Skip to main content
×
×
Home

Evaluation of the effects of different diets on microbiome diversity and fatty acid composition of rumen liquor in dairy goat

  • P. Cremonesi (a1), G. Conte (a2), M. Severgnini (a3), F. Turri (a1), A. Monni (a1), E. Capra (a1), L. Rapetti (a4), S. Colombini (a4), S. Chessa (a1), G. Battelli (a5), S. P. Alves (a6), M. Mele (a2) and B. Castiglioni (a1)...
Abstract

Fat supplementation plays an important role in defining milk fatty acids (FA) composition of ruminant products. The use of sources rich in linoleic and α-linolenic acid favors the accumulation of conjugated linoleic acids isomers, increasing the healthy properties of milk. Ruminal microbiota plays a pivotal role in defining milk FA composition, and its profile is affected by diet composition. The aim of this study was to investigate the responses of rumen FA production and microbial structure to hemp or linseed supplementation in diets of dairy goats. Ruminal microbiota composition was determined by 16S amplicon sequencing, whereas FA composition was obtained by gas-chromatography technique. In all, 18 pluriparous Alpine goats fed the same pre-treatment diet for 40±7 days were, then, arranged to three dietary treatments consisting of control, linseed and hemp seeds supplemented diets. Independently from sampling time and diets, bacterial community of ruminal fluid was dominated by Bacteroidetes (about 61.2%) and Firmicutes (24.2%) with a high abundance of Prevotellaceae (41.0%) and Veillonellaceae (9.4%) and a low presence of Ruminococcaceae (5.0%) and Lachnospiraceae (4.3%). Linseed supplementation affected ruminal bacteria population, with a significant reduction of biodiversity; in particular, relative abundance of Prevotella was reduced (−12.0%), whereas that of Succinivibrio and Fibrobacter was increased (+50.0% and +75.0%, respectively). No statistically significant differences were found among the average relative abundance of archaeal genera between each dietary group. Moreover, the addition of linseed and hemp seed induced significant changes in FA concentration in the rumen, as a consequence of shift from C18 : 2n-6 to C18 : 3n-3 biohydrogenation pathway. Furthermore, dimethylacetal composition was affected by fat supplementation, as consequence of ruminal bacteria population modification. Finally, the association study between the rumen FA profile and the bacterial microbiome revealed that Fibrobacteriaceae is the bacterial family showing the highest and significant correlation with FA involved in the biohydrogenation pathway of C18 : 3n-3.

Copyright
Corresponding author
E-mail: cremonesi@ibba.cnr.it
Footnotes
Hide All
a

These authors contributed equally to this work.

