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FEMS Microbiology Reviews Aug 2005The gut microbiota is a complex ecosystem composed of hundreds of different bacterial species that altogether play an important role in the physiology of their host. In... (Review)
Review
The gut microbiota is a complex ecosystem composed of hundreds of different bacterial species that altogether play an important role in the physiology of their host. In the past few years the complete genome sequence of a number of bacterial strains isolated from the human gastrointestinal tract has been established including that of Bifidobacterium longum NCC2705 isolated from the feces of a healthy infant. Bifidobacteria are among the first species to colonise the human gastrointestinal tract and as such are believed to play an important role in gut homeostasis and normal development. The genome sequence of NCC2705 has revealed a number of features that suggest how this bacterium has adapted to its environment and that could help understanding how it interacts with its host. Here, we review general features of bifidobacteria and illustrate how genome-based approaches can help us better understand the biology of these organisms.
Topics: Animals; Bifidobacterium; DNA, Bacterial; Gastrointestinal Tract; Genome, Bacterial; Humans
PubMed: 15939502
DOI: 10.1016/j.femsre.2005.04.010 -
Bioscience, Biotechnology, and... 2010Bifidobacteria have many beneficial effects for human health. The gastrointestinal tract, where natural colonization of bifidobacteria occurs, is an environment poor in... (Review)
Review
Bifidobacteria have many beneficial effects for human health. The gastrointestinal tract, where natural colonization of bifidobacteria occurs, is an environment poor in nutrition and oxygen. Therefore, bifidobacteria have many unique glycosidases, transporters, and metabolic enzymes for sugar fermentation to utilize diverse carbohydrates that are not absorbed by host humans and animals. They have a unique, effective central fermentative pathway called bifid shunt. Recently, a novel metabolic pathway that utilizes both human milk oligosaccharides and host glycoconjugates was found. The galacto-N-biose/lacto-N-biose I metabolic pathway plays a key role in colonization in the infant gastrointestinal tract. These pathways involve many unique enzymes and proteins. This review focuses on their molecular mechanisms, as revealed by biochemical and crystallographic studies.
Topics: Animals; Bifidobacterium; Carbohydrate Metabolism; Carbohydrate Sequence; Carbohydrates; Extracellular Space; Glycoside Hydrolases; Humans; Metabolic Networks and Pathways; Milk, Human; Molecular Sequence Data
PubMed: 21150123
DOI: 10.1271/bbb.100494 -
Applied and Environmental Microbiology May 2022Antibiotic resistance is a serious medical issue driven by antibiotic misuse. Bifidobacteria may serve as a reservoir for antibiotic resistance genes (ARGs) that have...
Antibiotic resistance is a serious medical issue driven by antibiotic misuse. Bifidobacteria may serve as a reservoir for antibiotic resistance genes (ARGs) that have the potential risk of transfer to pathogens. The erythromycin resistance gene (X) is an ARG with high abundance in bifidobacteria, especially in Bifidobacterium longum species. However, the characteristics of the spread and integration of the gene (X) into the bifidobacteria genome are poorly understood. In this study, 10 W-positive bifidobacterial strains and 1 (X)-positive bifidobacterial strain were used to investigate the transfer of ARGs. Conjugation assays found that the (X) gene could transfer to five other bifidobacterial strains. Dimethyl sulfoxide (DMSO) and vorinostat significantly promoted the transfer of the (X) from strain Bifidobacterium catenulatum subsp. DSM 21854 to Bifidobacterium longum subsp. DSM 20211. Whole-genome sequencing and comparative genomic analysis revealed that the (X) gene was located on the genomic island BKGI1 and that BKGI1 was conjugally mobile and transferable. To our knowledge, this is the first report that a genomic island-mediated gene (X) transfer in bifidobacteria. Additionally, BKGI1 is very unstable in B. catenulatum subsp. DSM 21854 and transconjugant D2TC and is highly excisable and has an intermediate circular formation. analysis showed that the BKGI1 homologs were also present in other bifidobacterial strains and were especially abundant in B. longum strains. Thus, our results confirmed that genomic island BKGI1 was one of the vehicles for (X) spread. These findings suggest that genomic islands play an important role in the dissemination of the gene (X) among species. Bifidobacteria are a very important group of gut microbiota, and the presence of these bacteria has many beneficial effects for the host. Thus, bifidobacteria have attracted growing interest owing to their potential probiotic properties. Bifidobacteria have been widely exploited by the food industry as probiotic microorganisms, and some species have a long history of safe use in food and feed production. However, the presence of antibiotic resistance raises the risk of its application. In this study, we analyzed the transfer of the erythromycin resistance gene (X) and revealed that the molecular mechanism behind the spread of the gene (X) was mediated by genomic island BKGI1. To the best of our knowledge this is the first report to describe the transfer of the gene (X) via genomic islands among bifidobacteria. This may be an important way to disseminate the gene (X) among bifidobacteria.
