Immune cells and bugs make a sugary coat: Epithelial cells line the intestinal tract and help to keep the peace between our immune system and our trillions of gut microbes. Such peacekeeping requires glycosylated proteins (proteins with attached carbohydrate chains) present on the epithelial cell surface, but how glycosylation occurs is unclear. Goto et al. find that fucosylation (a type of glycosylation) of gut epithelial cells in mice requires gut microbes (see the Perspective by Hooper). This process also requires innate lymphoid cells there, which produce the cytokines interleukin-22 and lymphotoxin, presumably in response to microbial signals. These cytokines signal epithelial cells to add fucose to membrane proteins, which allows the détente between microbes and immune cells to continue. Science , this issue 10.1126/science.1254009 ; see also p. 1248

The human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16S rDNA libraries and a culture‐based method. Direct counts ranged from 1.9 × 10¹¹ to 4.0 × 10¹¹ cells/g (wet weight), and plate counts totaled 6.6 × 10¹⁰ to 1.2 × 10¹¹ CFU/g (wet weight). Sixty to seventy percent of the bacteria in the human intestinal tract cannot be cultured with currently available methods. The 16S rDNA libraries from three subjects were generated from total community DNA in the intestinal tract with universal primer sets. Randomly selected clones were partially sequenced. All purified colonies detected from the surface of the agar plate were used for a partial sequencing of 16S rDNA. On the basis of sequence similarities, the clones and colonies were classified into several clusters corresponding to the major phylum of the domain Bacteria. Among a total of 744 clones obtained, approximately 25% of them belonged to 31 known species. About 75% of the remaining clones were novel “phylotypes” (at least 98% similarity of clone sequence). The predominant intestinal microbial community consisted of 130 species or phylotypes according to the sequence data in this study. The 16S rDNA libraries and colonies included the Bacteroides group, Streptococcus group, Bifidobacterium group, and Clostridium rRNA clusters IV, IX, XIVa, and XVIII. Moreover, several previously uncharacterized and uncultured microorganisms were recognized in clone libraries and colonies. Our results also showed marked individual differences in the composition of intestinal microbiota.

Microbiota in gut contents of jejunum, ileum, caecum and recto-sigmoid colon obtained from three elderly individuals at autopsy were compared using 16S rRNA gene libraries and terminal restriction fragment length polymorphism (T-RFLP). Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets of total genomic DNA extracted from each sample of gut contents. An average of 90 randomly selected clones were partially sequenced (about 500 bp). T-RFLP analysis was performed using the 16S rRNA gene amplified from each sample. The lengths of the terminal restriction fragments were analysed after digestion with HhaI and MspI. The jejunal and ileal microbiota consisted of simple microbial communities of streptococci, lactobacilli, ‘Gammaproteobacteria', the Enterococcus group and the Bacteroides group. Most of the species were facultative anaerobes or aerobes. The Clostridium coccoides group and the Clostridium leptum subgroup, which are the most predominant groups in human faeces, were not detected in samples from the upper gastrointestinal tract. The caecal microbiota was more complex than the jejunal and ileal microbiota. The C. coccoides group, the C. leptum subgroup and the Bacteroides group were detected in the caecum. The recto-sigmoidal colonic microbiota consisted of complex microbial communities, with numerous species that belonged to the C. coccoides group, the C. leptum subgroup, the Bacteroides group, ‘Gammaproteobacteria', the Bifidobacterium group, streptococci and lactobacilli, and included more than 26 operational taxonomic units. The results showed marked individual differences in the composition of microbiota in each region.

Nine strains capable of metabolizing isoflavones to equol were isolated from human faeces. Four of the strains were characterized by determining phenotypic and biochemical features and their phylogenetic position based on 16S rRNA gene sequence analysis. These strains were related to Eggerthella sinensis HKU14^T with about 93 % 16S rRNA gene sequence similarity; they were asaccharolytic, obligately anaerobic, non-spore-forming, non-motile and Gram-positive coccobacilli. In enzyme activity tests, arginine dihydrolase, arginine and leucine arylamidases were positive but nitrate reduction, urease and β-glucosidase were negative. The major menaquinone was DMMK-6 (dimethylmenaquinone-6), while that of members of the genus Eggerthella was MMK-6 (methylmenaquinone-6). Furthermore, the cell-wall peptidoglycan type of these strains was A1γ, while that of members of the genus Eggerthella was A4γ. On the basis of these data, a new genus, Adlercreutzia gen. nov., is proposed with one species, Adlercreutzia equolifaciens sp. nov. The type strain of Adlercreutzia equolifaciens is FJC-B9^T (=JCM 14793^T =DSM 19450^T =CCUG 54925^T).

The characteristics of threeBacteroidesspecies,Bacteroides distasonis,Bacteroides goldsteiniiandBacteroides merdae, were examined. 16S rRNA gene sequence analysis showed thatB. distasonis,B. goldsteiniiandB. merdaeshould not be classified as species within the genusBacteroides. AlthoughB. distasonis,B. goldsteiniiandB. merdaewere phylogenetically related toTannerella forsythensis, the ratios of anteiso-C_15 : 0to iso-C_15 : 0in whole-cell methanolysates of the three species were different from that ofT. forsythensis. In addition, whereas the major menaquinones ofT. forsythensiswere MK-10 and MK-11, the major menaquinones ofB. distasonis,B. goldsteiniiandB. merdaewere MK-9 and MK-10. The three species were phenotypically similar toBacteroides sensu stricto, but phylogenetically distinct. Furthermore,B. distasonis,B. goldsteiniiandB. merdaecould be differentiated fromBacteroides sensu stricto(predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus,Parabacteroidesgen. nov., is proposed forB. distasonis,B. goldsteiniiandB. merdae, with three species,Parabacteroides distasonisgen. nov., comb. nov. (the type species),Parabacteroides goldsteiniicomb. nov. andParabacteroides merdaecomb. nov. The type strains ofP. distasonis,P. goldsteiniiandP. merdaeare JCM 5825^T(=CCUG 4941^T=DSM 20701^T=ATCC 8503^T), JCM 13446^T(=CCUG 48944^T) and JCM 9497^T(=CCUG 38734^T=ATCC 43184^T), respectively.

A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7H^T, grew at 20–45 °C (optimum 35–40 °C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain LIND7H^T used cellobiose, glucose, lactose, mannose, maltose, peptone, rhamnose, raffinose, sucrose and xylose as electron donors. The main fermentation products from glucose metabolism were lactate, acetate, butyrate and isobutyrate. The predominant cellular fatty acids were anteiso-C_15 : 0, C_15 : 0, C_17 : 0 2-OH and a summed feature consisting of C_18 : 2ω6,9c and/or anteiso-C_18 : 0, and the major menaquinones were MK-9, MK-9(H₂) and MK-10. The G+C content of the genomic DNA was 41.4 mol%. Although the closest phylogenetic relatives of strain LIND7H^T were Parabacteroides merdae , Parabacteroides goldsteinii and Parabacteroides gordonii , analysis of the hsp60 gene sequence showed that strain LIND7H^T was not a member of the genus Parabacteroides . On the basis of phylogenetic inference and phenotypic properties, strain LIND7H^T ( = CCUG 60892^T = DSM 23697^T = JCM 16313^T) is proposed as the type strain of a novel species in a new genus within the family Porphyromonadaceae , Macellibacteroides fermentans gen. nov., sp. nov.