Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota

Abstract

A strictly anaerobic, cellulolytic strain, designated 18P13 T , was isolated from a human faecal sample. Cells were Gram-positive non-motile cocci. Strain 18P13 T was able to degrade microcrystalline cellulose but the utilization of soluble sugars was restricted to cellobiose. Acetate and succinate were the major end products of cellulose and cellobiose fermentation. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Ruminococcus of the family Ruminococcaceae. The closest phylogenetic relative was the ruminal cellulolytic strain Ruminococcus flavefaciens ATCC 19208 T (,95 % 16S rRNA gene sequence similarity). The DNA G+C content of strain 18P13 T was 53.05±0.7 mol%. On the basis of phylogenetic analysis, and morphological and physiological data, strain 18P13 T can be differentiated from other members of the genus Ruminococcus with validly published names. The name Ruminococcus champanellensis sp. nov. is proposed, with 18P13 T (5DSM 18848 T 5JCM 17042 T ) as the type strain.The human large intestine harbours a large diversity of bacterial communities that play a key role in health and disease through their involvement in nutrition, pathogenesis and immunology (Cummings & Macfarlane, 1991;Salminen et al., 1998). A proper understanding of the diversity and functionality of species in the human gut ecosystem is therefore of considerable importance. Over the past 20 years, the microbiota composition has been investigated using both culture-and molecular-based methods and results have revealed the extensive diversity of this ecosystem (Eckburg et al., 2005;Chassard et al., 2008b;Qin et al., 2010). The microbiota is mainly composed of bacteria belonging to three major phyla: 'Bacteroidetes', 'Firmicutes' and 'Actinobacteria'. The genus Ruminococcus represents an important phylogenetic taxon, belonging to phylum 'Firmicutes', and corresponds to 5-15 % of the total bacterial population in the colon (Chassard et al., 2008b; Ramirez-Farias et al., 2009).Presently, the genus Ruminococcus is not monophyletic and is divided into two phylogenetically separate groups.Group I is located within rRNA cluster IV and includes Ruminococcus flavefaciens, the type species of the genus. In the latest edition of Bergey's Manual of Systematic Bacteriology, members of group I were included in the family Ruminococcaceae and should be considered as Ruminococcus sensu stricto (Rainey, 2009a). Members of group II are located within rRNA cluster XIVa, which is now recognized as the family Lachnospiraceae, a large group of phenotypic and phylogenetic heterogeneous genera (Rainey, 2009b). Recently, a number of misclassified Ruminococcus species and a Clostridium species in group II were reclassified in the genus Blautia (Liu et al., 2008). The remaining ruminococci within group II most likely constitute the nuclei of novel genera and should not be considered true ruminococci.The genus Ruminococcus comprises anaerobic Grampositive cocci with a fermentative metabolism for which carbohydrates, but not amino acids, serve...

Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association

“…the Ruminococcus species within the Lachnospiraceae ) to avoid confusion in the literature. The topology of our phylogenetic analyses also matches partial phylogenetic analyses performed for recently described species (Chassard et al , 2012; Wegmann et al , 2014) and offers some insights. For example, R. bromii appears less related to all other true ruminococci, as determined in our pairwise 16S rRNA similarity comparisons (88–89 % 16S identity; Table S8).…”

“…Some species are cellulolytic, including the rumen isolates R. flavefaciens and Ruminococcus albus (Hungate, 1957), and the recently described human isolate Ruminococcus champanellensis (Chassard et al , 2012), which is the only known bacterial species isolated from the human colon capable of degrading crystalline cellulose (Moraïs et al , 2016). Others are non-cellulolytic and utilize polysaccharides like resistant starches in the case of R. bromii (Ze et al , 2012), or selectively use various plant hemicelluloses in the case of Ruminococcus callidus (Lay et al , 2005) and ‘ Ruminococcus bicirculans ’ (Wegmann et al , 2014).…”

Biogas production from wheat straw: community structure of cellulose-degrading bacteria

“…The T-RF 168 bp (OTU04) was only observed in the digester operating at 44°C (R 44 SS). This clone was most closely related to Ruminococcus champanellensis (61.8% identity), a cellulolytic bacterium isolated from human faeces that ferments cellulose, cellobiose and xylan, produces acetate and succinate as the main fermentation products and grows optimally from 33°C to 39°C (optimum 39°C) [41]. In a previous study, the abundance of Ruminococcus in a biogas digester was shown to increase after pre-treatment of sludge from a wastewater plant [32].…”

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

“…There are strong indications, however, that this family has a primary role in the degradation of particulate substrates, as it includes cellulolytic species, such as R. flavefaciens and R. albus, described from the rumen (Stewart et al, 1997;Flint et al, 2008), and R. champanellensis isolated from the human large intestine (Chassard et al, 2011). The breakdown of plant fiber in the rumen is dependent on such cellulolytic microorganisms, with many other species utilizing the solubilized products (Dehority, 1991).…”