restrained in a handling area using nets and leather gloves. Chemical restraint was then performed through intramuscular administration of a combination of ketamine (9 mg/kg), midazolam (0.3 mg/kg), and tramadol (2 mg/kg). Throughout the anesthetic procedure, the animals were monitored until full recovery, at which point they were returned to their original stall or paddock.

After collection, the swabs were placed in sterile test tubes containing 2.0 mL of enrichment broth (10.0g tryptone/L and 2.5g yeast extract/L), transported to the Veterinary Microbiology Laboratory (LMV/UFPI) and incubated at 35 ± 2 ºC in a bacteriological incubator for 24 hours. Subsequently, aliquots were plated on HE and MAC agar, both selective for Gram-negative enteric bacteria. The culture conditions and selective media were intentionally designed to favor the focus of this investigation. Colonies showing distinct macroscopic morphologies after 24 hours of incubation at 35 ± 2 ºC were selected, recultivated in Brain Heart Infusion (BHI) broth supplemented with 20% sterile glycerol, and stored at -80 ºC.

The bacterial isolates were sent to the Paulo de Góes Institute of Microbiology at the Federal University of Rio de Janeiro (Brazil), for identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Analyses were conducted with a Bruker Daltonics Microflex LT/SH system (Bruker Daltonics, Bremen, Germany), operated using the MALDI Biotyper Compass Explorer software, version 4.1.

The spectra obtained were compared against the MBT Compass Library (MBT BDAL 13.0, Bruker Daltonics), which includes 12,160 bacterial reference spectra from clinically and environmentally relevant microorganisms. Each isolate was spotted in duplicate (two independent positions per colony), and mass spectra were acquired in linear positive mode.

Identification scores were interpreted according to the manufacturer’s criteria: score ≥ 2.0 were accepted for reliable identification at the species and genus levels; scores between 1.7 and 1.99 indicated probable genus identification; and scores < 1.7 were considered unreliable. Taxonomic validation of the identified species was performed based on the List of Prokaryotic names with Standing in Nomenclature - LPSN [10].

RESULTS

A total of 114 colonies were selected and submitted to MALDI-TOF. From these isolates, species belonging to six different orders were identified, with a prevalence of the order Enterobacterales (48/114; 42.11%), followed by the orders Pseudomonadales (27/114; 23.68%), Lysobacterales (18/114; 15.79%), Rhizobiales (15/114; 13.16%), Burkholderiales (5/114; 4.39%) and Sphingomonadales (1/114; 0.88%). Table 1 shows the frequency and classification of the Gram-negative bacteria identified.

Table 1
Frequency of Gram-negative bacteria in the intestinal microbiota of collared peccaries

DISCUSSION

Microbial identification methodologies have advanced significantly over the last few decades. The transition from traditional phenotypic biochemical tests to more advanced techniques, such as molecular biology and mass spectrometry, enabled a rapid and accurate identification of microorganisms, with greater sensitivity and specificity [11,12].

However, despite all the progress, the use of MALDI-TOF as a tool for identifying microorganisms faces specific challenges, especially when applied to samples of animal origin. One of the main obstacles is the representativeness of the database used for comparing spectra. Frequently, these banks may not encompass a sufficient variety of microorganisms found in the animal microbiota, which may result in inaccurate identifications or even failures [13].

The animal microbial diversity itself, which includes less common or understudied species, makes the task of identifying even more complex. Furthermore, proper preparation is crucial, since the presence of contaminants can affect the results. In addition, it has already been noted that mass spectrometry is not always able to correctly identify all the microorganisms present in polymicrobial cultures [14,15].

As shown in a systematic review, there have been few studies dedicated to characterising the microbiota of collared peccaries [9]. From 1970 to 2022, only 13 papers were registered, and nine of these focused on the gastrointestinal microbial community. To date, according to this survey, the largest number of species identified was 11, utilising phenotypic biochemical tests [18]. In this study, 32 different species were identified using mass spectrometry, 88.60 per cent (101/114) of these scored above 2.0 (safety at genus and species level), and 11.40 per cent (13/114) between 1.70 and 1.99 (genus safety).

