Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis

Daugaliyeva, Аida; Daugaliyeva, Saule; Ashanin, Alexander; Kanatbayev, Serik G.; Beltramo, Chiara; Peletto, Simone

doi:10.1038/s41598-022-20732-4

Cited by 4 publications

(4 citation statements)

References 29 publications

(34 reference statements)

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“…For this purpose, fecal samples were taken rectally from 37 cattle heads from 4 regions of Kazakhstan (Western, Southern, Northern, and Southeast Kazakhstan). As a result of the studies, it was found that methanogenic bacteria were less present in animals from the Western region grazing in the pasture compared with animals from other regions kept in the stall [22].…”

Section: Discussionmentioning

confidence: 95%

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

Daugaliyeva

Ashanin

et al. 2022

Life

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In this study, we analyzed the microbial composition of the rumen contents of cattle from Kazakhstan. Specifically, samples of the liquid and solid fractions of the rumen were collected to determine the quantitative and qualitative composition of methanogenic archaea. Cattle were six steers receiving hay-concentrate feeding. Methane emission was determined by repeated measurements for each animal. Rumen samples were then taken from fistulas and analyzed using 16S metabarcoding via Next-Generation Sequencing (NGS). The difference between the rumen fractions was investigated, resulting in differential distribution of the families Streptococccaceae, Lactobacillaceae, Desulfobulbaceae, and Succinivibrionaceae, which were more abundant in the liquid fraction, while Thalassospiraceae showed a higher presence in the solid fraction. These differences can be explained by the fact that fibrolytic bacteria are associated with the solid fraction compared to the liquid. A relationship between methane emission and methanogenic microbiota was also observed. Steers producing more methane showed microbiota richer in methanogens; specifically, most Mathanobacteriaceae resided in the liquid fraction and solid fraction of animals 1 and 6, respectively. The same animals carried most of the Methanobrevibacter and Methanosphaera genera. On the contrary, animals 2, 3, and 5 hosted a lower amount of methanogens, which also agreed with the data on methane emissions. In conclusion, this study demonstrated a relationship between methane emission and the content of methanogenic archaea in different rumen fractions collected from cattle in Kazakhstan. As a result of the studies, it was found that the solid fraction of the rumen contained more genera of methanogens than the liquid fraction of the rumen. These results prove that taking rumen contents through a fistula is more useful than taking it through a probe. The presented data may be of interest to scientists from all over the world engaged in similar research in a comparative aspect.

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Section: Discussionmentioning

confidence: 95%

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

Daugaliyeva

Ashanin

et al. 2022

Life

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“…These innovative and powerful technologies are used in different fields for the detection of food frauds, identification of fish species or inspection of the dietary diversity of animals. However, bacteria are more frequently the target of the study, compared to parasites (20,(30)(31)(32)(33). For example, Ludwig, A. et al, and Howells et al described the presence of microorganisms such as parasites in the meat, but it was not possible for them to establish potential co-carriage, due to the technologies used, hence the interest of our study [5,9].…”

Section: Discussionmentioning

confidence: 99%

Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Workflow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

MATOUTE,

MAESTRI,

SAOUT

et al. 2024

Preprint

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French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there are few data available on the description of parasites circulating in this area, especially on protozoan belonging to the phy-lum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on Oxford Nanopore Technologies sequencing platform using the 18S gene of fourteen Apicomplexa-positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify as Apicom-plexa-positive 10 samples out of 14 and reveal the presence of co-carriages. The same samples were also sequenced with Illumina platform, for validation purposes. On samples identified as Apicomplexa-positive by both platforms, a strong positive correlation at up to genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detec-tion, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

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“…These innovative and powerful technologies are used in different fields for the detection of food frauds, identification of fish species or inspection of the dietary diversity of animals. However, bacteria are more frequently the target of the study, compared to parasites [19,[31][32][33][34]. For example, Ludwig, A. et al, and Howells et al described the presence of microorganisms such as parasites in meat, but it was not possible for them to establish potential co-carriage, due to the technologies used, hence the interest of our study [5,8].…”

Section: Discussionmentioning

confidence: 99%

Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

Matoute,

Maestri,

Saout

et al. 2024

CIMB

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French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.

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Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis

Cited by 4 publications

References 29 publications

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Workflow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana

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