Comparison of Different DNA Sampling and Extraction Protocols for Bacterial and Archaeal Populations Analysis in Water Buffalo

Authors

  • Maria Chiara La Mantia CREA, Research Center for Animal Production and Aquaculture, via Salaria 31, 00015 Monterotondo, Italy
  • Massimo Calì CREA, Research Center for Animal Production and Aquaculture, via Salaria 31, 00015 Monterotondo, Italy
  • Emanuela Rossi CREA, Research Center for Animal Production and Aquaculture, via Salaria 31, 00015 Monterotondo, Italy
  • David Meo Zilio CREA, Research Center for Animal Production and Aquaculture, via Salaria 31, 00015 Monterotondo, Italy https://orcid.org/0000-0002-8182-1833
  • Enrico Santangelo CREA, Research Centre for Engineering and Agro-Food Processing, Via della Pascolare, 16, 00015 Monterotondo, Italy https://orcid.org/0000-0001-5156-9430
  • Antonella Chiariotti CREA, Research Center for Animal Production and Aquaculture, via Salaria 31, 00015 Monterotondo, Italy

DOI:

https://doi.org/10.6000/1927-520X.2024.13.13

Keywords:

Rumen cannula, rumen microbiome, feces, buccal swabs, methane emission

Abstract

Methane (CH4) is a potent greenhouse gas, and ruminants are a significant source of agricultural emissions. It has been hypothesized that the host's genome controls rumen microbial communities, but robust results require numerous samples. The feasibility of a research project will depend on the ease and representativeness of the sampling method, as well as the cost-efficiency of large-scale sequencing. This study aimed to compare different protocols to investigate whether non-invasive samples could serve as a substitute for ruminal digesta. DNA recovery was tested in various matrices (whole rumen content, feces, and buccal swabs) from five cannulated buffalo cows. Three types of buccal swabs were tested, as well as feces in different forms (as-is, pelleted, or in a glycerol solution) and the rumen content. The study compared different protocols for DNA extraction, including WUR protocol, Maxwell®, and Quick Extract™, and two sampling times. Saliva was a challenging matrix to process, obtaining unsatisfactory DNA yield. Feces showed higher yields when pelleted but lower than rumen. The highest amount of DNA was obtained from whole rumen content using all three DNA extraction methods. Quick Extract was the easiest method to perform, while WUR resulted in the highest yield of DNA, swabs excluded. The Maxwell® method gave satisfactory results with all three matrices. However, further metagenomic analysis is required to verify if the species composition is comparable.

References

Mcallister TA, Meale SJ, Valle E, Guan LL, Zhou M, Kelly WJ, et al. Ruminant Nutrition Symposium: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis to support international efforts to develop CH4 mitigation and rumen adaptation technologies. J Anim Sci [Internet] 2015; 93: 1431-49. https://doi.org/10.2527/jas.2014-8329 DOI: https://doi.org/10.2527/jas.2014-8329

Li F, Li C, Chen Y, Liu J, Zhang C, Irving B, et al. Host genetics influence the rumen microbiota and heritable rumen microbial features associated with feed efficiency in cattle. Microbiome 2019; 7(1). https://doi.org/10.1186/s40168-019-0699-1 DOI: https://doi.org/10.1186/s40168-019-0699-1

Abbas W, Howard JT, Paz HA, Hales KE, Wells JE, Kuehn LA, et al. Influence of host genetics in shaping the rumen bacterial community in beef cattle. Sci Rep 2020; 10(1). https://doi.org/10.1038/s41598-020-72011-9 DOI: https://doi.org/10.1038/s41598-020-72011-9

Wegl G, Grabner N, Köstelbauer A, Klose V, Ghanbari M. Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. Front Microbiol 2021; 12. https://doi.org/10.3389/fmicb.2021.627539 DOI: https://doi.org/10.3389/fmicb.2021.627539

Henderson G, Cox F, Ganesh S, Jonker A, Young W, Janssen PH, et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 2015; 5.

Pitta D, Indugu N, Narayan K, Hennessy M. Symposium review: Understanding the role of the rumen microbiome in enteric methane mitigation and productivity in dairy cows. J of Dairy Sci. Elsevier Inc.; 2022; 105: 8569-85. https://doi.org/10.3168/jds.2021-21466 DOI: https://doi.org/10.3168/jds.2021-21466

Welch CB, Lourenco JM, Davis DB, Krause TR, Carmichael MN, Rothrock MJ, et al. The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot 1. Available from: https://academic.oup.com/jas/article-abstract/doi/10.1093/jas/skaa230/5873892

Lourenco JM, Kieran TJ, Seidel DS, Glenn TC, Da Silveira MF, Callaway TR, et al. Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate. PLoS One 2020; 15(4). https://doi.org/10.1371/journal.pone.0231533 DOI: https://doi.org/10.1371/journal.pone.0231533

