Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 May 2:15:1393153.
doi: 10.3389/fmicb.2024.1393153. eCollection 2024.

Identification and classification of the genomes of novel microviruses in poultry slaughterhouse

Keming Xie #  1   2 , Benfu Lin #  3 , Xinyu Sun  1 , Peng Zhu  2   4 , Chang Liu  2 , Guangfeng Liu  2 , Xudong Cao  5 , Jingqi Pan  1 , Suiping Qiu  1 , Xiaoqi Yuan  1 , Mengshi Liang  1 , Jingzhe Jiang  1   2 , Lihong Yuan  1
Affiliations

Identification and classification of the genomes of novel microviruses in poultry slaughterhouse

Keming Xie et al. Front Microbiol. .

Abstract

Microviridae is a family of phages with circular ssDNA genomes and they are widely found in various environments and organisms. In this study, virome techniques were employed to explore potential members of Microviridae in a poultry slaughterhouse, leading to the identification of 98 novel and complete microvirus genomes. Using a similarity clustering network classification approach, these viruses were found to belong to at least 6 new subfamilies within Microviridae and 3 higher-level taxonomic units. Genome size, GC content and genome structure of these new taxa showed evident regularities, validating the rationality of our classification method. Our method can divide microviruses into about 45 additional detailed clusters, which may serve as a new standard for classifying Microviridae members. Furthermore, by addressing the scarcity of host information for microviruses, the current study significantly broadened their host range and discovered over 20 possible new hosts, including important pathogenic bacteria such as Helicobacter pylori and Vibrio cholerae, as well as different taxa demonstrated different host specificities. The findings of this study effectively expand the diversity of the Microviridae family, providing new insights for their classification and identification. Additionally, it offers a novel perspective for monitoring and controlling pathogenic microorganisms in poultry slaughterhouse environments.

