Metaprofiling of the bacterial community in sorghum silages inoculated with lactic acid bacteria.
L. paracasei
L. plantarum
P. pentosaceus
NGS
inoculants
profiling
silage
sorghum
Journal
Journal of applied microbiology
ISSN: 1365-2672
Titre abrégé: J Appl Microbiol
Pays: England
ID NLM: 9706280
Informations de publication
Date de publication:
Oct 2022
Oct 2022
Historique:
revised:
13
05
2022
received:
16
02
2022
accepted:
28
06
2022
pubmed:
3
7
2022
medline:
28
9
2022
entrez:
2
7
2022
Statut:
ppublish
Résumé
To characterize the fermentation process and bacterial diversity of sorghum silage inoculated with Lactiplantibacillus plantarum LpAv, Pediococcus pentosaceus PpM and Lacticaseibacillus paracasei LcAv. Chopped sorghum was ensiled using the selected strains. Physicochemical parameters (Ammonia Nitrogen/Total Nitrogen, Dry Matter, Crude Protein, Acid Detergent Fibre, Neutral Detergent Fibre, Acid Detergent Lignin, Ether Extract and Ashes), bacterial counts, cell cytometry and 16sRNA sequencing were performed to characterize the ensiling process and an animal trial (BALB/c mice) was conducted in order to preliminary explore the potential of sorghum silage to promote animal gut health. After 30 days of ensiling, the genus Lactobacillus comprised 68.4 ± 2.3% and 73.5 ± 1.8% of relative abundance, in control and inoculated silages respectively. Richness (Chao1 index) in inoculated samples, but not in control silages, diminished along ensiling, suggesting the domination of fermentation by the inoculated LAB. A trend in conferring enhanced protection against Salmonella infection was observed in the mouse model used to explore the potential to promote gut health of sorghum silage. The LAB strains used in this study were able to dominate sorghum fermentation. This is the first report using metaprofiling of 16sRNA to characterize sorghum silage, showing a microbiological insight where resident and inoculated LAB strains overwhelmed the epiphytic microbiota, inhibiting potential pathogens of the genus Klebsiella.
Substances chimiques
Detergents
0
Ethers
0
Plant Extracts
0
Ammonia
7664-41-7
Lignin
9005-53-2
Nitrogen
N762921K75
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2375-2389Subventions
Organisme : Agencia Nacional de Promoción Científica y Tecnológica
ID : PICT-2016-0256
Informations de copyright
© 2022 Society for Applied Microbiology.
Références
Alhaag, H., Yuan, X., Mala, A., Bai, J. & Shao, T. (2019) Fermentation characteristics of Lactobacillus plantarum and Pediococcus species isolated from sweet sorghum silage and their application as silage inoculants. Applied Sciences (Switzerland), 9(6), 1-17. https://doi.org/10.3390/app9061247
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
Bai, C., Wang, C., Sun, L., Xu, H., Jiang, Y., Na, N. et al. (2021) Dynamics of bacterial and fungal communities and metabolites during aerobic exposure in whole-plant corn silages with two different moisture levels. Frontiers in Microbiology, 12, 1-12. https://doi.org/10.3389/fmicb.2021.663895
Bao, W., Mi, Z., Xu, H., Zheng, Y., Kwok, L.Y., Zhang, H. et al. (2016) Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters. Scientific Reports, 6, 1-8. https://doi.org/10.1038/srep28358
Blajman, J.E., 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. Muck, 2010, 1655-1669. https://doi.org/10.1111/jam.14084
Blajman, J.E., Vinderola, G., Páez, R. & Signorini, M.L. (2020) The role of homofermentative and heterofermentative lactic acid bacteria for alfalfa silage: a meta-analysis. The Journal of Agricultural Science, 158(1-2), 107-118. https://doi.org/10.1017/S0021859620000386
Callahan, B.J., Sankaran, K., Fukuyama, J.A., McMurdie, P.J. & Holmes, S.P. (2016) Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; referees: 3 approved]. F1000Research, 5(3). https://doi.org/10.12688/F1000RESEARCH.8986.1
Calle, M.L. (2019) Statistical analysis of metagenomics data. Genomics and Informatics, 17(1), 1-9. https://doi.org/10.5808/GI.2019.17.1.e6
