Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken

LAYING RATE WAS CORRELATED WITH MICROBIAL Fecal microbiota transplantation improves the laying performance by changing the gut microbiota composition in late laying period

This research investigated the differences and succession patterns of microbes in different ages, the performance of laying hens, and the effect of Fecal Microbiota Transplantation (FMT) on aged laying hens. First, based on the different laying rates and age, we divided the laying hens into four groups: 75-week-old high-yield (OH, laying rate (LR) > 90%), 75-week-old low-yield (OL, LR < 60%), 75-week-old non-laying hens (OZ, LR = 0%) and 35-week-old high-yield (YH, LR > 90%) with 5 replicates in each group and 6 chickens in each replicate. The microbial metabolic patterns between different ages and laying rates were determined using 16S rDNA technology. Then, to verify the results of microbiome research, we utilized FMT technology to transplant the gut microbiota from OH to OZ (OZFMT-OH), thereby revealing the connection between gut microbes and production performance. The results showed that high-yielding hens (YH and OH groups) had higher levels of Superoxide dismutase (SOD) and Immunoglobulin A (IgA) compared to OL and OZ groups. The Villus height to Crypt depth ratio(V/C) was significantly higher in the YH group than in 75-week-old hens (P < 0.05). Alpha diversity indicated higher microbial diversity in the YH group compared to older hens (P < 0.05), with YH hens harboring more Megamonas, OH hens more Bacteroides, and OL and OZ groups showing higher levels of harmful bacteria. The villus height, V/C, mucosal layer thickness, cup cell number acetic acid level, and LR in the OZFMT-OH group were significantly higher than those in the OZ group (P < 0.05), while the IL-2 level, crypt depth and cecal intestinal wall thickness were significantly lower than those in OZ group (P < 0.05). FMT also changed the morphological structure of grade follicles and small yellow follicles, improved the microbe composition of cecum and increased Bacteroides abundance. In the late laying period, if the intestinal flora cannot maintain the dynamic balance and carry out timely replacement, the production performance may be decreased, and the increase of Bacteroides abundance in the intestinal tract can improve the intestinal health and production performance of laying hens in the late laying period.

Bacteroides rhinocerotis sp. nov., isolated from the fresh feces of rhinoceros in Beijing Zoo

A Gram-negative strain, anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain named as NGMCC 1.200684 ^T was isolated from the fresh feces of rhinoceros in Beijing Zoo. Based on 16S rRNA gene sequences, phylogenetic analysis indicated that strain NGMCC 1.200684 ^T belonged to the genus Bacteroides and was most strongly related to the type strain of Bacteroides uniformis ATCC 8492 ^T (96.88%). The G + C content of the genomic DNA was determined to be 46.62%. Between strains NGMCC 1.200684 ^T and B. uniformis ATCC 8492 ^T, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 93.89 and 67.60%, respectively. Strain NGMCC 1.200684 ^T can produce acid from fermentation of several substrates, including glucose, mannitol, lactose, saccharose, maltose, salicin, xylose, cellobiose, mannose, raffinose, sorbitol, trehalose, D-galactose, and maltotriose. The major cellular fatty acids (> 10%) were identified as anteiso-C_15:0, iso-C_15:0, iso-C_14:0, and iso-C_17:0 3-OH. The polar lipid profiles of strain NGMCC 1.200684 ^T were determined to contain diphosphatidyl glycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, and two unknown amino-phospholipids. Based on phenotypic, phylogenetic, and chemotaxonomic characteristics, a novel species of the genus Bacteroides, Bacteroides rhinocerotis sp. nov. is proposed. The type strain is NGMCC 1.200684 ^T (= CGMCC 1.18013 ^T = JCM 35702 ^T).

Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma

A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104^T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C_15 : 0 and C_15 : 0 as the major fatty acids. The genome size of strain 14-104^T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929^T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104^T and P. abscessus CCUG 55929^T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104^T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104^T (=BCRC 81305^T= NBRC 115041^T).

