Keywords
pathogens
agroindustrial residual
silage
nutritional value
next generation sequencing
Bacterias ácido lácticas
patógeno
residuo agroindustrial
ensilaje
valor nutricional
secuenciación de nueva generación
How to Cite
Abstract
Introduction: King grass (Cenchrus purpureus (Schumach.) Morrone, syn. Pennisetum purpuphoides) and pineapple peel (Ananas comosus) silages are food alternatives for livestock in conditions of feed shortage. Objective: To describe the dynamics of the microbiota present in king grass and pineapple silage during the fermentation process using next generation sequencing (NGS) and to evaluate the protective effect of Lacticaseibacillus paracasei_6714 as a silage inoculum against Listeria monocytogenes. Methods: We used an unrestricted randomized design to characterize the microbiota present in silages made from king grass harvested 70 days after regrowth and pineapple peel. We inoculated mixtures of grass and peel with L. paracasei_6714 or L. monocytogenes, or both, with a non-inoculated treatment as control. The nutritional and fermentative profile was evaluated after 30 days. After 15 and 30 days of fermentation, we used 16S rRNA analysis to determine the dynamics and diversity of the microbiota in the inoculated and control silages. Result: Dry matter content and digestibility did not differ significantly; however, there were differences in crude protein, pH and organic acids. We obtained 4432 amplicon sequence variants of Proteobacteria, Firmicutes, Bacterioidetes, Actinobacteria, Verrucomicrobia, Planctomycetes and Patescibacteria. The relative abundance of each phylum varied depending on the material and fermentation period. Phylum similarity was over 70 % (but not greater than 50 % with Bray-Curtis at the species level). Conclusion: These bacterial communities seem to have an important role during silage fermentation. Proper management of silage processing can reduce or eliminate pathogenic bacteria.
References
Alfaro, E., & Quesada, A. (2010). Ocurrencia de ciclones tropicales en el Mar Caribe y sus impactos sobre Centroamérica. Intersedes, 11, 136–153.
Araya, M., & Boschini, C. (2005). Producción de forraje y calidad nutricional de variedades de Pennisetum purpureum en la Meseta Central de Costa Rica. Agronomia Mesoamericana, 16, 37–43.
Association of Official Analytical Chemist (AOAC). (1998). Official Methods of Analysis of AOAC International (16th ed). AOAC.
Auerbach, H., & Nadeau, E. (2020). Effects of additive type on fermentation and aerobic stability and its interaction with air exposure on silage nutritive value. Agronomy, 10, 1229.
Ávila, C., & Carvalho, B. (2019). Silage fermentation-update focusing on the performance of micro-organisms. Journal of Applied Microbiology, 128, 966–984.
Birnboim, H. C., & Doly, J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Research, 7, 1513–1523.
Blajman, J. E., Páez, R. B., Vinderola, C. G., Lingua, M. S., & Signorini, M. L. (2018). A meta-analysis on the effectiveness of homofermentative and heterofermentative lactic acid bacteria for corn silage. Journal Applied Microbiology, 125, 1655–1669.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., ... & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, 37(8), 852–857.
Callahan, B., McMurdie, P., Rosen, M., Han, A., Johnson, A. J., & Holmes, S. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Gonzales Peña, A., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, B. D., Pirrung, M., ... & Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature methods, 7(5), 335–336.
Carvalho, B. F., Ávila, C. L., Bernardes, T. F., Pereira, M. N., Santos, C., & Schwan, R. F. (2017). Fermentation profile and identification of lactic acid bacteria and yeasts of rehydrated corn kernel silage. Journal of Applied Microbiology, 122, 589–600.
Cao, Y., Cai, Y., Takahashi, T., Yoshida, N., Tohno, M., Uegaki, R., Nonaka, K., & Terada, F. (2011). Effect of lactic acid bacteria inoculant and beet pulp addition on fermentation characteristics and in vitro ruminal digestion of vegetable residue silage. Journal Dairy Science, 94, 3902–3912.