The data revealed a higher prevalence of bacteria belonging to the Enterobacteriaceae family (42/114, 36.84%). Eight species were identified, with Klebsiella pneumoniae and Escherichia coli being the most notable. The presence of this family in the intestinal microbiota of collared peccaries has already been recognised and documented, as mentioned previously [16-18]. However, the evaluation of this taxonomic group, from their frequency to the diversity of species found, should always be emphasised. Possible variations in the occurrence and number of species may indicate an imbalance in the normal microbial composition, or an adaptive response to specific environmental or health conditions. The state of conservation of the animal itself, whether in situ or ex situ, may be a factor that indicates the variability of the microbiota. Also noteworthy is the pathogenic potential of many species belonging to the Enterobacteriaceae family, as well as their ability to harbour antimicrobial resistance genes [19,20].

Of the nine families characterised in this study, five of them had never been reported in the microbiota of tayassuids, to the best of our knowledge, due to the complexity of identification by conventional techniques: Brucellaceae (15/114), Sphingomonadaceae (1/114), Alcaligenaceae (5/114), Moraxellaceae (9/114) and Lysobacteraceae (18/114). The identification of these species contributes to the formation of a database, fundamental for future research and practical applications, as well as providing valuable insights into microbial biodiversity and their interactions with their hosts and environments [21].

Nonfermenting Gram-negative bacilli (NFGNB) were also found in the intestinal microbiota of collared peccaries. The greatest diversity appeared within the genus Pseudomonas, with seven species identified, and the genera Acinetobacter, Stenotrophomonas and Achromobacter were also detected. These microorganisms are commonly isolated in different habitats, from the aquatic environment to the soil, and in the gastrointestinal tract of mammals, birds, fish and reptiles [22].

Precisely due to the ubiquity of the NFGNB and their high environmental adaptability, their identification becomes even more important. This bacterial group has been recognized by the World Health Organization (WHO) and by the Centre for Disease Control and Prevention (CDC) as a major global public health concern due to its association with hospital-acquired infections and antimicrobial resistance, particularly involving P. aeruginosa and A. baumannii [23-25].

Although three species of the Ochrobactrum genus have been identified, the nomenclature of this taxonomic group has already undergone the suggested changes, after a phylogenetic analysis of genomic sequences [26]. The names Brucella intemedia, Brucella tritici and Brucella anthropi are proposed for O. intermedium, O. tritici and O. anthropi, respectively [10]. This information highlights the importance of maintaining and updating databases which feed the mass spectrometers in their identification process.

Only one isolate of Sphingobacterium thalpophilum was identified. This Gram-negative microorganism has been found in different environments and is rarely identified as responsible for infectious processes in humans and animals [27,28]. The presence of this species in the intestinal microbiota of collared peccaries highlights its adaptation to different ecological niches.

The present study provides new insights into the intestinal microbiota of Pecari tajacu, revealing a diverse composition of Gram-negative bacteria, including taxa with pathogenic and zoonotic potential. Using MALDI-TOF MS, we were able to identify a greater diversity of species than previously reported in tayassuids, reinforcing the effectiveness of this technique for microbiota characterization in wildlife species.

It is important to acknowledge that the methodological approach employed in this study - particularly the use of enrichment broth and selective culture media under aerobic conditions - was designed to favor the isolation of aerobic and facultative Gram-negative bacteria. Consequently, this strategy may have introduced a selective bias, potentially underrepresenting strict anaerobes or Gram-positive species that are also part of the intestinal microbiota. However, this selective enrichment was intentional, as the primary objective of this investigation was to characterize the diversity of Gram-negative bacteria inhabiting the intestinal tract of collared peccaries. Therefore, the findings presented here should be interpreted within this defined microbial scope, while future studies employing metagenomic or anaerobic culture approaches may further expand our understanding of the full microbiota composition in this species.