Topics: Anti-Bacterial Agents; Bifidobacterium; Erythromycin; Genomic Islands
PubMed: 35477272
DOI: 10.1128/aem.00410-22 -
Microbial Genomics Jun 2021Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good...
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of and species. The species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated and .
Topics: Amidohydrolases; Animals; Bifidobacterium; Gastrointestinal Microbiome; Gastrointestinal Tract; Genome, Bacterial; Genomics; Humans; Lactobacillus; Life Style; Mice; Phylogeny; Probiotics; RNA, Ribosomal, 16S
PubMed: 34100697
DOI: 10.1099/mgen.0.000581 -
Gut Microbes 2024Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short-...
Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health. species are important commensals capable of dominating the infant gut microbiome and are known to be less prone to possess antimicrobial resistance genes than other taxa that may colonize infants. We aimed to study the association between -dominated infant gut microbiota and the antibiotic resistant gene load in neonates, and to ascertain the perinatal factors that may contribute to the antibiotic resistance acquisition. Two hundred infant fecal samples at 7 days and 1 month of age from the MAMI birth cohort were included in the study and for whom maternal-neonatal clinical records were available. Microbiota profiling was carried out by 16S rRNA amplicon sequencing, and targeted antibiotic resistance genes (ARGs) including and were quantified by qPCR. Infant microbiota clustered into two distinct groups according to their genus abundance: high and low. The main separation of groups or clusters at each time point was performed with an unsupervised non-linear algorithm of k-means partitioning to cluster data by time points based on genus relative abundance. Microbiota composition differed significantly between both groups, and specific bifidobacterial species were enriched in each cluster. Lower abundance of in the infant gut was associated with a higher load of antibiotic resistance genes. Our results highlight the relevance of genus in the early acquisition and establishment of antibiotic resistance in the gut. Further studies are needed to develop strategies to promote a healthy early colonization and fight against the spread of antibiotic resistances.
Topics: Humans; Bifidobacterium; Infant, Newborn; Gastrointestinal Microbiome; Feces; Anti-Bacterial Agents; Female; RNA, Ribosomal, 16S; Drug Resistance, Bacterial; Male; Infant
PubMed: 38798019
DOI: 10.1080/19490976.2024.2357176 -
Genes Apr 2021has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of is dissimilar... (Comparative Study)
Comparative Study
has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts' dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts' feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts' dietary pattern is the key determinant of the distribution and evolution of GH genes.
Topics: Animals; Base Composition; Bifidobacterium; Dietary Carbohydrates; Gene Expression Regulation, Bacterial; Genome Size; Genome, Bacterial; Glycoside Hydrolases; Host-Pathogen Interactions; Multigene Family; Phylogeny
PubMed: 33924280
DOI: 10.3390/genes12040609 -
Asia Pacific Journal of Clinical... 2006The human intestine is colonized by a large number of microorganisms, collectively termed microbiota, which support a variety of physiological functions. As the major... (Review)
Review
The human intestine is colonized by a large number of microorganisms, collectively termed microbiota, which support a variety of physiological functions. As the major part of the microbiota has not yet been cultured, molecular methods are required to determine microbial composition and the impact of specific dietary components including probiotics. Probiotics are viable microbial food supplements, which have a beneficial impact on human health. Health-promoting properties have been demonstrated for specific probiotic products. The most significant demonstrations for probiotic efficacy include prevention and treatment of antibiotic associated diarrhea, rotavirus diarrhea and allergy prevention. Lactobacillus rhamnosus GG (=ATCC 53103) and Bifidobacterium lactis Bb12 are the among the best-characterized and most studied probiotic strains with demonstrated impact on human health. New complex targets for probiotics include irritable bowel syndrome and Helicobacter pylori infection. For future probiotics the most important target is a demonstrated clinical benefit supported by knowledge on the mechanistic actions in the microbiota of the target population. Molecular and genomics-based knowledge of the composition and functions of the microbiota, as well as deviations from the balanced microbiota, will advance the selection of new and specific probiotics. Potential combinations of specific probiotics may prove to be the next step to reduce the risk on intestinal diseases and reconstruct specific microbial deviations.
Topics: Bifidobacterium; Humans; Intestinal Diseases; Intestines; Lactobacillus; Probiotics
PubMed: 17077076
DOI: No ID Found -
BMC Microbiology Sep 2020Bifidobacteria are important probiotics; some of the beneficial effects of bifidobacteria are achieved by the hydrolysis of glycans in the human gut. However, because...