Contreras-Govea, F., Muck, R. E., Broderick, G. A., & Weimer, P. J. (2013). Lactobacillus plantarum effects on silage fermentation and in vitro microbial yield. Animal Feed Science Technology, 179, 61–68.
Dhama, K., Karthik, K., Tiwari, R., Shabbir, M. Z., Barbuddhe, S., Veer, S., & Singh, R. K. (2015). Listeriosis in animals, its public health significance (food-borne zoonosis) and advances in diagnosis and control: a comprehensive review. Veterinary Quarterly, 35, 211–235.
Driehuis, F., & Oude-Elferink, S. J. W. H. (2000). The impact of the quality of silage on animal health and food safety: a review. Veterinary Quarterly, 22, 212–216.
Driehuis, F., Oude-Elferink, S. J. W. H., & Van Wikselaar, P. G. (2002). Fermentation characteristics and aerobic stability of grass silage inoculated with Lactobacillus buchheri, with or without homofermentative lactic acid bacteria. Grass Forage Science, 56, 330–343.
Duniere, L., Xu, S., Long, J., Elekwachi, C., Wang, Y., Turkington, K., Forster, R., & McAllister, T. A. (2017). Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage. BMC microbiology, 17(1), 1–16.
Guan, H., Ke, W., Yan, Y., Shuai, Y., Li, X., Ran, Q., Yang, Z., Wang, X., Cai, Y., & Zhang, X. (2020). Screening of natural lactic acid bacteria with potential effect on silage fermentation, aerobic stability and aflatoxin B1 in hot and humid area. Journal of Applied Microbiology, 128, 1301–1311.
Gutierrez, F., Rojas-Bourrillón, A., Dormond, H., Poore, M., & WingChing-Jones, R. (2003). Características nutricionales y fermentativas de mezclas ensiladas de desechos de piña y avícolas. Agronomía Costarrincense, 27(1), 79–89.
He, L., Lv, H., Xing, Y., Wang, C., You, X., Chen, X., & Zhang, Q. (2020). The nutrients in Moringa oleifera leaf contribute to the improvement of stylo and alfalfa silage: Fermentation, nutrition and bacterial community. Bioresource Technology, 301, 122733.
Huyen, N., Martinez, I., & Pellikaan, W. (2020). Using lactic acid bacteria as silage inoculants or direct-fed microbials to improve in vitro degradability and reduce methane emissions in dairy cows. Agronomy, 10, 1482.
Idland, L., Granquist, E. G., Aspholm, M., & Lindbäck, T. (2022). The prevalence of Campylobacter spp., Listeria monocytogenes and Shiga toxin‐producing Escherichia coli in Norwegian dairy cattle farms: A comparison between free stall and tie stall housing systems. Journal of Applied Microbiology, 132(5), 3959–3972.
Keshri, J., Chen, Y., Pinto, R., Kroupitski, Y., Weinberg, Z. G., & Sela-Saldinger, S. (2018). Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant. Applied Microbiology and Biotechnology, 102, 4025–4037.
Keshri, J., Chen, Y., Pinto, R., Kroupitski, Y., Weinberg, Z. G., Sela-Saldinger, S. (2019). Bacterial dynamics of wheat silage. Frontiers in Microbiology, 10, 1532.
Kim, D., Lee, K., & Choi, K. (2020). Role of LAN in silage fermentation: Effect on nutritional quality and organic acid production-An overview. AIMS Agriculture and Food, 6, 216–234.
Kleinschmit, D. H., & Kung, L. J. (2006). A meta-analysis of the effects of Lactobacillus buchneri on the fermentation and aerobic stability of corn and grass and small-grain silages. Journal of Dairy Science, 89, 4005–13.
Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic acids research, 41(1), e1–e1.
Leiva., A., & Granados-Chinchilla, F. (2020). Fatty acid profiling in animal feed and related food matrixes using a fast GC/MS method and in situ derivatization. International Journal of Agriculture, Environment and Food Sciences, 4, 70–89.