Zhou X, Ma Y, Yang C, Zhao Z, Ding Y, Zhang Y, et al. Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake. Microorganisms 2023; 11(2). https://doi.org/10.3390/microorganisms11020358 DOI: https://doi.org/10.3390/microorganisms11020358

Kittelmann S, Naylor GE, Koolaard JP, Janssen PH. A proposed taxonomy of anaerobic fungi (class neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis. PLoS One 2012; 7(5). https://doi.org/10.1371/journal.pone.0036866 DOI: https://doi.org/10.1371/journal.pone.0036866

Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, et al. Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS One 2013; 8(2). https://doi.org/10.1371/journal.pone.0047879 DOI: https://doi.org/10.1371/journal.pone.0047879

Jeyanathan J, Kirs M, Ronimus RS, Hoskin SO, Janssen PH. Methanogen community structure in the rumens of farmed sheep, cattle, and red deer fed different diets. FEMS Microbiol Ecol 2011; 76(2): 311-26. https://doi.org/10.1111/j.1574-6941.2011.01056.x DOI: https://doi.org/10.1111/j.1574-6941.2011.01056.x

Bertoni A, Napolitano F, Mota-Rojas D, Sabia E, Álvarez-Macías A, Mora-Medina P, et al. Similarities and differences between river buffaloes and cattle: Health, physiological, behavioral and productivity aspects. J Buffalo Sci 2020; 9: 92-109. https://doi.org/10.6000/1927-520X.2020.09.12 DOI: https://doi.org/10.6000/1927-520X.2020.09.12

Tong F, Wang T, Gao NL, Liu Z, Cui K, Duan Y, et al. The microbiome of the buffalo digestive tract. Nat Commun 2022; 13(1). https://doi.org/10.1038/s41467-022-28402-9 DOI: https://doi.org/10.1038/s41467-022-28402-9

Kittelmann S, Kirk MR, Jonker A, McCulloch A, Janssen PH. Buccal swabbing as a non-invasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen. Appl Environ Microbiol 2015; 81(21): 7470-83. https://doi.org/10.1128/AEM.02385-15 DOI: https://doi.org/10.1128/AEM.02385-15

Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, et al. Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. PLoS One 2016; 11(3). https://doi.org/10.1371/journal.pone.0151220 DOI: https://doi.org/10.1371/journal.pone.0151220

Van Soest PJ, Robertson JB, Lewis BA. Methods for Dietary Fiber, Neutral Detergent Fiber, and Nonstarch Polysaccharides in Relation to Animal Nutrition. J Dairy Sci 1991; 74(10): 3583-97. https://doi.org/10.3168/jds.S0022-0302(91)78551-2 DOI: https://doi.org/10.3168/jds.S0022-0302(91)78551-2

Martillotti F, Antongiovanni M, Rizzi L, Santi E, Bittante G. Metodi di analisi per gli alimenti d’impiego zootecnico. CNR-IPRA, editor. Roma; 1987; Vol. 8.

APAT, Istituto di ricerca sulle acque. Metodi analitici per le acque. 3, Sezione 6000. Metodi microbiologici : parte generale ; Sezione 7000 ; Determinazione di microorganismi ; Sezione 8000 : Metodi ecotossicologici ; Sezione 9000 : Indicatori biologici. APAT 2003.

van Lingen HJ, Edwards JE, Vaidya JD, van Gastelen S, Saccenti E, van den Bogert B, et al. Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen. Front Microbiol 2017; 8(MAR): 425. https://doi.org/10.3389/fmicb.2017.00425 DOI: https://doi.org/10.3389/fmicb.2017.00425

Maeda H, Fujimoto C, Haruki Y, Maeda T, Kokeguchi S, Petelin M, et al. Quantitative real-time PCR using TaqMan and SYBR Green for Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, tetQ gene and total bacteria. FEMS Immunol Med Microbiol 2003; 39(1): 81-6. https://doi.org/10.1016/S0928-8244(03)00224-4 DOI: https://doi.org/10.1016/S0928-8244(03)00224-4

Hook SE, Wright AD, McBride BW. Methanogens: methane producers of the rumen and mitigation strategies. Archaea 2010; 2010. https://doi.org/10.1155/2010/945785 DOI: https://doi.org/10.1155/2010/945785

Huws SA, Lee MRF, Muetzel SM, Scott MB, Wallace RJ, Scollan ND. Forage type and fish oil cause shifts in rumen bacterial diversity. FEMS Microbiol Ecol 2010; 73(2): 396-407. https://doi.org/10.1111/j.1574-6941.2010.00892.x DOI: https://doi.org/10.1111/j.1574-6941.2010.00892.x

Baraka TA. Rumen Constituents and Ciliates Generic & Species Composition in Water Buffaloes (Bubalus bubalis) in Egypt [Internet]. J of American Sci 2011; 7.

