Characterization of the rumen microbial community composition of buffalo breeds consuming diets typical of dairy production systems in Southern China

https://doi.org/10.1016/j.anifeedsci.2015.06.013Get rights and content

Highlights

Abstract

Murrah and Nili-Ravi are water buffalo breeds widely used as dairy animals in Asian countries. In this study, we investigated the diversity of ruminal microbes in six Murrah and six Nili-Ravi water buffaloes consuming diets typical of those used in Southern China which had forage to concentrate ratios of 3.2 and 1.6. After feeding the diets for 25 days, ruminal fluid was sampled by stomach tube before the morning feeding. Bacterial and archaeal 16S rRNA genes and the ciliate protozoal 18S rRNA genes were PCR-amplified from DNA extracted from rumen samples, sequenced using 454 Titanium pyrosequencing, and analyzed using the QIIME software package. Our results showed that, at the phylum level, Bacteroidetes was the predominant bacterial group, accounting for 42–72% of total bacteria, followed by Firmicutes, Fibrobacteres, Proteobacteria and Spirochaetes. At genus level, Prevotella dominated, accounting for 22–58% of total bacteria, followed by Fibrobacter, Paludibacter, and Ruminococcus. While there were differences between the bacterial community compositions of different animals, there was no obvious correlation of bacterial community composition at the phylum or genus level with the diets or with buffalo breeds. Methanobrevibacter-related organisms were the dominant archaeal group, accounting for around 80% of the total, followed by Methanomassiliicoccales (Rumen Cluster C (RCC), 15%) and Methanosphaera (3%). Similar to the bacterial community, there was no obvious correlation of archaeal community profiles with diet or buffalo breed. The ciliate protozoal communities differed between the samples analyzed, and Entodinium was the most abundant group of ciliates in every sample, accounting for more than 40% of total protozoa. The second largest ciliate group varied in different samples, with Isotricha, Polyplastron or Dasytricha being the most dominant genera after Entodinium.

Introduction

Water buffaloes (Bubalus bubalis) are an important livestock species for milk and meat production worldwide, and are second in milk production only to dairy cows. Buffaloes are adapted to hot climates and high roughage feeding, and consequently they are often farmed in tropical and subtropical regions. In fact, about 90% of the world's buffaloes are found in Asian countries, mainly in subtropical areas (FAO, 2007). There are large physiological, genetic and behavioral differences between buffaloes and dairy cows, which make them an interesting ruminant species for comparative studies. Early nutritional investigations on buffaloes showed that they ingest about the same amount as cattle on a dry matter basis, but they spend around 50% more time ruminating, which results in a larger pool of fine feed particles and a 30% lower mean residence time of particulate matter in the rumen (McSweeney et al., 1989). Other studies have shown that buffaloes digest fibrous feeds more efficiently (Norton et al., 1979), resulting in higher digestibility of organic matter compared to cattle (Franzolin, 1994, Calabrò et al., 2008). Therefore, digestion of fibre in the rumen of buffaloes has attracted some attention, prompting an interest in understanding fibre-degrading microbes from the buffalo rumen, the enzymatic activities involved in lignocellulose breakdown, and the consequences for rumen methanogens and methane production.

The number of studies describing the composition of the rumen microbial communities in buffaloes is small compared with those from other ruminant species such as sheep and cattle. Most of the studies on buffaloes report the occurrence of well-known rumen bacteria and archaea and show strong similarities between rumen microbial profiles of buffaloes and other ruminants (Imai et al., 1995, Calabrò et al., 2005, Wanapat and Cherdthong, 2009, Foiklang et al., 2011, Huws et al., 2012, Lwin et al., 2012). A study of Mediterranean buffaloes on a variety of diets showed that the archaeal populations in the rumen were dominated by sequences associated with Methanobrevibacter species, with smaller numbers of sequences associated with Methanosphaera and Methanobacterium species (Franzolin et al., 2012), typical of methanogen communities found in other ruminants. However, there are several reports from India and Pakistan that indicate that the archaeal communities of Surti and Murrah buffaloes are different, being dominated by members of the genus Methanomicrobium (Chaudhary and Sirohi, 2009; Chaudhary et al., 2011, Singh et al., 2011a, Singh et al., 2012). The reasons for these differences are not clear, but diet, buffalo breed or the primers used to amplify methanogen 16S RNA genes may be contributing factors.

In China, native water buffalo have traditionally been used as draught animals, but in recent times there has been a strong drive to develop a dairy buffalo industry, based on imported breeds such as the Murrah and Nili-Ravi. The buffaloes are fed on pastures and by-products of crops and supplemented with some concentrates (Yang et al., 2007). In the southern regions, they are typically fed on fresh or conserved fodder crops, such as corn or cassava and they are also offered varying amounts of grains or waste products from processed plant material. Therefore, depending on the availability of feeds, dairy buffaloes can experience a variety of diets, often varying widely in forage:concentrate ratio, and quite unlike the fibrous diets that wild buffaloes encounter naturally. Comparing the rumen microbial communities of these dairy production buffaloes with those of better studied bovine species, and examining how these communities are affected by diet, is being studied to give a better understanding of the ruminal processes that underpin their unusual utilization of forage material and the rumen conditions that select for different methanogen communities. In the study reported here, Murrah and Nili-Ravi buffalo were fed on two diets of contrasting forage:concentrate ratio to represent the range of diets typically encountered by dairy buffaloes in this region. Rumen content samples were collected and analyzed via barcoded pyrosequencing to define their rumen microbial community composition to allow comparison with previously published data.