BACKGROUND
Bifidobacteria are important probiotics; some of the beneficial effects of bifidobacteria are achieved by the hydrolysis of glycans in the human gut. However, because the diet of breastfed infants typically lacks plant-derived glycans, in the gut environment of mothers and their breastfed infants, the mother will intake a variety of plant-derived glycans, such as from onions and bananas, through her diet. Under this assumption, we are interested in whether the same species of bifidobacteria isolated from mother-infant pairs present a distinction in their hydrolysis of plant-derived carbohydrates.
RESULTS
Among the 36 Bifidobacterium strains, bifidobacterial carbohydrate utilization showed two trends related to the intestinal environment where the bacteria lived. Compared with infant-type bifidobacterial strains, adult-type bifidobacterial strains preferred to use plant-derived glycans. Of these strains, 10 isolates, 2 Bifidobacterium pseudocatenulatum (B. pseudocatenulatum), 2 Bifidobacterium pseudolongum (B. pseudolongum), 2 Bifidobacterium bifidum (B. bifidum), 2 Bifidobacterium breve (B. breve), and 2 Bifidobacterium longum (B. longum), were shared between the mother-infant pairs. Moreover, the repetitive sequence-based polymerase chain reaction (rep-PCR) results illustrated that B. pseudolongum and B. bifidum showed genotypic similarities of 95.3 and 98.2%, respectively. Combined with the carbohydrate fermentation study, these results indicated that the adult-type strains have a stronger ability to use plant-derived glycans than infant-type strains. Our work suggests that bifidobacterial carbohydrate metabolism differences resulted in the selective adaptation to the distinct intestinal environment of an adult or breastfed infant.
CONCLUSIONS
The present study revealed that the different gut environments can lead to the differences in the polysaccharide utilization in the same strains of bifidobacterial strains, suggesting a further goal of investigating the exact expression of certain enzymes in response to specific carbon sources.
Topics: Adult; Bifidobacterium; Breast Feeding; Carbohydrate Metabolism; Feces; Gastrointestinal Microbiome; Genotyping Techniques; Humans; Infant; Mothers; Plants; Polysaccharides; Species Specificity
PubMed: 32912151
DOI: 10.1186/s12866-020-01962-w -
Microbiology and Molecular Biology... Sep 2010Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role... (Review)
Review
Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.
Topics: Amino Acyl-tRNA Synthetases; Animals; Bacterial Proteins; Bifidobacterium; Genetic Variation; Genome, Bacterial; Genomics; Humans; RNA, Transfer
PubMed: 20805404
DOI: 10.1128/MMBR.00004-10 -
BMC Microbiology Oct 2013The study of a production chain of raw milk cheeses (St Marcellin, Vercors area, France) led to the isolation of two Bifidobacterium populations: B. crudilactis and B....
BACKGROUND
The study of a production chain of raw milk cheeses (St Marcellin, Vercors area, France) led to the isolation of two Bifidobacterium populations: B. crudilactis and B. mongoliense, that were able to grow along the production chain. The aims of this study were to further detect and characterize these bacteria along the process and evaluate the ability of some strains to survive or grow in adverse conditions.
RESULTS
Using PCR coupled with restriction fragment length polymorphism, B. crudilactis and B. mongoliense were detected in respectively 77% and 30% of St Marcellin cheeses from production chain after 21 days of ripening. They were present in more than half of all analyzed retail cheeses with counts going from 1.6 to 5 log cfu g-1 for B. crudilactis and 1.4 to 7 log cfu g-1 for B. mongoliense. Bifidobacterium mongoliense was sensitive to pH 2, with an observed decrease of at least 3 log for both studied strains (FR49/f/2 and FR41/2) after 1 h incubation. At pH 3, no significant decrease was observed. Good survival was observed for the same strains in presence of pancreatic juice with a decrease of less than one log. Survival of strain FR49/f/2 was better than FR41/2 with a decrease of 3 logarithms (in presence of 1% bile salts) and almost 2 logarithms (in presence of 0.5% bile salts). The genotypic analyses using total DNA-DNA hybridization, GC% content, 16S rRNA gene sequencing and multilocus sequencing analysis (MLSA) confirmed the classification of Bifidobacterium. crudilactis and B. mongoliense into two different clusters well separated from other bifidobacteria clusters.
CONCLUSIONS
According to the observed characteristics such as survival in adverse conditions and their ability to grow under 12 °C during the manufacturing process of the cheeses, which has never been described for bifidobacteria and which is a very interesting technological asset, these B. crudilactis and B. mongoliense strains should be further investigated for a potential use in new food or in food supplements.
Topics: Animals; Bacterial Load; Bifidobacterium; Cheese; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; France; Hydrogen-Ion Concentration; Microbial Viability; Milk; Molecular Sequence Data; Nucleic Acid Hybridization; Phylogeny; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 24164698
DOI: 10.1186/1471-2180-13-239