López-Herrera, M., Rojas-Bourrillón, A., & Castillo-Umaña, M. (2019). Efecto de la sustitución de King grass (Cenchrus purpureus) por yuca (Manihot esculenta crantz) sobre la calidad del ensilaje. Nutrición Animal Tropical, 13, 21–42.
López-Herrera, M., WingChing-Jones, R., & Rojas-Bourrillón, A. (2014). Meta análisis de los subproductos de piña (Ananas comosus) para la alimentación animal. Agronomia Mesoamericana, 25(2), 383–392.
McDonald, P. (1981). The biochemistry of silage. John Wiley Ltd.
Meng, J., & Doyle. M. P. (1997). Emerging issues in microbiological food safety. Annual Review of Nutrition, 17, 255–275.
Muraro, G. B., de Almeida-Carvalho-Estrada, P., de Oliveira-Pasetti, M. H., Santos, M. C., & Nussio, L. G. (2021). Bacterial dynamics of sugarcane silage in the tropics. Environmental Microbiology, 23(10), 5979–5991.
Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and environmental microbiology, 59(3), 695–700.
National Research Council (NRC). (2001). Nutrient requirements of dairy catlle (7th rev. ed.) National academy press.
Ni, K., Wang, Y., Cai, Y., & Pang, H. (2015). Natural lactic acid bacteria population and silage fermentation of whole-crop wheat. Asian-Australasian Journal of Animal Sciences, 28, 1123–1132.
Nightingale, K. K., Schukken, Y. H., Nightingale, C. R., Fortes, E. D., Ho, A. J., Her, Z., Grohn, Y. T., & Wiedmann, M. (2004). Ecology and transmission of Listeria monocytogenes infecting ruminants and in the farm environment. Applied and Environmental Microbiology, 70(8), 4458–4467.
Pulido, R., García, E., Beltrán, I., Daza, J., Keim, J., & Castillo, I. (2020). Effect of a homofermentative lactic acid bacteria additive on the quality of sugar-beet pulp silage and animal response of dairy cows with restricted access to pasture. Chilean Journal of Agricultural Research, 80(2), 234–240.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web‐based tools. Nucleic Acids Research, 41(D1), D590–D596.
Queiroz, O., Ogunade, I., Weinberg, Z., & Adesogan, T. (2018). Silage review: Foodborne pathogens in silage and their mitigation by silage additives. Journal of Dairy Science, 101, 4132–4142.
Rahman, M. M., Abdullah, R. B., Khadijah, W. E., Nakagawa, T., & Akashi, R. (2014). Feed intake and growth performance of goats supplemented with soy waste. Pesquisa Agropecuária Brasileira, 49, 554–558.
Ren, H., Wang, C., Fan, W., Zhang, B., Li, Z., & Li, D. (2018). Effects of formic acid or acetic acid on the mixed-storage quality of air-dried maize stover and cabbage wastes and microbial community analysis. Food Technolgy and Biotechnology, 56, 71–82.
Romero, J. J., Zhao, Y., Balseca-Paredes, M. A., Tiezzi, F., Gutierrez-Rodriguez, E., & Castillo, M. S. (2017). Laboratory silo type and inoculation effects on nutritional composition, fermentation, and bacterial and fungal communities of oat silage. Journal of Dairy Science, 100, 1812–1828.
Ronquist, F., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
SAS Institute Inc. (2011). Base SAS Procedures Guide: Statistical Procedures. SAS Institute Inc.
Santos, A. O., Ávila, C. L. S., & Schwan, R. F. (2013). Selection of tropical lactic acid bacteria for enhancing the quality of maize silage. Journal of Dairy Science, 96, 7777–7789.
