Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus

Structure of Extracellular Vesicles and Their Effect on Bacterial Biofilms Change with the Development of Antibiotic Resistance in the Probiotic Strain Lactiplantibacillus plantarum 8p-a3

Significant changes in lactobacillus-derived extracellular membrane vesicles, which transfer lipids, polysaccharides, proteins, and nucleic acids, were for the first time observed to accompany the development of resistance to antibiotics (amoxicillin and clarithromycin) in vitro in the probiotic strain Lactiplantibacillus plantarum 8p-a3. The changes occur together with large-scale genome rearrangements, changes in the profile of phenotypic sensitivity to antimicrobials of various groups, and evolution of virulence. Changes in vesicles affected their structure, composition, and activity against biofilms of opportunistic bacteria. The data provide for a better understanding of the molecular mechanisms of microbial survival under selective pressure of antimicrobials, the functional potential of probiotic vesicles, and probiotic safety assessments.

Genomic Characterization and Safety Assessment of Bifidobacterium breve BS2-PB3 as Functional Food

Our group had isolated Bifidobacterium breve strain BS2-PB3 from human breast milk. In this study, we sequenced the whole genome of B. breve BS2-PB3, and with a focus on its safety profile, various probiotic characteristics (presence of antibiotic resistance genes, virulence factors, and mobile elements) were then determined through bioinformatic analyses. The antibiotic resistance profile of B. breve BS2-PB3 was also evaluated. The whole genome of B. breve BS2-PB3 consisted of 2,268,931 base pairs with a G-C content of 58.89% and 2,108 coding regions. The average nucleotide identity and whole-genome phylogenetic analyses supported the classification of B. breve BS2-PB3. According to our in silico assessment, B. breve BS2-PB3 possesses antioxidant and immunomodulation properties in addition to various genes related to the probiotic properties of heat, cold, and acid stress, bile tolerance, and adhesion. Antibiotic susceptibility was evaluated using the Kirby-Bauer disk-diffusion test, in which the minimum inhibitory concentrations for selected antibiotics were subsequently tested using the Epsilometer test. B. breve BS2-PB3 only exhibited selected resistance phenotypes, i.e., to mupirocin (minimum inhibitory concentration/MIC >1,024 μg/ml), sulfamethoxazole (MIC >1,024 μg/ml), and oxacillin (MIC >3 μg/ml). The resistance genes against those antibiotics, i.e., ileS, mupB, sul4, mecC and ramA, were detected within its genome as well. While no virulence factor was detected, four insertion sequences were identified within the genome but were located away from the identified antibiotic resistance genes. In conclusion, B. breve BS2-PB3 demonstrated a sufficient safety profile, making it a promising candidate for further development as a potential functional food.

Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota

The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.

A Mendelian Randomization Study: Roles of Gut Microbiota in Sepsis - Who is the Angle?

Gut microbiota (GM) is a crucial underlying player during sepsis pathogenesis. However, the causal relationship is unclear and remains to be determined. A two-sample Mendelian randomization study was implemented. The statistical data about sepsis together with GM summarized from genome-wide association studies were evaluated. Instrumental variables were defined as single-nucleotide polymorphisms with prominent correlations with exposure. The inverse-variance-weighted test was employed as a major approach of Mendelian randomization analysis to estimate of causal relationships. The inverse-variance-weighted analysis results demonstrated that at different taxa levels, Actinobacteria and Bifidobacteriaceae influence sepsis. Actinobacteria had negative relationships to sepsis risk at the phylum (β = -0.34, SE = 0.10, p = 0.0008) and class (β = -0.23, SE = 0.07, p = 0.0011) levels in outcome coded ieu-b-69. Actinobacteria at the phylum level (β = -0.22, SE = 0.10, p = 0.027) was also negatively associated with sepsis in outcome coded ieu-b-4980. Bifidobacteriaceae at the order (β = -0.20, SE = 0.06, p = 0.0021), family (β = -0.20, SE = 0.06, p = 0.0021), and genus (β = -0.20, SE = 0.06, p = 0.0007) levels were all negatively correlated with the risk of sepsis in outcome coded ieu-b-69. The results of the Wald ratio model showed that Tyzzerella genus (OR (95%CI) = 0.6902[0.4907,0.9708], p = 0.0331) and Gastranaerophilales order (OR (95%CI) = 0.5907[0.3516,0.9926], p = 0.0468) were negatively connected with sepsis. This study implied at different taxa levels Actinobacteria and Bifidobacteriaceae, Tyzzerella genus, and Gastranaerophilales order have a causal relationship with sepsis, indicating that they are protective factors for the incidence of sepsis.

Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China

Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.

Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments

BACKGROUND

Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent.

METHODS

We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis.

FINDINGS

The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes.

INTERPRETATION

Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.

FUNDING

Odd-Berg Group, Northern Norway Regional Health Authority.

Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence

Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the "Lactobacterin" probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.

Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome

Background

Different feeding regimens in infancy alter the gastrointestinal (gut) microbial environment. The fecal microbiota in turn influences gastrointestinal homeostasis including metabolism, immune function, and extra-/intra-intestinal signaling. Advances in next generation sequencing (NGS) have enhanced our ability to study the gut microbiome of breast-fed (BF) and formula-fed (FF) infants with a data-driven hypothesis approach.

Methods

Next generation sequencing libraries were constructed from fecal samples of BF (n=24) and FF (n=10) infants and sequenced on an Illumina HiSeq 2500. Taxonomic classification of the NGS data was performed using the Sunbeam/Kraken pipeline and a functional analysis at the gene level was performed using publicly available algorithms, including BLAST, and custom scripts. Differentially represented genera, genes, and NCBI Clusters of Orthologous Genes (COG) were determined between cohorts using count data and R (statistical packages edgeR and DESeq2).

Results

Thirty-nine genera were found to be differentially represented between the BF and FF cohorts (FDR ≤ 0.01) including Parabacteroides, Enterococcus, Haemophilus, Gardnerella, and Staphylococcus. A Welch t-test of the Shannon diversity index for BF and FF samples approached significance (p=0.061). Bray-Curtis and Jaccard distance analyses demonstrated clustering and overlap in each analysis. Sixty COGs were significantly overrepresented and those most significantly represented in BF vs. FF samples showed dichotomy of categories representing gene functions. Over 1,700 genes were found to be differentially represented (abundance) between the BF and FF cohorts.

Conclusions

Fecal samples analyzed from BF and FF infants demonstrated differences in microbiota genera. The BF cohort includes greater presence of beneficial genus Bifidobacterium. Several genes were identified as present at different abundances between cohorts indicating differences in functional pathways such as cellular defense mechanisms and carbohydrate metabolism influenced by feeding. Confirmation of gene level NGS data via PCR and electrophoresis analysis revealed distinct differences in gene abundances associated with important biologic pathways.

Comparative effects of environmental factors on bacterial communities in two types of indoor dust: Potential risks to university students

University students are constantly exposed to potential bacterial pathogens and environmental pollutants in indoor environment because they spend most of their time indoors. University dormitory and printing shop are two typical indoor environments frequented by university students. However, little is known about the characteristics of bacterial community as well as the effect of indoor environmental factors on them. 16S rRNA gene sequencing was used to reveal the bacterial community in indoor dust, electronic devices were recorded during dust sampling, and polybrominated diphenyl ethers (PBDEs) were detected by gas chromatography mass spectrometry (GC-MS). Proteobacteria, Actinobacteria and Firmicutes were leading phyla, and Acinetobacter, Paracoccus and Kocuria were dominating genera. The predominant genera showed Acinetobacter > Paracoccus > unidentified Corynebacteriaceae in indoor dusts from university dormitories, whereas Paracoccus > unidentified Cyanobacteria > Acinetobacter in printing shops. The occurrence of Acinetobacter, Kocuria, Corynebacterium, Pseudomonas, and Bacillus suggested the health risks of potential pathogenic bacteria to university students. Significant differences of microbial composition and diversity were proved between university dormitories and printing shops. Chemoheterotrophy and aerobic chemoheterotrophy were dominant bacterial functions, and the seven primary bacterial functions displayed university dormitory > printing shop. BDE 138 and BDE 66 were main environmental parameters affecting the indoor dust bacterial community in university dormitory, while printer and BDE 47 played dominating role in shaping microorganism in printing shop. The complex biotic (potential bacterial pathogens) and abiotic factors (electronic equipment and chemical pollutants) in indoor dusts may pose potential health risks to university students.

