Can rumen bacteria communicate to each other?

Abstract

Background: The rumen contains a myriad of microbes whose primary role is to degrade and ferment dietary nutrients, which then provide the host with energy and nutrients. Rumen microbes commonly attach to ingested plant materials and form biofilms for effective plant degradation. Quorum sensing (QS) is a well-recognised form of bacterial communication in most biofilm communities, with homoserine lactone (AHL)-based QS commonly being used by Gram-negative bacteria alone and AI-2 Lux-based QS communication being used to communicate across Gram-negative and Gram-positive bacteria. However, bacterial cell to cell communication in the rumen is poorly understood. In this study, rumen bacterial genomes from the Hungate collection and Genbank were prospected for QS-related genes. To check that the discovered QS genes are actually expressed in the rumen, we investigated expression levels in rumen metatranscriptome datasets.

Results: A total of 448 rumen bacterial genomes from the Hungate collection and Genbank, comprised of 311 Gram-positive, 136 Gram-negative and 1 Gram stain variable bacterium, were analysed. Abundance and distribution of AHL and AI-2 signalling genes showed that only one species (Citrobacter sp. NLAE-zl-C269) of a Gram-negative bacteria appeared to possess an AHL synthase gene, while the Lux-based genes (AI-2 QS) were identified in both Gram-positive and Gram-positive bacteria (191 genomes representing 38.2% of total genomes). Of these 192 genomes, 139 are from Gram-positive bactreetteria and 53 from Gram-negative bacteria. We also found that the genera Butyrivibrio, Prevotella, Ruminococcus and Pseudobutyrivibrio, which are well known as the most abundant bacterial genera in the rumen, possessed the most lux-based AI-2 QS genes. Gene expression levels within the metatranscriptome dataset showed that Prevotella, in particular, expressed high levels of LuxS synthase suggesting that this genus plays an important role in QS within the rumen.

Conclusion: This is the most comprehensive study of QS in the rumen microbiome to date. This study shows that AI-2-based QS is rife in the rumen. These results allow a greater understanding on plant-microbe interactions in the rumen.

Keywords: AI-2; Acyl-homoserine lactone; Bacteria; LuxS; Quorum sensing; Rumen.

Fig. 1

Percentage occurrence of putative AI-2 LuxS-based quorum sensing proteins in the genomes of Gram-positive and Gram-negative rumen bacteria [13]. a Proportional representation of LuxS and LuxR in the genomes of the Gram-positive and Gram-negative genomes. b Proportional representation of LuxS in the genomes of the Gram-positive and Gram-negative genomes. c Proportional representation of LuxR in the genomes of the Gram-positive and Gram-negative genomes. Numbers in brackets show total number of bacterial genomes in which the corresponding gene was found

Fig. 2

Distribution and abundance of LuxS proteins relating to AI-2-based quorum sensing across 448 rumen bacterial genomes [13]

Fig. 3

Comparative phylogenetic tree of all putative LuxS proteins detected within the genomes of 171 rumen bacterial species. Two standards (Vibrio harveyi and Streptococcus pneumoniae) were used for comparison with other samples (highlighted with grey colour). Most abundant four groups were highlighted with colours (orange: Pseudobutyrivibrio, yellow: Prevotella, green: Butyrivibrio and blue: Ruminococcus). Sequences denoted by a square and beginning with MG are those identified by Ghali et al. [9] from rumen metagenomic sequences and those with MT also being derived from the same study using a metatranscriptome dataset

Fig. 4

Average expression of LuxS genes identified in the bacterial genomes within rumen bacterial metatranscriptome datasets [16]. Expression is shown as reads per kilobase of transcript per million (RKPM). Where RKPM was < 0.1, the expression data was grouped as “other”. Other essentially contained the expression of the LuxS synthase genes discovered within Lachnobacterium bovis DSM, Ruminococcus gnavus AGR2154, Actinobacillus succinogenes 130Z, Streptococcus sp. NLAE-zl-C503, Butyrivibrio sp. AD3002, Butyrivibrio sp. INlla18, Pseudobutyrivibrio ruminis DSM, Bifidobacterium bifidum Calf96, Butyrivibrio sp. TB, Butyrivibrio sp. WCD2001, Succinimonas_amylolytica DSM 2873, Pseudobutyrivibrio sp. JW11, Ruminococcus flavefaciens 17, Pseudobutyrivibrio sp. LB2011, Ruminococcus albus SY3, Pseudobutyrivibrio sp. MD2005, Butyrivibrio sp. NC3005, Clostridium mangenotii LM2, Cellulomonas sp. KH9, Clostridium aerotolerans DSM, Butyrivibrio fibrisolvens YRB2005, Butyrivibrio fibrisolvens MD2001, Kandleria vitulina WCE2011 and Butyrivibrio sp. YAB300