Weimer PJ. Degradation of Cellulose and Hemicellulose by Ruminal Microorganisms. Vol. 10, Microorganisms. MDPI; 2022. https://doi.org/10.3390/microorganisms10122345 DOI: https://doi.org/10.3390/microorganisms10122345

Warner ACI. Some Factors Influencing the Rumen Microbial Population. J Gen Microbiol 1962; Vol. 28. https://doi.org/10.1099/00221287-28-1-129 DOI: https://doi.org/10.1099/00221287-28-1-129

Belanche A, Palma-Hidalgo JM, Nejjam I, Serrano R, Jiménez E, Martín-García I, et al. In vitro assessment of the factors that determine the activity of the rumen microbiota for further applications as inoculum. J Sci Food Agric 2019; 99(1): 163-72. https://doi.org/10.1002/jsfa.9157 DOI: https://doi.org/10.1002/jsfa.9157

Indugu N, Hennessy M, Kaplan-Shabtai VS, de Assis Lage CF, Räisänen SE, Melgar A, Nedelkov K, Chen X, Oh J, Vecchiarelli B, Bender JS. Comparing non-invasive sampling techniques with standard cannula sampling method for ruminal microbial analysis. JDS Communications 2021; 2(6): 329-33. https://doi.org/10.3168/jdsc.2021-0094 DOI: https://doi.org/10.3168/jdsc.2021-0094

Rogers NL, Cole SA, Lan HC, Crossa A. New saliva DNA collection method compared to buccal cell collection techniques for epidemiological studies. American Journal of Human Biology 2007; 19(3): 319-26. https://doi.org/10.1002/ajhb.20586 DOI: https://doi.org/10.1002/ajhb.20586

Sa G, Xiong X, Wu T, Yang J, He S, Zhao Y. Histological features of oral epithelium in seven animal species: As a reference for selecting animal models. European Journal of Pharmaceutical Sciences 2016; 81: 10-7. https://doi.org/10.1016/j.ejps.2015.09.019 DOI: https://doi.org/10.1016/j.ejps.2015.09.019

Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protoc 2008; 3(6): 1101-8. https://doi.org/10.1038/nprot.2008.73 DOI: https://doi.org/10.1038/nprot.2008.73

Alhaddad H, Maraqa T, Alabdulghafour S, Alaskar H, Alaqeely R, Almathen F, et al. Quality and quantity of dromedary camel DNA sampled from whole blood, saliva, and tail hair. PLoS One 2019; 14(1). https://doi.org/10.1371/journal.pone.0211743 DOI: https://doi.org/10.1371/journal.pone.0211743

Imai S, Abdullahb N, Hob YW, Jalaludinb S, Hussainc HY, Onoderac R, et al. Comparative study on the rumen ciliate populations in small experimental herds of water buffalo and Kedah Kelantan cattle in Malaysia.Animal Feed Sci and Tech 1995; 52. https://doi.org/10.1016/0377-8401(94)00726-P DOI: https://doi.org/10.1016/0377-8401(94)00726-P

Jouany JP, Ushida K. The role of protozoa in feed digestion-Review. Asian-Australasian Journal of Animal Sciences 1999; 12(1): 113-28. DOI: https://doi.org/10.5713/ajas.1999.113

Ushida by K, Ha J P Jouany JK, Ushida K. The Roleof Protozoa in Feed Digestion* *-Review-"Rumen Microorganisms and Application to the Improvement of Ruminant Production" at the 8th. 1998.

Wallace RJ, Rooke JA, Duthie CA, Hyslop JJ, Ross DW, McKain N, et al. Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle. Sci Rep 2014; 4. https://doi.org/10.1038/srep05892 DOI: https://doi.org/10.1038/srep05892

Coleman GS. Rumen ciliate protozoa. Advances in Parasitology 1980; 18: 121-73. DOI: https://doi.org/10.1016/S0065-308X(08)60399-1

Morgavi DP, Martin C, Jouany JP, Ranilla MJ. Rumen protozoa and methanogenesis: Not a simple cause-effect relationship. British Journal of Nutrition 2012; 107(3): 388-97. https://doi.org/10.1017/S0007114511002935 DOI: https://doi.org/10.1017/S0007114511002935

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Published

2024-09-19

How to Cite

La Mantia, M. C. ., Calì, M. ., Rossi, E. ., Zilio, D. M. ., Santangelo, E. ., & Chiariotti, A. . (2024). Comparison of Different DNA Sampling and Extraction Protocols for Bacterial and Archaeal Populations Analysis in Water Buffalo. Journal of Buffalo Science, 13, 116–124. https://doi.org/10.6000/1927-520X.2024.13.13

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Editorial: Dedicated to Articles Presented at the World Buffalo Congress, Caracas, Venezuela, 2023, November 22-24

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