Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Effect of a Co-Feed Liquid Whey-Integrated Diet on Crossbred Pigs' Fecal Microbiota

This study assessed the potential effect of a co-feed liquid whey-integrated diet on the fecal microbiota of 14 crossbred pigs. The experimental design was as follows: seven pigs were in the control group, fed with a control feed, and seven were in the experimental group, fed with the same control feed supplemented daily with liquid whey. The collection of fecal samples was conducted on each animal before the dietary treatment (T0) and one (T1), and two (T2) months after the beginning of the co-feed integration. In addition, blood samples were collected from each pig at the same time points in order to evaluate the physiological parameters. Taxonomic analysis showed a bacterial community dominated by Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria phyla that populated the crossbred pig feces. The diversity metrics suggested that the co-feed supplementation affected some alpha diversity indexes of the fecal microbiota. In addition, the differential abundance analysis at the genus level revealed significant differences for various genera, suggesting that the liquid whey supplementation potentially influenced a part of the bacterial community over time. Spearman's correlations revealed that the differential abundant genera identified are positively or negatively correlated with the physiological parameters.

Limosilactobacillus caccae sp. nov., a new bacterial species isolated from the human gut microbiota

Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95-96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.

Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives

Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.

Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

Anaerococcus marasmi sp. nov., a new bacterium isolated from human gut microbiota

Anaerococcus marasmi sp. nov. strain Marseille-P3557T is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557T was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was Anaerococcus prevotii strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557T as the type strain of Anaerococcus marasmi sp. nov., a new species within the genus Anaerococcus.

Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient

Using the taxono-genomics concept, we describe here a strictly anaerobic Gram-positive bacillus. This strain was isolated from the stool sample of a 50-year-old healthy Bedouin woman. The 16S rRNA gene sequence analysis and the whole-genome sequencing showed that this isolate belonged to the genus Gordonibacter in the family Eggerthellaceae. Based on these criteria, we propose the creation of Gordonibacter massiliensis sp. nov., strain Marseille-P2775T (= CSUR P2775).

Linseed oil and heated linseed grain supplements have different effects on rumen bacterial community structures and fatty acid profiles in cashmere kids1

This study investigated the effects of dietary supplementation with alternative sources of α-linolenic acid on growth, the composition of rumen microbiota, and the interactions between rumen microbiota and long-chain fatty acid (FA) concentrations, in goat kids. Sixty 4-month-old castrated male Albas white cashmere kids (average BW 18.6 ± 0.1 kg) were randomly allocated among three dietary treatments: (i) basal diet without supplementation (Control), (ii) basal diet supplemented with linseed oil (LSO), (iii) basal diet supplemented with heated linseed grain (HLS). The concentrate:forage ratio was 5:5 and the LSO and HLS treatments provided the kids with similar dietary FA profiles. The diets were fed for 104 d, consisting of 14 d for adaptation followed by 90 d of experimental observation. Treatment did not significantly influence BW, DMI, or bacterial richness or diversity. On the other hand, the relative abundance of bacteria participating in hydrogenation differed significantly among the three groups: the Veillonellaceae and Christensenellaceae were more abundant in LSO kids, Prevotellaceae were more abundant in HLS kids, and the Fibrobacteriaceae were more abundant in Control kids (P < 0.05). Spearman correlation analysis indicated that Ruminobacter, Selenomonas_1, Fretibacterium, Prevotellaceae_UCG-001, Succinimonas, and Ruminococcaceae_NK4A214_group were the genera that participated in hydrogenation of long-chain FAs. HLS-fed kids had a lower relative abundance of Ruminobacter, but a higher abundance of Prevotellaceae_UCG-001 and Fretibacterium than LSO-fed kids. These changes were associated with greater rumen concentrations of C18:3n3 and n-3 PUFA, but lower concentrations of n-6 PUFA and lower n-6/n-3 ratios, in HLS than in LSO-fed kids. In conclusion, feeding kids with HLS increased rumen concentrations of C18:3n3 and n-3 PUFA, but decreased the n-6/n-3 ratio by decreasing the abundance of bacteria that hydrogenate C18:3n3 and increasing the abundance of bacteria that hydrogenate C18:2n6.