Carvalho, B.F., Sales, G.F.C., Schwan, R.F. & Ávila, C.L.S. (2021) Criteria for lactic acid bacteria screening to enhance silage quality. Journal of Applied Microbiology, 130(2), 341-355. https://doi.org/10.1111/jam.14833
Charan, J. & Kantharia, N. (2013) How to calculate sample size in animal studies? Journal of Pharmacology and Pharmacotherapeutics, 4(4), 303-306. https://doi.org/10.4103/0976-500X.119726
Cheng, J., Zhou, M., Nobrega, D.B., Barkema, H.W., Xu, S., Li, M. et al. (2021) Genetic diversity and molecular epidemiology of outbreaks of Klebsiella pneumoniae mastitis on two large Chinese dairy farms. Journal of Dairy Science, 104(1), 762-775. https://doi.org/10.3168/jds.2020-19325
Correa Deza, M., Grillo-Puertas, M., Salva, S., Rapisarda, V., Gerez, C. & Font de Valdez, G. (2017) Inorganic salts and intracellular polyphosphate inclusions play a role in the thermotolerance of the immunobiotic lactobacillus rhamnosus CRL 1505. PLoS One, 12(6), e0179242. https://doi.org/10.1371/journal.pone.0179242
dos Santos Leandro, E., Ginani, V.C., de Alencar, E.R., Pereira, O.G., Rose, E.C.P., do Vale, H.M.M. et al. (2020) Isolation, identification, and screening of lactic acid bacteria with probiotic potential in silage of different species of forage plants, cocoa beans, and artisanal salami. Probiotics and Antimicrobial Proteins, 13, 173-186. https://doi.org/10.1007/s12602-020-09679-y
Driehuis, F., Wilkinson, J.M., Jiang, Y., Ogunade, I. & Adesogan, A.T. (2018) Silage review: animal and human health risks from silage. Journal of Dairy Science, 101(5), 4093-4110. https://doi.org/10.3168/jds.2017-13836
Duniere, L., Xu, S., Long, J., Elekwachi, C., Wang, Y., Turkington, K. et al. (2017) Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage. BMC Microbiology, 17(1), 1-16. https://doi.org/10.1186/s12866-017-0947-0
Edgar, R. (2016) UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv, 3476-3482. https://doi.org/10.1101/081257
Edgar, R.C. (2018) Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics, 34(14), 2371-2375. https://doi.org/10.1093/bioinformatics/bty113
Edgar, R.C. & Flyvbjerg, H. (2015) Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics, 31(21), 3476-3482. https://doi.org/10.1093/bioinformatics/btv401
Eikmeyer, F.G., Köfinger, P., Poschenel, A., Jünemann, S., Zakrzewski, M., Heinl, S. et al. (2013) Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial community involved in grass ensiling. Journal of Biotechnology, 167(3), 334-343. https://doi.org/10.1016/j.jbiotec.2013.07.021
Fabiszewska, A.U., Zielińska, K.J. & Wróbel, B. (2019) Trends in designing microbial silage quality by biotechnological methods using lactic acid bacteria inoculants: a minireview. World Journal of Microbiology and Biotechnology, 35(5), 1-8. https://doi.org/10.1007/s11274-019-2649-2
Gallagher, D., Parker, D., Allen, D.J. & Tsesmetzis, N. (2018) Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production. Bioresource Technology, 264, 163-173. https://doi.org/10.1016/j.biortech.2018.05.053
Gharechahi, J., Kharazian, Z.A., Sarikhan, S., Jouzani, G.S., Aghdasi, M. & Hosseini Salekdeh, G. (2017) The dynamics of the bacterial communities developed in maize silage. Microbial Biotechnology, 10(6), 1663-1676. https://doi.org/10.1111/1751-7915.12751
Guan, H., Yan, Y., Li, X., Li, X., Shuai, Y., Feng, G. et al. (2018) Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China. Bioresource Technology, 265, 282-290. https://doi.org/10.1016/j.biortech.2018.06.018
Guo, X.S., Ke, W.C., Ding, W.R., Ding, L.M., Xu, D.M., Wang, W.W. et al. (2018) Profiling of metabolome and bacterial community dynamics in ensiled Medicago sativa inoculated without or with Lactobacillus plantarum or Lactobacillus buchneri. Scientific Reports, 8(1), 1-10. https://doi.org/10.1038/s41598-017-18348-0
Hammer, Ø., Harper, D.A.T. & Ryan, P.D. (2001) Past: paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4(1), 1-9.