Footnotes
References
Hide All
Alves, SP, Santos-Silva, J, Cabrita, ARJ, Fonseca, AMJ and Bessa, RJB 2013. Detailed dimethylacetal and fatty acid composition of rumen content from lambs fed lucerne or concentrate supplemented with soybean oil. PLOS one 3, e58386.
Association of Official Analytical Chemists International 1995. Official Methods of Analysis, 15th ed. AOAC International, Washington, DC, USA.
Belenguer, A, Toral, PG, Frutos, P and Hervás, G 2010. Changes in the rumen bacterial community in response to sunflower oil and fish oil supplements in the diet of dairy sheep. Journal of Dairy Science 93, 32753286.
Buccioni, A, Decandia, M, Minieri, S, Molle, G and Cabiddu, A 2012. Lipid metabolism in the rumen: New insights on lipolysis and biohydrogenation with an emphasis on the role of endogenous plant factors. Animal Feed Science and Technology 174, 125.
Caporaso, JG, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK, Fierer, N, Peña, AG, Goodrich, JK, Gordon, JI, Huttley, GA, Kelley, ST, Knights, D, Koenig, JE, Ley, RE, Lozupone, CA, McDonald, D, Muegge, BD, Pirrung, M, Reeder, J, Sevinsky, JR, Turnbaugh, PJ, Walters, WA, Widmann, J, Yatsunenko, T, Zaneveld, J and Knight, R 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335336.
Caporaso, JG, Lauber, CL, Walters, WA, Berg-Lyons, D and Lozupone, CA 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of National Academy of Science 108, 45164522.
Castro-Carrera, T, Toral, PG, Frutos, P, Mcewan, NR, Hervás, G, Abecia, L, Pinloche, E, Girdwood, SE and Belenguer, A 2014. Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae. Journal of Dairy Science 97, 16611669.
Chilliard, Y, Ferlay, A, Rouel, J and Lamberet, G 2003. A review of nutritional and physiological factors affecting goat milk lipid synthesis and lipolysis. Journal of Dairy Science 86, 17511770.
Chilliard, Y and Ferlay, A 2004. Dietary lipids and forages interactions on cow and goat milk fatty acid composition and sensory properties. Reproduction Nutrition Development 44, 467492.
Chilliard, Y, Glasser, F, Ferlay, A, Bernard, L, Rouel, J and Doreau, M 2007. Diet, rumen biohydrogenation and nutritional quality of cow and goat milk fat. European Journal of Lipid Science and Technology 109, 828855.
Christie, WW 1993. Advances in lipid methodology. Oily Press, Dundee, UK. pp. 69111.
Cunha, IS, Barreto, CC, Costa, OY, Bomfim, MA, Castro, AP, Kruger, RH and Quirino, BF 2011. Bacteria and Archaea community structure in the rumen microbiome of goats (Capra hircus) from the semiarid region of Brazil. Anaerobe 17, 118124.
Demirel, G, Wachira, AM, Sinclair, LA, Wilkinson, RG, Wood, JD and Enser, M 2004. Effects of dietary n-3 polyun- saturated fatty acids, breed and dietary vitamin E on the fatty acids of lamb muscle, liver and adipose tissue. British Journal of Nutrition 91, 551565.
Devillard, E, McIntosh, FM, Duncan, SH and Wallace, RJ 2007. Metabolism of linoleic acid by human gut bacteria: different routes for biosynthesis of conjugated linoleic acid. Journal of Bacteriology 189, 25662570.
Fernando, SC, Purvis, HT, Najar, FZ, Sukharnikov, LO, Krehbiel, CR, Nagaraja, TG, Roe, BA and DeSilva, U 2010. Rumen microbial population dynamics during adaptation to a high-grain diet. Applied and Environmental Microbiology 76, 74827490.
Fievez, V, Colman, E, Castro-Montoya, JM, Stefanov, I and Vlaeminck, B 2012. Milk odd- and branched-chain fatty acids as biomarkers of rumen function – an update. Animal Feed Science and Technology 172, 5165.
Frey, JC, Pell, AN, Berthiaume, R, Lapierre, H, Lee, S, Ha, JK, Mendell, JE and Angert, ER 2010. Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows. Journal of Applied Microbiology 108, 19821993.
Goldfine, H 2010. The appearance, disappearance and reappearance of plasmalogens in evolution. Progress in Lipid Research 49, 493498.
Harfoot, CG and Hazlewood, GP 1997. Lipid metabolism in the rumen. In The rumen microbial ecosystem (ed. PN Hobson), pp. 382426. Elsevier, London.
Huws, SA, Kim, EJ, Lee, MRF, Scott, MB, Tweed, JKS, Pinloche, E, Wallace, RJ and Scollan, ND 2011. As yet uncul- tured bacteria phylogenetically classified as Prevotella, Lachnospiraceae incertae sedis and unclassified Bacteroidales, Clostridiales and Ruminococcaceae may play a predominant role in ruminal bio-hydrogenation. Environmental Microbiology 13, 15001512.
International Organization for Standardization 1976. Milk: determination of fat content (Gerber method). ISO, Geneva, Switzerland.
International Organization for Standardization 2006. Milk: Determination of urea content. Enzymatic method using difference in pH (Reference method). ISO, Geneva, Switzerland.
Jewell, KA, McCormick, CA, Odt, CL, Weimer, PJ and Suen, G 2015. Ruminal bacteria community composition in dairy cows is dynamic over the course of two lactation and correlates with feed efficiency. Applied and Environmental Microbiology 81, 46974710.