Although several of the bacterial species identified in this study are recognized as clinically relevant and potentially antimicrobial-resistant, phenotypic antimicrobial susceptibility testing (AST) was not included within the scope of this work. The primary objective of this study was to characterize and identify Gram-negative bacteria using MALDI-TOF MS as a rapid and accurate tool for wildlife microbiota studies. However, all relevant isolates - including Klebsiella pneumoniae, Escherichia coli, Pseudomonas spp., and Acinetobacter spp. - have been preserved and are currently under evaluation in a complementary investigation. This ongoing study aims to determine antimicrobial resistance profiles using disk diffusion and MIC methods according to CLSI guidelines. These results will provide an important follow-up to the present work, contributing to the One Health perspective by integrating microbial ecology, wildlife health, and antimicrobial resistance surveillance.

From an applied perspective, the detection of pathogenic and zoonotic bacterial species in the intestinal microbiota of clinically healthy collared peccaries provides valuable insights for improving sanitary management in captive wildlife. These findings reinforce the need for implementing continuous microbiological monitoring programs aimed at detecting early changes in microbial composition and the emergence of potentially harmful taxa. Regular assessment of intestinal microbiota, together with strict hygiene routines, controlled animal density, and adequate waste management, can help prevent the spread of opportunistic and resistant bacteria among animals and staff. Such practices are essential to ensure animal welfare, reduce pathogen circulation in ex situ environments, and promote sustainable management in wildlife conservation centers [9].

Furthermore, these results highlight the importance of understanding wildlife microbiota through the lens of the One Health framework. The detection of potentially pathogenic and zoonotic microorganisms emphasizes the interconnectedness of human, animal, and environmental health. Continuous monitoring of microbial diversity in wildlife populations is essential for safeguarding animal health and reducing the risks of zoonotic transmission and antimicrobial resistance spread. Integrating microbiological monitoring into wildlife management practices supports broader One Health strategies by linking biodiversity conservation, public health, and environmental stability [29].

In this context, the presence of bacterial species with pathogenic and zoonotic potential in the microbiota of clinically healthy collared peccaries underscores the complex interactions between microorganisms, their hosts, and the surrounding environment. These animals may act as reservoirs or vectors of infectious agents, representing potential risks to both wildlife and humans, particularly in ex situ environments where interactions are more frequent. Therefore, integrated surveillance and biosecurity measures aligned with the principles of One Health are essential to monitor and mitigate zoonotic risks, contributing to global health protection and the ecological balance of natural and managed ecosystems.

CONCLUSION

To our knowledge, this is the first study to use the MALDI-TOF technique to assess the microbiota of clinically healthy peccaries, revealing a substantial bacterial diversity, as well as the role of these wild mammals as a potential reservoir of pathogenic bacteria. Future research should focus on evaluating the antimicrobial susceptibility and resistance patterns of these microorganisms. Furthermore, the effectiveness of the MALDI-TOF technique for accurately identifying the microbiota in wild animals was demonstrated in this study, emphasizing its value for microbiological research and One Health monitoring.

  • Funding:
    This research received no external funding.
  • Institutional Review Board Statement:
    The animal study protocol was approved by Ethics Committee for the Use of Animals of the FEDERAL UNIVERSITY OF PIAUÍ (CEUA/UFPI - Register N° 680/21), and of the Chico Mendes Institute for Biodiversity Conservation / Biodiversity Authorization and Information System (ICMBio/SISBIO-Register Nº 78643-1).
  • Informed Consent Statement:
    Not applicable.

Acknowledgments:

The authors have no acknowledgments to declare.

Use of Generative Artificial Intelligence:

The authors declare that no generative artificial intelligence (AI) or AI-assisted technologies were used to generate or modify the scientific content of this manuscript, including the conception of the study, data collection, data analysis, interpretation of results, or creation of original text, figures, tables or graphical abstracts, apart from routine tools for spelling, grammar checking and reference management that do not create original scholarly content.

Data Availability Statement:

Research data are available in the body of the manuscript.

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  • Editor-in-Chief:
    Paulo Vitor Farago
  • Associate Editor:
    Marcos Pileggi

Publication Dates

  • Publication in this collection
    12 June 2026
  • Date of issue
    2026

History

  • Received
    04 Nov 2025
  • Accepted
    31 Dec 2025
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