Section snippets

Animals, feed and management

The buffalo feeding experiment was conducted at the buffalo farm of the Buffalo Research Institute, the Chinese Academy of Agricultural Sciences, in Nanning, Guangxi, China, from 1 December 2012 to 10 January 2013. High and low concentrate diets were used to simulate the typical range of feeding that buffaloes experience when farmed in Southern China, and the diet nutritional composition is shown in Table 1. The following AOAC methods (AOAC, 1997) were used to determine diet composition: dry

Ruminal fermentation parameters

The rumen fermentation characteristics of the Murrah and Nili-Ravi buffaloes fed the high concentrate (HC) or low concentrate (LC) diets are shown in Table 3. There were no differences observed in rumen pH between buffalo breeds, but the diets showed a significant difference, being approximately 0.2 pH units lower in the HC diet. Ruminal ammonia nitrogen concentrations were significantly different by both diet and buffalo breed (P < 0.05), and were higher in the HC diet and in Nili-Ravi buffalo.

Discussion

The composition of the microbial community in ruminants has previously been linked with animal production traits (Jami et al., 2014; Kittelmann et al., 2014) therefore it is reasonable to expect that comparison of buffalo rumen microbial profiles with those of other bovine species involved in dairy production will help identify the main ruminal microbes that contribute to the buffalo's digestion of forage material. Moreover, it may offer insights into the rumen conditions that select for

Conclusion

In conclusion, the results from this study indicate that the microbial community structure in the rumen of buffaloes consuming diets with different forage:concentrate ratios are similar to other ruminants. The buffalo rumen bacterial communities are dominated by Prevotella, while the archaeal and protozoal communities are dominated by Methanobrevibacter and Entodinium, respectively. Methanomicrobium was not a significant methanogen in the animals sampled and while Dasytricha were detected in

Conflict of interest

None declared.

Acknowledgments

This work was supported by a Livestock Emissions Abatement Research Network (LEARN) Postdoctoral Fellowship award funded by the Ministry of Primary Industries of the New Zealand Government, and the Guangxi Natural Science Foundation (2012GXNSFDA053012 and 2013GXNSFBA019114) of China. We also appreciate the support and advice of the Global Rumen Census, which is funded by the New Zealand Government to support the objectives of the Livestock Research Group of the Global Research Alliance on

References (53)

  • P.J. Weimer et al.

    Host specificity of the ruminal bacterial community in the dairy cow following near-total exchange of ruminal contents

    J. Dairy Sci.

    (2010)
  • D.G. Welkie et al.

    ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle

    Anaerobe

    (2010)
  • C.M. Zhang et al.

    Effect of octadeca carbon fatty acids on microbial fermentation methanogenesis and microbial flora in vitro

    Anim. Feed Sci. Technol.

    (2008)
  • AOAC

    Official Methods of Analysis

    (1997)
  • A.K. Benson et al.

    Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

    Proc. Natl. Acad. Sci.

    (2010)
  • S. Calabrò et al.

    Rumen fermentation and degradability in buffalo and cattle using the in vitro gas production technique

    J. Anim. Physiol. An. N.

    (2008)
  • J.G. Caporaso et al.

    QIIME allows analysis of high-throughput community sequencing data

    Nat. Methods

    (2010)
  • P.P. Chaudhary et al.

    Dominance of Methanomicrobium phylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis)

    Lett. Appl. Microbiol.

    (2009)
  • P.P. Chaudhary et al.

    Methyl coenzyme M reductase (mcrA) gene based phylogenetic analysis of methanogens population in Murrah buffaloes (Bubalus bubalis)

    J. Microbiol.

    (2011)
  • FAO

    FAO Yearbook

    (2007)
  • R. Franzolin

    Feed efficiency a comparison between buffalo and cattle

    Buffalo J.

    (1994)
  • R. Franzolin et al.

    Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets

    Microb. Ecol.

    (2012)
  • S. Foiklang et al.

    Effects of various plant protein sources in high-quality feed block on feed intake, rumen fermentation, and microbial population in swamp buffalo

    Trop. Anim. Health. Pro.

    (2011)
  • Y.B. Gurung et al.

    Rumen ciliate faunae of water buffalo (Bubalus bubalis) and goat (Capra hircus) in Nepal

    J. Vet. Med. Sci.

    (2002)
  • G. Henderson et al.

    Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities

    PLoS ONE

    (2013)
  • S.A. Huws et al.

    Effects of feeding Mediterranean buffalo sorghum silage versus maize silage on the rumen microbiota and milk fatty acid content

    J. Gen. Appl. Microbiol.

    (2012)
  • Cited by (23)

    • Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau

      2017, Systematic and Applied Microbiology
      Citation Excerpt :

      In this present study, the diversity of prokaryotes was significantly lower in TMR groups than in NG groups (Table 2). Lin et al. [44] found a higher Shannon diversity index for bacteria in a low concentrate diet group (forage:concentrate ratio, 3.24:1) than in a high concentrate diet group (1.58:1). Liu et al. [47] discovered significantly higher diversity of a ruminal epithelial bacterial community in goats fed with a hay diet than in those fed with a high-grain diet, indicating that feed composition may influence the diversity index of microorganisms.

    • Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau

      2016, Livestock Science
      Citation Excerpt :

      This study found that Methanobacteriales was the predominant archaea of rumen microbiota in the natural grazing yaks in Sichuan; Huang et al. (2012) found that Methanomassiliicoccales was the dominant methanogens in domesticated yaks in Gansu. Lin et al. (2015) found no obvious correlation between archaeal and bacterial community profiles and Buffalo diet. But Zhou et al. (2009) indicated that methanogen communities differed between cattle herds of different feed efficiency, which may be an important factor causing their difference in CH4 production.

    View all citing articles on Scopus
    View full text