Santoso, B., Hariadi, B. T., & Jeni, J. (2015). Fermentation quality of king grass silage treated with liquid or dried inoculants of lactic bacteria. Journal of the Indonesian Tropical Animal Agriculture, 40(4), 208–214.
da Silva, N. C., Nascimento, C. F., Nascimento, F. A., de Resende, F. D., Daniel, J. L. P., & Siqueira, G. R. (2018). Fermentation and aerobic stability of rehydrated corn grain silage treated with different doses of Lactobacillus buchneri or a combination of Lactobacillus plantarum and Pediococcus acidilactici. Journal Dairy Science, 101, 4158–4167.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729.
Thierry, A., Deutsch, S. M., Falentin, H., Dalmasso, M., Cousin, F. J., & Jan, G. (2011). New insights into physiology and metabolism of Propionibacterium freudenreichii. International Journal of Food Microbiology, 149(1), 19–27.
Tobía, C., Rojas, A., Villalobos, E., Soto, H., & Uribe, L. (2004). Use of soybean silage to partially substitute balanced concentrate and its effects on dairy milk production and quality, in the wet tropics of Costa Rica. Agronomia Costarricense, 28, 27–35.
Van-Soest, P. J., & Robertson, J. B. (1985). Analysis of forages and fibrous foods: a laboratory manual for animal science. Cornell University.
Villalobos-Villalobos, L., Arce-Cordero, J., WingChing-Jones, R. (2015). Costos de producción de ensilados de pastos tropicales elaborados en lecherías de Costa Rica. Nutrición Animal Tropical, 9, 27–48.
Wang, X., Haruta, S., Wang, P., Ishii, M., Igarashi, Y., & Cui, Z. (2006). Diversity of a stable enrichment culture which is useful for silage inoculant and its succession in alfalfa silage. FEMS Microbiology Ecology, 57(1), 106–115.
Wang, S., Shao, T., Li, J., Zhao, J., & Dong, Z. (2022). Fermentation profiles, bacterial community compositions, and their predicted functional characteristics of grass silage in response to epiphytic microbiota on legume forages. Frontiers in Microbiology, 13, 830888.
Wang, Y. S., Shi, W., Huang, L. T., Ding, C. L., Dai, C. C. (2016). The effect of lactic acid bacterial starter culture and chemical additives on wilted rice straw silage. Animal Science Journal, 87(4), 525–535.
WingChing-Jones, R., Redondo-Solano, M., Usaga, J., Uribe, L., & Barboza, N. (2021). Tipificación con secuencias multilocus en Lactobacillus casei procedentes de ensilados de cáscara de piña. Agronomía Mesoamericana, 32, 508–522.
Wu-Wu, J., Redondo-Solano, M., Uribe, L., WingChing-Jones, R., Usaga, J., & Barboza, N. (2021). First characterization of the probiotic potential of lactic acid bacteria isolated from Costa Rican pineapple silages. PeerJ, 9, e12437.
Yang, L., Yuan, X., Li, J., Dong, Z., & Shao, T. (2019). Dynamics of microbial community and fermentation quality during ensiling of sterile and nonsterile alfalfa with or without Lactobacillus plantarum inoculant. Bioresource Technology, 275, 280–287.
Yoon, S. H., Ha, S. M., Kwon, S., Lim, J., Kim, Y., Seo, H., & Chun, J. (2017). Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67(5), 1613–1617.
Yoshida, T., Kato, Y., Sato, M., & Hirai, K. (1998). Sources and routes of contamination of raw milk with Listeria monocytogenes and its control. The Journal of Veterinary Medical Science, 60, 1165–1168.
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M., Harris, H. M., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., Wantanabe, K., Wuyts, S., Felis, G. E., Gänzle, M. G., & Lebeer, S. (2020). A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. International journal of systematic and evolutionary microbiology, 70(4), 2782–2858.
Zi, X., Li, M., Chen, Y., Lv, R., Zhou, H., & Tang, J. (2021). Effects of citric acid and Lactobacillus plantarum on silage quality and bacterial diversity of king grass Silage. Frontiers in Microbiology, 12, 631096.
Comments
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright (c) 2023 Revista de Biología Tropical