Environmental Determination of Indigenous Bifidobacteria of the Human Intestine

The environmental determination of indigenous (constantly present) bifidobacteria of the human large intestine is considered in this review. Environmental determination (from the Latin determinere, "I determine") is understood as a set of natural phenomena of a habitat (biotope) that determine the role of indigenous microorganisms in the microbiocenosis. Using the symbiotic approach, an attempt is made to identify the environmental conditions for the habitat of bifidobacteria and their physiological effects in the microsymbiocenosis. The features of indigenous bifidobacteria in terms of their nature have been established: evolutionary-genetic (phylogenetic remoteness, genome conservation, metabolic specialization), biochemical (lysozyme resistance, constitutive acetate production), and physiological (microbial "friend-foe" identification, immunoregulation), which are important in adaptation (persistence) and the provision of mutualistic effects and stability of the bifidoflora in the population.

Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool

Lactic acid bacteria (LAB) and bifidobacteria may serve as reservoirs of antimicrobial resistance, but the risk posed by strains intentionally introduced into the agro-food chain has not yet been thoroughly investigated. The aim of our study was to evaluate whether probiotics, starter and protective cultures, and feed additives represent a risk to human health. In addition to commercial strains of LAB and bifidobacteria, isolates from human milk or colostrum, intestinal mucosa or feces, and fermented products were analyzed. Phenotypic susceptibility data of 474 strains showed that antimicrobial resistance was more common in intestinal isolates than in commercial strains. Antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were characterized in the whole genome sequences of 1114 strains using comparative genomics. Intrinsic ARGs were abundant in enterococci, bifidobacteria, and lactococci but were considered non-risky due to the absence of MGEs. The results revealed that 13.8% of commercial strains contained acquired ARGs, most frequently for tetracycline. We associated 75.5% of the acquired ARGs with known or novel MGEs, and their potential for transmission was assessed by examining metagenomic sequences. We confirmed that ARGs and MGEs were not as abundant or diverse in commercial strains as in human intestinal isolates or isolates from human milk, suggesting that strains intentionally introduced into the agro-food chain do not pose a significant threat. However, attention should be paid especially to individual probiotic strains containing elements that have been shown to have high potential for transferability in the gut microbiota.Abbreviations: ARG, antimicrobial resistance gene; ICE, integrative and conjugative element; IME, integrative and mobilizable element; LAB, lactic acid bacteria; MDR, multidrug resistance; MIC, minimum inhibitory concentration; MGE, mobile genetic element; TRRPP, tetracycline-resistant ribosomal protection protein; WGS, whole genome sequences.

Exploring the Genomic Diversity and Antimicrobial Susceptibility of Bifidobacterium pseudocatenulatum in a Vietnamese Population

Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and specific variants of B. pseudocatenulatum have been associated with health benefits such as improving gut integrity and reducing inflammatory responses. Here, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum cells found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intraclonal variation attributed largely to a gain or loss of carbohydrate-utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases predicted to target plant-based nondigestible carbohydrates (GH13, GH43) but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed extensive genetic diversity and was subject to a high degree of genetic modification. Antimicrobial susceptibility profiling revealed that the Vietnamese B. pseudocatenulatum cells were uniformly susceptible to beta-lactams but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin, and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with a mutation(s) in the quinolone resistance-determining region (GyrA, S115, and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which can be exploited for the rational design of probiotics. IMPORTANCE Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features. Population-specific beneficial microbes represent a promising avenue for the development of potential probiotics, as they may exhibit a more suitable profile in the target population. This study investigates the underexplored diversity of B. pseudocatenulatum in Vietnam and provides more understanding of its genomic diversity, metabolic potential, and antimicrobial susceptibility. Such data from indigenous populations are essential for selecting probiotic candidates that can be accelerated into further preclinical and clinical investigations.

