Citation: Šakarnyt ˙ e, L.; Šiugždinien ˙ e, R.; Žymantien ˙ e, J.; Ruzauskas, M. Comparison of Oral Microbial Composition and Determinants Encoding Antimicrobial Resistance in Dogs and Their Owners. Antibiotics 2023, 12, 1554. https://doi.org/ 10.3390/antibiotics12101554 Academic Editor: Jonathan Frye Received: 17 August 2023 Revised: 14 September 2023 Accepted: 19 October 2023 Published: 20 October 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). antibiotics Article Comparison of Oral Microbial Composition and Determinants Encoding Antimicrobial Resistance in Dogs and Their Owners Laura Šakarnyt ˙ e 1 , Rita Šiugždinien ˙ e 1 , Judita Žymantien ˙ e 2 and Modestas Ruzauskas 1,2, * 1 Microbiology and Virology Institute, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; laura.sakarnyte@lsmu.lt (L.Š.); rita.siugzdiniene@lsmu.lt (R.Š.) 2 Department of Anatomy and Physiology, Veterinary Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania; judita.zymantiene@lsmu.lt * Correspondence: modestas.ruzauskas@lsmu.lt; Tel.: +370-615-15240 Abstract: Consolidated studies on animal, human, and environmental health have become very important for understanding emerging zoonotic diseases and the spread of antimicrobial resis- tance (AMR). The aim of this study was to analyse the oral microbiomes of healthy dogs and their owners, including determinants of AMR. Shotgun metagenomic sequencing detected 299 bacterial species in pets and their owners, from which 70 species were carried by dogs and 229 species by humans. Results demonstrated a unique microbial composition of dogs and their owners. At an order level, Bacteroidales were the most prevalent oral microbiota of dogs with significantly lower prevalence in their owners where Actinomycetales and Lactobacillales predominated. Porphyromonas and Corynebacterium were the most prevalent genera in dogs, whereas Streptococcus and Actinomyces were in animal owners. The resistances to macrolides, tetracyclines, lincosamides and Cfx family A class broad-spectrum β-lactamase were detected in both animal and human microbiomes. Resistance determinants to amphenicols, aminoglycosides, sulphonamides, and quaternary ammonium com- pounds were detected exceptionally in dogs. In conclusion, the study demonstrated different bacterial composition in oral microbiomes of healthy dogs without clinical signs of periodontal disease and their owners. Due to the low numbers of the samples tested, further investigations with an increased number of samples should be performed. Keywords: bacteria; zoonoses; antimicrobial resistance; pets; microbiome; resistome 1. Introduction Zoonotic infections are caused by a wide variety of microorganisms and are transmit- ted naturally from animals to humans and vice versa. Recently, it was indicated that more than 60% of human pathogens are zoonotic in origin [1]. The One Health concept is focused on consequences, responses, and actions at the animal–human–ecosystem interfaces, espe- cially for emerging zoonoses [2,3] and antimicrobial resistance (AMR), which can spread between humans and animals [4]. A collaborative and multi-disciplinary approach, cutting across boundaries of animal, human, and environmental health, is needed to understand the ecology of each emerging zoonotic disease and the spread of AMR determinants to undertake a risk assessment, and to develop plans for response and control [5]. Periodontitis is an infection caused by microorganisms that damage the gingiva and, without treatment, can cause bone loss around teeth, which may lead to tooth loss. This pathology is widespread in humans and especially in dogs, which is reported to be the most common disease affecting dogs (and cats) worldwide [6,7]. Previously, it was reported that 63% of pet owners have never had their pets’ teeth cleaned [8], suggesting a high risk of bacterial infections in dogs and humans they come into contact with. A study performed in Japan in 2012 concluded that close contact could contribute to the transmission of bacteria such as Eikenella corrodens, Porphyromonas gulae, Treponema forsythia, and T. denticola Antibiotics 2023, 12, 1554. https://doi.org/10.3390/antibiotics12101554 https://www.mdpi.com/journal/antibiotics