Kramer, JKG, Hernandez, M, Cruz-Hernandez, C, Kraft, J and Dugan, MER 2008. Combining results of two GC separations partly achieves determination of all cis and trans 16:1, 18:1, 18:2 and 18:3 except CLA isomers of milk fat as demonstrated using Ag-Ion SPE Fractionation. Lipids 43, 259273.
Loor, JJ, Ferlay, A, Ollier, A, Ueda, K, Doreau, M and Chilliard, Y 2005. High-concentrate diets and polyunsaturated oils alter trans and conjugated isomers in bovine rumen, blood, and milk. Journal of Dairy Science 88, 39863999.
Lozupone, C and Knight, R 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71, 82288235.
Masella, AP, Bartram, AK, Truszkowski, JM, Brown, DG and Neufeld, JD 2012. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics 13, 31.
Mele, M 2009. Designing milk fat to improve healthfulness and functional properties of dairy products: from feeding strategies to a genetic approach. Italian Journal of Animal Science 8, 365373.
Mertens, DR 2002. Gravimetric determination of amylase-treated neutral detergent fiber in feeds using refluxing in beakers or crucibles: collaborative study. Journal of AOAC International 85, 12171240.
Min, BR, Wright, C, Ho, P, Eun, JS, Gurung, N and Shange, R 2014. The effect of phytochemical tannins-containing diet on rumen fermentation characteristics and microbial diversity dynamics in goats using 16S rDNA amplicon pyrosequencing. Agricultural Food and Analytical Bacteriology 4, 311.
Paillard, D, McKain, N, Chaudhary, LC, Walker, ND, Pizette, F, Koppova, I, McEwan, NR, Kopecny, J, Vercoe, PE, Louis, P and Wallace, RJ 2007. Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria from the rumen. Antonie van Leeuwenhoek 91, 417422.
Palmquist, DL, Lock, AL, Shingfield, KJ and Bauman, DE 2005. Biosynthesis of conjugated linoleic acid in ruminants and humans. Advances in Food and Nutrition Research 50, 179217.
Paul, SS, Deb, SM, Dey, A, Somvanshi, SP, Singh, D, Rathore, R and Stiverson, J 2015. 16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo. Anaerobe 35, 310.
Revello Chion, A, Tabacco, E, Giaccone, D, Peiretti, PG, Battelli, G and Borreani, G 2010. Variation of fatty acid and terpene profiles in mountain milk and ‘Toma piemontese’ cheese as affected by diet composition in different seasons. Food Chemistry 121, 393399.
Saluzzi, L, Stewart, CS, Flint, HJ and Smith, A 1995. Plasmalogens of microbial communities associated with barley straw and clover in the rumen. FEMS Microbiology Ecology 17, 4756.
Shah, HN and Collins, MD 1983. Megamonas hypermegas gen. nov., comb. nov. In Validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 10. International Journal of Systemic and Bacteriology 33, 438440.
Shingfield, KJ, Bernard, L, Leroux, C and Chilliard, Y 2010. Role of trans fatty acids in the nutritional regulation of mammary lipogenesis in ruminants. Animal 7, 11401166.
Shingfield, KJ, Kairenius Äröla, PA, Paillard, D, Muetzel, S, Ahvenjärvi, S, Vanhatalo, A, Huhtanen, P, Toivonen, V, Griinari, JM and Wallace, RJ 2012. Dietary fish oil supplements modify ruminal biohydrogenation, alter the flow of fatty acids at the oma- sum, and induce changes in the ruminal Butyrivibrio population in lactating cows. Journal of Nutrition 142, 14371448.
Sirohi, SK, Chaudhary, PP, Singh, N, Singh, D and Puniya, AK 2013. The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet. Gene 523, 161166.
Toral, PG, Belenguer, A, Shingfield, KJ, Hervás, G, Toivonen, V and Frutos, P 2012. Fatty acid composition and bacterial community changes in the rumen fluid of lactating sheep fed sunflower oil plus incremental levels of marine algae. Journal of Dairy Science 95, 794806.
Toral, PG, Bernard, L, Belenguer, A, Rouel, J, Hervás, G, Chilliard, Y and Frutos, P 2016. Comparison of ruminal lipid metabolism in dairy cows and goats fed diets supplemented with starch, plant oil, or fish oil. Journal of Dairy Science 99, 301316.
Vlaeminck, B, Fievez, V, Cabrita, ARJ, Fonseca, AJM and Dewhurst, RJ 2006. Factors affecting odd- and branched-chain fatty acids in milk: a review. Animal Feed Science and Technology 131, 389417.
Wang, Q, Garrity, GM, Tiedje, JM and Cole, JR 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73, 52615267.
Yu, Z and Morrison, M 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 36, 808812.
Zened, A, Combes, S, Cauquil, L, Mariette, J, Klopp, C, Bouchez, O, Troegeler-Meynadier, A and Enjalbert, F 2013. Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets. FEMS Microbiology and Ecology 83, 504514.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

animal
  • ISSN: 1751-7311
  • EISSN: 1751-732X
  • URL: /core/journals/animal
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Keywords

Type Description Title
WORD
Supplementary materials

Cremonesi et al. supplementary material
Figures S1-S5

 Word (2.7 MB)
2.7 MB

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 16
Total number of PDF views: 129 *
Loading metrics...

Abstract views

Total abstract views: 540 *
Loading metrics...

* Views captured on Cambridge Core between 8th January 2018 - 19th July 2018. This data will be updated every 24 hours.