Hill, C., Guarner, F., Reid, G., Gibson, G.R., Merenstein, D.J., Pot, B. et al. (2014) Expert consensus document: the international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology and Hepatology, 11, 506-514. https://doi.org/10.1038/nrgastro.2014.66
Hughes, J.B., Hellmann, J.J., Ricketts, T.H., Bohannan, B.J.M., Sinclair, L., Osman, O.A. et al. (2016) Counting the uncountable: statistical approaches to estimating microbial diversity MINIREVIEW counting the uncountable: statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology, 10(1), 4399-4406. https://doi.org/10.1128/AEM.67.10.4399
Kraut-Cohen, J., Tripathi, V., Chen, Y., Gatica, J., Volchinski, V., Sela, S. et al. (2016) Temporal and spatial assessment of microbial communities in commercial silages from bunker silos. Applied Microbiology and Biotechnology, 100(15), 6827-6835. https://doi.org/10.1007/s00253-016-7512-x
Logares, R. (2017) No title. Ramalok/Amplicon_processing: workflow for Analysing MiSeq amplicons based on Uparse. Zenodo. https://doi.org/10.5281/zenodo.259579
Li, Y. & Nishino, N. (2011) Monitoring the bacterial community of maize silage stored in a bunker silo inoculated with Enterococcus faecium, Lactobacillus plantarum and Lactobacillus buchneri. Journal of Applied Microbiology, 110(6), 1561-1570. https://doi.org/10.1111/j.1365-2672.2011.05010.x
Liu, B., Huan, H., Gu, H., Xu, N., Shen, Q. & Ding, C. (2019) Dynamics of amicrobial community during ensiling and upon aerobic exposure in lactic acid bacteria inoculation-treated and untreated barley silages. Bioresource Technology, 273(50), 212-219. https://doi.org/10.1016/j.biortech.2018.10.041
Liu, B., Yang, Z., Huan, H., Gu, H., Xu, N. & Ding, C. (2020) Impact of molasses and microbial inoculants on fermentation quality, aerobic stability, and bacterial and fungal microbiomes of barley silage. Scientific Reports, 10(1), 1-10. https://doi.org/10.1038/s41598-020-62290-7
Marco, M.L., Sanders, M.E., Ganzle, M., Arrieta, M.C., Cotter, P.D., De Vuyst, L. et al. (2021) The international scientific Association for Probiotics and Prebiotics (ISSAP) consensus statement on fermented foods. Nature Reviews Gastroenterology and Hepatology, 18, 196-208. https://doi.org/10.1038/s41575-020-00390-5
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R. & Delgado, S. (2014) Impact of next generation sequencing techniques in food microbiology. Current Genomics, 15(4), 293-309. https://doi.org/10.2174/1389202915666140616233211
McAllister, T.A., Dunière, L., Drouin, P., Xu, S., Wang, Y., Munns, K. et al. (2018) Silage review: using molecular approaches to define the microbial ecology of silage. Journal of Dairy Science, 101(5), 4060-4074. https://doi.org/10.3168/jds.2017-13704
McCary, C.L., Vyas, D., Faciola, A.P. & Ferraretto, L.F. (2020) Graduate student literature review: current perspectives on whole-plant sorghum silage production and utilization by lactating dairy cows. Journal of Dairy Science, 103(6), 5783-5790. https://doi.org/10.3168/jds.2019-18122
Mogodiniyai Kasmaei, K., Dicksved, J., Spörndly, R. & Udén, P. (2017) Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability. Grass and Forage Science, 72(2), 281-289. https://doi.org/10.1111/gfs.12238
Muck, R.E., Nadeau, E.M.G., McAllister, T.A., Contreras-Govea, F.E., Santos, M.C. & Kung, L. (2018) Silage review: recent advances and future uses of silage additives. Journal of Dairy Science, 101(5), 3980-4000. https://doi.org/10.3168/jds.2017-13839
Munoz, M.A., Welcome, F.L., Schukken, Y.H. & Zadoks, R.N. (2007) Molecular epidemiology of two Klebsiella pneumoniae mastitis outbreaks on a dairy farm in New York state. Journal of Clinical Microbiology, 45(12), 3964-3971. https://doi.org/10.1128/JCM.00795-07
Ni, K., Minh, T.T., Tu, T.T.M., Tsuruta, T., Pang, H. & Nishino, N. (2017) Comparative microbiota assessment of wilted Italian ryegrass, whole crop corn, and wilted alfalfa silage using denaturing gradient gel electrophoresis and next-generation sequencing. Applied Microbiology and Biotechnology, 101(4), 1385-1394. https://doi.org/10.1007/s00253-016-7900-2
Nikolenko, S.I., Korobeynikov, A.I. & Alekseyev, M.A. (2013) BAYESHAMMER: Bayesian subclustering for error correction in single cell sequencing. BMC Genomics, 14(Suppl 1), 1-11. http://www.biomedcentral.com/1471-2164/14/S1/S7
Oddi, S., Binetti, A., Burns, P., Cuatrin, A., Reinheimer, J., Salminen, S. et al. (2020) Occurrence of bacteria with technological and probiotic potential in Argentinian breast-milk. Beneficial Microbes, 11(7), 685-702. https://doi.org/10.3920/BM2020.0054
Ogunade, I.M., Jiang, Y., Kim, D.H., Cervantes, A.A.P., Arriola, K.G., Vyas, D. et al. (2017) Fate of Escherichia coli O157:H7 and bacterial diversity in corn silage contaminated with the pathogen and treated with chemical or microbial additives. Journal of Dairy Science, 100(3), 1780-1794. https://doi.org/10.3168/jds.2016-11745
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H., Szoecs, E., & Wagner, H. (2013). Vegan: community ecology package. R package version 2.0-9. http://cran.r-project.org/package=vegan
Oude Elferink, S.J.W.H., Driehuis, F., Gottschal, J.C. & Spoelstra, S.F. (2000) Silage fermentation processes and their manipulation. In: FAO plant production and protection papers, January, pp. 17-30.