Mobile Antimicrobial Resistance Genes in Probiotics

Even though people worldwide tend to consume probiotic products for their beneficial health effects on a daily basis, recently, concerns were outlined regarding the uptake and potential intestinal colonisation of the bacteria that they carry. These bacteria are capable of executing horizontal gene transfer (HGT) which facilitates the movement of various genes, including antimicrobial resistance genes (ARGs), among the donor and recipient bacterial populations. Within our study, 47 shotgun sequencing datasets deriving from various probiotic samples (isolated strains and metagenomes) were bioinformatically analysed. We detected more than 70 ARGs, out of which rpoB mutants conferring resistance to rifampicin, tet(W/N/W) and potentially extended-spectrum beta-lactamase (ESBL) coding TEM-116 were the most common. Numerous ARGs were associated with integrated mobile genetic elements, plasmids or phages promoting the HGT. Our findings raise clinical and public health concerns as the consumption of probiotic products may lead to the transfer of ARGs to human gut bacteria.

Amoxicillin-Clavulanic Acid Resistance in the Genus Bifidobacterium

Amoxicillin-clavulanic acid (AMC) is one of the most frequently prescribed antibiotic formulations in the Western world. Extensive oral use of this antimicrobial combination influences the gut microbiota. One of the most abundant early colonizers of the human gut microbiota is represented by different taxa of the Bifidobacterium genus, which include many members that are considered to bestow beneficial effects upon their host. In the current study, we investigated the impact of AMC administration on the gut microbiota composition, comparing the gut microbiota of 23 children that had undergone AMC antibiotic therapy to that of 19 children that had not been treated with antibiotics during the preceding 6 months. Moreover, we evaluated AMC sensitivity by MIC test of 261 bifidobacterial strains, including reference strains for the currently recognized 64 bifidobacterial (sub)species, as well as 197 bifidobacterial isolates of human origin. These assessments allowed the identification of four bifidobacterial strains that exhibit a high level of AMC insensitivity, which were subjected to genomic and transcriptomic analyses to identify the putative genetic determinants responsible for this AMC insensitivity. Furthermore, we investigated the ecological role of AMC-resistant bifidobacterial strains by in vitro batch cultures.IMPORTANCE Based on our results, we observed a drastic reduction in gut microbiota diversity of children treated with antibiotics, which also affected the abundance of Bifidobacterium, a bacterial genus commonly found in the infant gut. MIC experiments revealed that more than 98% of bifidobacterial strains tested were shown to be inhibited by the AMC antibiotic. Isolation of four insensitive strains and sequencing of their genomes revealed the identity of possible genes involved in AMC resistance mechanisms. Moreover, gut-simulating in vitro experiments revealed that one strain, i.e., Bifidobacterium breve PRL2020, is able to persist in the presence of a complex microbiota combined with AMC antibiotic.

The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host

Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.

Decoding the Genomic Variability among Members of the Bifidobacterium dentium Species

Members of the Bifidobacterium dentium species are usually identified in the oral cavity of humans and associated with the development of plaque and dental caries. Nevertheless, they have also been detected from fecal samples, highlighting a widespread distribution among mammals. To explore the genetic variability of this species, we isolated and sequenced the genomes of 18 different B. dentium strains collected from fecal samples of several primate species and an Ursus arctos. Thus, we investigated the genomic variability and metabolic abilities of the new B. dentium isolates together with 20 public genome sequences. Comparative genomic analyses provided insights into the vast metabolic repertoire of the species, highlighting 19 glycosyl hydrolases families shared between each analyzed strain. Phylogenetic analysis of the B. dentium taxon, involving 1140 conserved genes, revealed a very close phylogenetic relatedness among members of this species. Furthermore, low genomic variability between strains was also confirmed by an average nucleotide identity analysis showing values higher than 98.2%. Investigating the genetic features of each strain, few putative functional mobile elements were identified. Besides, a consistent occurrence of defense mechanisms such as CRISPR-Cas and restriction-modification systems may be responsible for the high genome synteny identified among members of this taxon.

Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium

Bifidobacteria are typical commensals inhabiting the human intestine and are beneficial to the host because of their probiotic properties. One of the risks concerning probiotics is the potential of introducing antibiotic resistance genes (ARGs) to the host gut pathogens. This study was aimed to depict the general antibiotic resistance characteristics of the genus Bifidobacterium by combining the reported phenotype dataset and in silico genotype prediction. Bifidobacteria were mostly reported to be sensitive to beta-lactams, glycopeptides, chloramphenicol, and rifampicin, but resistant to aminoglycosides, polypeptides, quinolones, and mupirocin. Generally, the resistance phenotypes to erythromycin, tetracycline, fusidic acid, metronidazole, clindamycin, and trimethoprim were variable. Besides cmX and tetQ, characterized in bifidobacterial resident plasmids, 3520 putative ARGs were identified from 831 bifidobacterial genomes through BLASTP search. The identified ARGs matched thirty-eight reference ARGs, four of which seemed to be mutant housekeeping genes. The two high-abundant ARGs, tetW and ermX, were found to have different distribution traits. The predicted ARGs reasonably explained most of the corresponding resistant phenotypes in the published literature.

Antibiotic resistance propagation through probiotics

INTRODUCTION

The widespread use of probiotics globally has established an argument against their safety profile. Recent studies investigated the gastrointestinal tract (GIT) as a reservoir for antibiotic resistance genes and horizontal gene transfer (HGT) amongst opportunistic pathogens, probiotics, and the normal microbiota which might cause severe clinical implications.

AREAS COVERED

In this review, we aimed to discuss the potential role of probiotics in spreading antibiotic resistance. All relevant data were found through online/updated databases such as PubMed, Google Scholar, and Clinicaltrials.gov. This review is based on the studies undertaken over the past two decades (2000-2020).

EXPERT OPINION

Microorganisms are capable of transferring resistance genes to survive against antimicrobial medications. Transference of resistance genes among pathogens, probiotics, and gut microbiota in the GIT through HGT endow probiotics as a possible source for antimicrobial resistance genes, which is responsible for the development of the antibiotic resistance crisis. According to the expression of genes in mechanisms of antibiotics resistance and probiotics HGT, the hypothesis of the role of these microorganisms in personalized medicine and gene therapy could also be considered.

The Diversity of the CRISPR-Cas System and Prophages Present in the Genome Reveals the Co-evolution of Bifidobacterium pseudocatenulatum and Phages

Diverse CRISPR-Cas systems constitute an indispensable part of the bacterial adaptive immune system against viral infections. However, to escape from this immune system, bacteriophages have also evolved corresponding anti-defense measures. We investigated the diversity of CRISPR-Cas systems and the presence of prophages in the genomes of 66 Bifidobacterium pseudocatenulatum strains. Our findings revealed a high occurrence of complete CRISPR-Cas systems (62%, 41/66) in the B. pseudocatenulatum genomes. Subtypes I-C, I-U and II-A, were found to be widespread in this species. No significant association was found between the number of bacterial CRISPR spacers and its host's age. This study on prophages within B. pseudocatenulatum genomes revealed that prophage genes related to distinct functional modules became degraded at different levels, indicating that these prophages were not likely to enter lytic cycle spontaneously. Further, the evolutionary analysis of prophages in this study revealed that they might be derived from different phage ancestors. Notably, self-targeting phenomenon within B. pseudocatenulatum and Anti-CRISPR (Acr) coding genes in prophages was observed. Overall, our results indicate that the competition between B. pseudocatenulatum and phages is a major driving factor for the genomic diversity of both partners.