Keywords: clustering; genome; host; microviruses; poultry slaughterhouse.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Similarity clustering network of Cap of microviruses from poultry slaughterhouses and related microvirus groups. The network includes identified microvirus Cap sequences from the DSV data (n = 98), along with related Cap sequences from the NR data (n = 459) and microvirus Cap sequences from the ICTV data (n = 20). The similarity clustering network was constructed using Gephi (version 0.9.7) based on Diamond (version 0.9.14.115) alignment score. Gray connections represent Diamond Blastp score > 480.
Figure 2
Figure 2
The host types and quantity statistics of microviruses from poultry slaughterhouses and related groups. (A) hostG (Shang and Sun, 2021) results of DSV sequences. (B) hostG results of NR sequences. (C) Cherry (Shang and Sun, 2022) results of DSV sequences. (D) Cherry results of NR sequences. Score > 0.7. (E) Host types and quantity predicted by cherry for corresponding DSV sequences. AS (All soil and sludge of slaughterhouse); Soil (Soil of slaughterhouse); Sludge (Sludge of slaughterhouse); SS (Swab of slaughterhouse workshop); ST (Swab of poultry transport vehicle); SCD (Oral and cloacal swabs of chickens and ducks).
Figure 3
Figure 3
Genomic features of each cluster of microviruses from poultry slaughterhouses and related groups. (A) Distribution of microviruses genome sizes in each cluster from Result 3.1. (B) Distribution of microviruses genome %GC content in each cluster from Result 3.1. Red, blue, green, yellow, and black correspond to Family_Red, Family_Blue, Family_Green, Family_Yellow, and Bullavirinae, respectively. Turkey’s test was used, where p < 0.05 indicates significant differences, and p > 0.05 indicates no significant differences. In the group where the maximum mean value is located, mark it with the letter “a.” Then, compare this mean value with the mean values of other groups one by one. If there is no significant difference, label them with the same letter “a.” Continue this process until encountering a mean value with a significant difference, then label it with the letter “b.” Subsequently, use “b” as the standard for further comparisons. Repeat this process, labeling consecutive mean values with the letters “b” until encountering a mean value with a significant difference, which is then labeled as the letter “c.” This pattern continues for subsequent comparisons. The plot displays median values, 25th and 75th percentiles, 1.5 interquartile ranges, and outlier data points.
Figure 4
Figure 4
Phylogenetic tree, hosts, and genomic structure of cluster_1 microviruses from poultry slaughterhouse and related sources. The maximum likelihood phylogenetic tree was constructed based on the Cap sequences of Microviruses using IQtree (version 2.1.4). ModelFinder was set to MFP, and 1,000 ultrafast bootstrap replicates were performed, displaying bootstrap values >70. The red branches represent DSV microvirus sequences, green branches represent ICTV sequences, and black branches represent NR sequences. The third column shows host annotations predicted by Cherry, and the fourth column displays partial genomic structure diagrams.
Figure 5
Figure 5
Phylogenetic tree, hosts, and genomic structure of cluster_2 microviruses from poultry slaughterhouse and related sources. The maximum likelihood phylogenetic tree was constructed based on the Cap sequences of Microviruses using IQtree (version 2.1.4). ModelFinder was set to MFP, and 1,000 ultrafast bootstrap replicates were performed, displaying bootstrap values >70. The red branches represent DSV microvirus sequences, green branches represent ICTV sequences, and black branches represent NR sequences. The third column shows host annotations predicted by Cherry, and the fourth column displays partial genomic structure diagrams.
Figure 6
Figure 6
The microviruses collection with diverse taxa. Similarity clustering network was constructed using microviruses Cap sequences identified from DSV data (n = 98), along with related Cap sequences from NR (n = 459), ICTV microviruses Cap sequences (n = 20), and an additional set of Cap sequences reported by Kirchberger et al. (n = 4,007) [red dots represent DSV sequences, black dots represent NR sequences, and dark green dots represent ICTV sequences; other dots are colored based on the families defined by Kirchberger et al., 2022]. Clusters corresponding to those in Figure 1 are enclosed by ellipses of four different colors. Labels such as Pichovirinae, Shukshmavirinae, Group D, Alpavirinae, Gokushovirinae A/B/C correspond to subfamilies reported by previous studies (Krupovic and Forterre, 2011; Rosario et al., 2012; Roux et al., 2012; Tikhe and Husseneder, 2017) and suggested classifications by Kirchberger et al. (2022). The similarity clustering network graph was created using Gephi (version 0.9.7) based on Diamond (version 0.9.14.115) alignment score, with gray edges indicating Diamond Blastp score > 0.
Figure 7
Figure 7
Host specificity of different clusters of Microviruses. (A) Similarity clustering network constructed using microviruses Cap sequences identified in DSV data (n = 98), along with related Cap sequences from NR (n = 459), and microviruses Cap sequences from ICTV (n = 20), colored based on host types. (B) Based on the sequences in panel (A), an extended similarity clustering network was constructed by introducing Cap sequences reported by Kirchberssger et al. (n = 4,007), also colored according to host types. The similarity clustering network graph was created using Gephi (version 0.9.7) based on Diamond (version 0.9.14.115) alignment score, with gray edges indicating Diamond Blastp score > 0.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Abraham W.-R., Strömpl C., Meyer H., Lindholst S., Moore E. R. B., Christ R., et al. . (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int. J. Syst. Evol. Microbiol. 49, 1053–1073. doi: 10.1099/00207713-49-3-1053 - DOI - PubMed
    1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. doi: 10.1016/s0022-2836(05)80360-2 - DOI - PubMed
    1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., et al. . (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402. doi: 10.1093/nar/25.17.3389, PMID: - DOI - PMC - PubMed
    1. Angly F. E., Willner D., Prieto-Davó A., Edwards R. A., Schmieder R., Vega-Thurber R., et al. . (2009). The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol. 5:e1000593. doi: 10.1371/journal.pcbi.1000593, PMID: - DOI - PMC - PubMed
    1. Arzey G. G., Kirkland P. D., Arzey K. E., Frost M., Maywood P., Conaty S., et al. . (2012). Influenza virus a (H10N7) in chickens and poultry abattoir workers, Australia. Emerg. Infect. Dis. 18, 814–816. doi: 10.3201/eid1805.111852, PMID: - DOI - PMC - PubMed

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This project was supported by the Natural Science Foundation of China (nos. 31872499 and 31972847) to LY and JJ; the Innovation Team Project of Guangdong Universities (No. 2022KCXTD017) to LY; the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (nos. 2023TD44 and 2021SD05) to JJ. The funders had no role in the study design, data collection, and analysis, decision to publish, or manuscript preparation.
-