Pahlow, G., Muck, R.E., Driehuis, F., Oude Elferink, S.J.W.H. & Spoelstra, S.F. (2003) Microbiology of ensiling. In: Buxton, D.R., Muck, R.E. & Jarrison, J.H. (Eds.) Silage science and technology. Madison: American Society of Agronomy, pp. 31-93. https://doi.org/10.2134/agronmonogr42.c2
Pavanelo, D.B., Schröder, N.C.H., Pin Viso, N.D., Martins, L.A., Malossi, C.D., Galletti, M.F.B.M. et al. (2020) Comparative analysis of the midgut microbiota of two natural tick vectors of rickettsia rickettsii. Developmental and Comparative Immunology, 106(December 2019), 103606. https://doi.org/10.1016/j.dci.2019.103606
Podder, M.P., Rogers, L., Daley, P.K., Keefe, G.P., Whitney, H.G. & Tahlan, K. (2014) Klebsiella species associated with bovine mastitis in Newfoundland. PLoS One, 9(9), 1-5. https://doi.org/10.1371/journal.pone.0106518
Puntillo, M., Spotti, J., Salminen, S. & Vinderola, G. (2021) Narrowing down the number of potential plant-based probiotic candidates by successive in vitro, technological and in vivo assays. Beneficial Microbes, 12, 351-364.
Puntillo, M., Gaggiotti, M., Oteiza, J.M., Binetti, A., Massera, A. & Vinderola, G. (2020) Potential of lactic acid bacteria isolated from different forages as silage inoculants for improving fermentation quality and aerobic stability. Frontiers in Microbiology, 11, 1-17. https://doi.org/10.3389/fmicb.2020.586716
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(3), 1812-1828. https://doi.org/10.3168/jds.2016-11642
Salminen, S., Collado, M.C., Endo, A., Hill, C., Lebeer, S., Quigley, E.M.M. et al. (2021) The international scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nature Reviews Gastroenterology and Hepatology, 18(9), 649-667. https://doi.org/10.1038/s41575-021-00440-6
Shannon, C.E. (1948) A mathematical theory of communication. The Bell System Technical Journal, 27(3), 379-423.
Soundharrajan, I., Kim, D., Kuppusamy, P., Muthusamy, K., Lee, H.J. & Choi, K.C. (2019) Probiotic and triticale silage fermentation potential of pediococcus pentosaceus and lactobacillus brevis and their impacts on pathogenic bacteria. Microorganisms, 7(9), 1-19. https://doi.org/10.3390/microorganisms7090318
Sun, L., Bai, C., Xu, H., Na, N., Jiang, Y., Yin, G. et al. (2021) Succession of bacterial community during the initial aerobic, intense fermentation, and stable phases of whole-plant corn silages treated with lactic acid bacteria suspensions prepared from other silages. Frontiers in Microbiology, 12, 1-15. https://doi.org/10.3389/fmicb.2021.655095
Wilkinson, J. M., & Muck, R. E. (2019). Ensiling in 2050: Some challenges and opportunities. Grass and Forage Science, 74(2), 178-187. https://doi.org/10.1111/gfs.12418
Wu, J.W.F.W., Redondo-Solano, M., Uribe, L., Ching-Jones, R.W., Usaga, J. & Barboza, N. (2021) First characterization of the probiotic potential of lactic acid bacteria isolated from costa Rican pineapple silages. PeerJ, 9, 1-26. https://doi.org/10.7717/peerj.12437
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. https://doi.org/10.1016/j.biortech.2018.12.067
Zacarías, M.F., Reinheimer, J., Forzani, L., Grangette, C. & Vinderola, G. (2014) Mortality and translocation assay to study the protective capacity of Bifidobacterium lactis INL1 against salmonella typhimurium infecti. Beneficial Microbes, 5(4), 427-436. https://doi.org/10.3920/BM2013.0086
Zhao, X., Zhong, J., Wei, C., Lin, C.W. & Ding, T. (2017) Current perspectives on viable but non-culturable state in foodborne pathogens. Frontiers in Microbiology, 8, 1-16. https://doi.org/10.3389/fmicb.2017.00580