Comparison of different small molecular weight alcohols for sustaining sulfidogenic bioreactors maintained at moderately low pH

Sulfate-reducing bacteria (SRB) catalyse the dissimilatory reduction of sulfate to hydrogen sulfide using a wide range of small molecular weight organic compounds, and hydrogen, as electron donors. Here we report the effects of different combinations of small molecular weight alcohols on the performance and bacterial composition of a moderately low pH sulfidogenic bioreactor (pH 4.0–5.5) operated at 35°C in continuous flow mode. Ethanol alone and methanol or ethanol used in combination with glycerol were evaluated based on their equivalent amounts of carbon. Although evidenced that methanol was utilised as electron donor to fuel sulfidogenesis at pH 5.5, rates of sulfate reduction/sulfide production were negatively impacted when this alcohol was first introduced to the system, though these rates increased in subsequent phases as a result of adaptation of the microbial community. Further increased dosage of methanol again caused rates of sulfidogenesis to decrease. Methanol addition resulted in perturbations of the bioreactor microbial community, and species not previously detected were present in relatively large abundance, including the sulfate-reducer Desulfovibrio desulfuricans. Ethanol utilization was evidenced by the increase in rates of sulfidogenesis as the dosage of ethanol increased, with rates being highest when the bioreactor was fed with ethanol alone. Concentrations of acetate in the effluent liquor also increased (up to 8 mM) as a result of incomplete oxidation of ethanol. This alcohol continued to be used as the electron donor for sulfate reduction when the bioreactor pH was decreased incrementally (to pH 4.0), but rates of sulfidogenesis decreased. The relative abundance of Dv. desulfuricans diminished as the bioreactor pH was lowered, while that of the acidophilic Firmicute Desulfosporosinus acididurans increased. This study has shown that all three alcohols can be used to fuel microbial sulfidogenesis in moderately acidic liquors, though the cost-effectiveness, availability and toxicity to the microbial community will dictate the choice of substrate.

An Outdoor Access Period Improves Chicken Cecal Microbiota and Potentially Increases Micronutrient Biosynthesis

Characterizing the gut microbiota of free-range and alternative poultry production systems provides information, which can be used to improve poultry welfare, performance, and environmental sustainability. Gut microbiota influence not only the health and metabolism of the host but also the presence of zoonotic agents contaminating food of animal origin. In this study, the composition and diversity of the cecal microbiota community of free-range grown chickens were characterized by 16S rDNA high-throughput Illumina sequencing. Significant differences were observed in the composition of chicken cecal microbiota at the time points of 28 days of age (Indoor group) and 56 days of age (Outdoor group), i.e., before and after the outdoor access period of chicken groups. The Outdoor group showed a richer and more complex microbial community, characterized by the onset of new phyla such as Deferribacterota and Synergistota, while the Indoor group showed an increase in Campylobacterota. At the species level, it is noteworthy that the occurrence of Mucispirillum schaedleri in Outdoor group is known to potentially stimulate mucus layer formation in the distal intestinal tract, thus being associated with a healthy gut. We also report a significant decrease in the Outdoor group of Helicobacter pullorum, highlighting that the lower abundance at the age of slaughter reduced the possibility to contaminate chickens' carcasses and, consequently, its zoonotic potential. As revealed by a mutual exclusion study in network analysis, H. pullorum was present only if Bacteroides barnesiae, an uncultured organism of the genus Synergistes, and Bacteroides gallinaceum were absent. Finally, microbiome predictive analysis revealed an increase of vitamins and micronutrient biosyntheses such as queuosine (Q) and its precursor pre Q0, in the Outdoor group, suggesting that the outdoor evolved microbiota of chickens do contribute to the vitamin pool of the gut and the biosynthesis of micronutrients involved in vital cell processes.

Effects of Compound Probiotics on Cecal Microbiome and Metabolome of Shaoxing Duck

This experiment was conducted to investigate the effects of compound probiotics on intestinal microflora and metabolome of Shaoxing ducks. A total of 640 1-day-old Shaoxing ducks were randomly divided into two treatments with eight replicates and forty ducks for each replicate. The ducks were fed basal diet (Ctrl) and basal diet supplemented with 0.15% compound probiotics (MixP). The experiment lasted for 85 days. The results showed that the abundance of Bacteroidetes and Bacteroides in MixP was higher than that in Ctrl (P < 0.05). However, the abundance of Firmicutes and Oscillospira and Desulfovibrio in MixP was lower than that in Ctrl (P < 0.05). Concentrations of 71 metabolites differed significantly (P < 0.05) between the MixP and the Ctrl groups; for example, Pyridoxal (Vitamin B6), L-Arginine, and Betaine aldehyde were up-regulated (P < 0.05), and 7-oxocholesterol, 3-hydroxy-L-kynureni-ne, and N-acetyl-d-glucosamine were down-regulated (P < 0.05). KEGG was enriched in 15 metabolic pathways. The pathways of Vitamin B6 metabolism, Vascular smooth muscle contraction, Vitamin digestion and absorption, and Protein digestion and absorption were influenced by compound probiotics supplementation. Thus, supplementation of compound probiotics improved cecal heath through shifts in the cecal microbiome and metabolome.

Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure

Isolating relevant microorganisms is still a substantial challenge that limits the use of bacteria in the maintenance of human health. To confirm which media and which bacterial colony densities can enrich certain kinds of bacteria, we selected eight common media and used them to enrich the gut microorganisms on agar plates. Then, we calculated the numbers of bacterial colonies and collected the bacterial culture mixtures from each kind of medium. Using the Illumina HiSeq platform, we analyzed the composition and diversity of the culture-enriched gut bacterial community. Our data suggested that medium supplemented with blood could increase the diversity of the bacterial community. In addition, beef powder and peptone could significantly change the culture-enriched bacterial community. A moderate density (100-150 colony-forming units per plate) was optimal for obtaining the highest diversity on the agar. Similarly, membrane transport was significantly enriched in the moderate-density group, which indicated a more active metabolism in this density range. Overall, these results reveal the optimal culture conditions, including the densities of colonies and nutritional components for various gut bacteria, that provide a novel strategy for isolating bacteria in a way that is targeted and avoids blinded and repetitive work.

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.

Roles of intestinal bacteroides in human health and diseases

Bacteroides, an abundant genus in the intestines of mammals, has been recently considered as the next generation probiotics (NGP) candidate due to its potential role in promoting host health. However, the role of Bacteroides in the development of intestinal dysfunctions such as diarrhea, inflammatory bowel disease, and colorectal cancer should not be overlooked. In the present study, we focused on nine most widely occurred and abundant Bacteroides species and discussed their roles in host immunity, glucose and lipid metabolism and the prevention or induction of diseases. Besides, we also discussed the current methods used in the safety evaluation of Bacteroides species and key opinions about the concerns of these strains for the future use.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Fermented Momordica charantia L. juice modulates hyperglycemia, lipid profile, and gut microbiota in type 2 diabetic rats

The effect of Lactobacillus plantarum-fermentation on the anti-diabetic functionality of Momordica charantia was examined using a high-fat-diet and low-dose streptozocin-induced type 2 diabetic rat model. Fermented Momordica charantia juice (FMCJ) administration mitigated the hyperglycemia, hyperinsulinemia, hyperlipidemia, and oxidative stress in diabetic rats more favorably than the non-fermented counterpart. Treatments with FMCJ improved ergosterols and lysomonomethyl-phosphatidylethanolamines metabolisms more effectively. Supplement of FMCJ regulated the composition of the gut microbiota, such as increased the abundance of Bacteroides caecigallinarum, Oscillibacter ruminantium, Bacteroides thetaiotaomicron, Prevotella loescheii, Prevotella oralis, and Prevotella melaninogenica, in diabetic rats compared with untreated diabetic rats. Moreover, FMCJ-treated diabetic rats exhibited higher concentrations of acetic acid, propionic acid, butyric acid, total short-chain fatty acids and lower pH values in colonic contents than that in non-fermented juice-treated rats. These results demonstrated that Lactobacillus plantarum-fermentation enhanced the anti-diabetic property of MC juice by favoring the regulation of gut microbiota and the production of SCFAs.

Polysaccharide from fermented Momordica charantia L. with Lactobacillus plantarum NCU116 ameliorates type 2 diabetes in rats

The influence of Lactobacillus plantarum-fermentation on the structure and anti-diabetic effects of Momordica charantia polysaccharides were evaluated. High-fat diet and streptozotocin-induced type 2 diabetic rats were administrated with polysaccharides from fermented and non-fermented Momordica charantia (FP and NFP) for 4 weeks. Fermentation affected the physicochemical characterization, monosaccharide composition, molecular weight, and viscosity of Momordica charantia polysaccharides. Treatment with FP significantly ameliorated hyperglycemia, hyperinsulinemia, hyperlipidemia, and oxidative stress in diabetic rats compared with NFP. Moreover, the diversity and abundance of gut microbiota (Lactococcus laudensis and Prevotella loescheii) in diabetic rats were notably increased by treatment with FP in comparison to NFP. Meanwhile, FP-treated diabetic rats exhibited more colonic short-chain fatty acids (SCFAs) and lower pH values than that in NFP-treated rats. Overall, Lactobacillus plantarum-fermentation could enhance the anti-diabetes effects of Momordica charantia polysaccharides in rats by modifying the structure of polysaccharides to optimize gut microbiota and heighten the production of SCFAs.