Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems

Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion

In our study, we aimed to explore the genomic and phenotypic traits of Priestia megaterium strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of P. megaterium strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.IMPORTANCEBoth genomic and phenotypic analyses yielded valuable insights into the capacity of P. megaterium B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that P. megaterium members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.

Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis

In 2022, a novel disease similar to pear fire blight was found in a pear orchard in Zhangye City, Gansu Province, China. The disease mainly damages the branches, leaves, and fruits of the plant. To identify the pathogen, tissue isolation and pathogenicity testing (inoculating the potential pathogen on healthy plant tissues) were conducted. Furthermore, a comprehensive analysis encompassing the pathogen's morphological, physiological, and biochemical characteristics and whole-genome sequencing was conducted. The results showed that among the eight isolates, the symptoms on the detached leaves and fruits inoculated with isolate DE2 were identical to those observed in the field. Verifying Koch's postulates confirmed that DE2 was the pathogenic bacterium that causes the disease. Based on a 16S rRNA phylogenetic tree, isolate DE2 belongs to the genus Erwinia. Biolog and API 20E results also indicated that isolate DE2 is an undescribed species of Erwinia. Isolate DE2 was negative for oxidase. Subsequently, the complete genome sequence of isolate DE2 was determined and compared to the complete genome sequences of 29 other Erwinia species based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The ANI and dDDH values between strain DE2 and Erwinia species were both below the species thresholds (ANI < 95-96%, dDDH<70%), suggesting that isolate DE2 is a new species of Erwinia. We will temporarily name strain DE2 as Erwinia pyri sp. nov. There were 548 predicted virulence factors in the genome of strain DE2, comprising 534 on the chromosome and 5 in the plasmids. The whole genome sequence of strain DE2 has been submitted to the NCBI database (ASM3075845v1) with accession number GCA_030758455.1. The strain DE2 has been preserved at the China Center for Type Culture Collection (CCTCC) under the deposit number CCTCC AB 2024080. This study represents the initial report of a potentially new bacterial species in the genus Erwinia that causes a novel pear dieback disease. The findings provide a valuable strain resource for the study of the genus Erwinia and establish a robust theoretical foundation for the prevention and control of emerging pear dieback diseases.

Genome engineering of the human gut microbiome

The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.

GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010

Bifidobacteria are commensal microorganisms that typically inhabit the mammalian gut, including that of humans. As they may be vertically transmitted, they commonly colonize the human intestine from the very first day following birth and may persist until adulthood and old age, although generally at a reduced relative abundance and prevalence compared to infancy. The ability of bifidobacteria to persist in the human intestinal environment has been attributed to genes involved in adhesion to epithelial cells and the encoding of complex carbohydrate-degrading enzymes. Recently, a putative mucin-degrading glycosyl hydrolase belonging to the GH136 family and encoded by the perB gene has been implicated in gut persistence of certain bifidobacterial strains. In the current study, to better characterize the function of this gene, a comparative genomic analysis was performed, revealing the presence of perB homologues in just eight bifidobacterial species known to colonize the human gut, including Bifidobacterium bifidum and Bifidobacterium longum subsp. longum strains, or in non-human primates. Mucin-mediated growth and adhesion to human intestinal cells, in addition to a rodent model colonization assay, were performed using B. bifidum PRL2010 as a perB prototype and its isogenic perB-insertion mutant. These results demonstrate that perB inactivation reduces the ability of B. bifidum PRL2010 to grow on and adhere to mucin, as well as to persist in the rodent gut niche. These results corroborate the notion that the perB gene is one of the genetic determinants involved in the persistence of B. bifidum PRL2010 in the human gut.

Two extracellular α-arabinofuranosidases are required for cereal-derived arabinoxylan metabolism by Bifidobacterium longum subsp. longum

Members of the genus Bifidobacterium are commonly found in the human gut and are known to utilize complex carbohydrates that are indigestible by the human host. Members of the Bifidobacterium longum subsp. longum taxon can metabolize various plant-derived carbohydrates common to the human diet. To metabolize such polysaccharides, which include arabinoxylan, bifidobacteria need to encode appropriate carbohydrate-active enzymes in their genome. In the current study, we describe two GH43 family enzymes, denoted here as AxuA and AxuB, which are encoded by B. longum subsp. longum NCIMB 8809 and are shown to be required for cereal-derived arabinoxylan metabolism by this strain. Based on the observed hydrolytic activity of AxuA and AxuB, assessed by employing various synthetic and natural substrates, and based on in silico analyses, it is proposed that both AxuA and AxuB represent extracellular α-L-arabinofuranosidases with distinct substrate preferences. The variable presence of the axuA and axuB genes and other genes previously described to be involved in the metabolism of arabinose-containing glycans can in the majority cases explain the (in)ability of individual B. longum subsp. longum strains to grow on cereal-derived arabinoxylans and arabinan.

Gut microbiota and traumatic central nervous system injuries: Insights into pathophysiology and therapeutic approaches

Traumatic brain injury and spinal cord injury are two distinct but fundamentally similar types of acute insults to the central nervous system (CNS) that often culminate in death or cognitive and motor impairment. Over the past decade, researchers have tapped into research to discover the potential role being played by gut bacteria in CNS. After an acute CNS injury, the altered composition of the gut microbiota disturbs the balance of the bidirectional gut-brain axis, aggravating secondary CNS injury, motor dysfunctions, and cognitive deficits, which worsens the patient's prognosis. Some of the well-known therapeutic interventions which can also be used as adjuvant therapy for alleviating CNS injuries include, the use of pro and prebiotics, fecal microbiota transplantation, and microbial engineering. In this review, we aim to discuss the importance of gut microbes in our nervous system, anatomy, and signaling pathways involved in regulating the gut-brain axis, the alteration of the gut microbiome in CNS injuries, and the therapeutic strategies to target gut microbiomes in traumatic CNS injuries.

Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants

The species Bifidobacterium longum currently comprises four subspecies: B. longum subsp. longum , B. longum subsp. infantis , B. longum subsp. suis and B. longum subsp. suillum . Recently, several studies on B. longum suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to B. longum subsp. suis DSM 20210T and B. longum subsp. suillum JCM1995T [average nucleotide identity (ANI) of 98.1 %) while showed an ANI of 96.5 % with both B. longum subsp. infantis and B. longum subsp. longum . The current work describes five novel additional B. longum strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species B. longum with B. longum subsp. suis and B. longum subsp. suillum as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to B. longum subsp. infantis , show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies, B. longum subsp. suis and B. longum subsp. suillum . Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name Bifidobacterium longum subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T=CCOS 2034T), is proposed.

Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle

Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.

A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning

The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.

M-TUBE enables large-volume bacterial gene delivery using a high-throughput microfluidic electroporation platform

Conventional cuvette-based and microfluidics-based electroporation approaches for bacterial gene delivery have distinct advantages, but they are typically limited to relatively small sample volumes, reducing their utility for applications requiring high throughput such as the generation of mutant libraries. Here, we present a scalable, large-scale bacterial gene delivery approach enabled by a disposable, user-friendly microfluidic electroporation device requiring minimal device fabrication and straightforward operation. We demonstrate that the proposed device can outperform conventional cuvettes in a range of situations, including across Escherichia coli strains with a range of electroporation efficiencies, and we use its large-volume bacterial electroporation capability to generate a library of transposon mutants in the anaerobic gut commensal Bifidobacterium longum.

Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality

Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

SUMMARY

Taxonomic analysis of microbial communities is well supported at the level of species and strains. However, species can contain significant phenotypic diversity and strains are rarely widely shared across global populations. Stratifying the diversity between species and strains can identify 'subspecies', which are a useful intermediary. High-throughput identification and profiling of subspecies is not yet supported in the microbiome field. Here, we use an operational definition of subspecies based on single nucleotide variant (SNV) patterns within species to identify and profile subspecies in metagenomes, along with their distinctive SNVs and genes. We incorporate this method into metaSNV v2, which extends existing SNV-calling software to support further SNV interpretation for population genetics. These new features support microbiome analyses to link SNV profiles with host phenotype or environment and niche-specificity. We demonstrate subspecies identification in marine and fecal metagenomes. In the latter, we analyze 70 species in 7524 adult and infant subjects, supporting a common subspecies population structure in the human gut microbiome and illustrating some limits in subspecies calling.

AVAILABILITY AND IMPLEMENTATION

Source code, documentation, tutorials and test data are available at https://github.com/metasnv-tool/metaSNV and https://metasnv.embl.de.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota

Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies longum, as observed in phylogenetic analysis. B. longum SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among longum subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that B. longum M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of B. longum subsp. longum to colonize the human gut microbiota.

Galacto-oligosaccharides as infant prebiotics: production, application, bioactive activities and future perspectives

Galacto-oligosaccharides (GOS) are non-digestible oligosaccharides characterized by a mix of structures that vary in their degree of polymerization (DP) and glycosidic linkage between the galactose moieties or between galactose and glucose. They have enjoyed extensive scientific scrutiny, and their health-promoting effects are supported by a large number of scientific and clinical studies. A variety of GOS-associated health-promoting effects have been reported, such as growth promotion of beneficial bacteria, in particular bifidobacteria and lactobacilli, inhibition of pathogen adhesion and improvement of gut barrier function. GOS have attracted significant interest from food industries for their versatility as a bioactive ingredient and in particular as a functional component of infant formulations. These oligosaccharides are produced in a kinetically-controlled reaction involving lactose transgalactosylation, being catalyzed by particular β-galactosidases of bacterial or fungal origin. Despite the well-established technology applied for GOS production, this process may still meet with technological challenges when employed at an industrial scale. The current review will cover relevant scientific literature on the beneficial physiological properties of GOS as a prebiotic for the infant gut microbiota, details of GOS structures, the associated reaction mechanism of β-galactosidase, and its (large-scale) production.

Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons

Bifidobacterium longum is one of the most widely distributed and abundant Bifidobacterium in the human intestine, and has been proven to have a variety of physiological functions. In this study, 80 strains of B. longum isolated from human subjects were classified into subspecies by ANI and phylogenetic analyses, and the functional genes were compared. The results showed that there were significant differences in carbohydrate metabolism between the two subspecies, which determined their preference for human milk oligosaccharides or plant-derived carbohydrates. The predicted exopolysaccharide (EPS) gene clusters had large variability within species but without difference at the subspecies level. Four subtype CRISPR-Cas systems presented in B. longum, while the subtypes I-U and II-C only existed in B. longum subsp. longum. The bacteriocin operons in B. longum subsp. infantis were more widely distributed compared with B. longum subsp. longum. In conclusion, this study revealed the similarities and differences between B. longum subsp. infantis and B. longum subsp. longum, which could provide a theoretical basis for further exploring the probiotic characteristics of B. longum.

Comparative genomics and in silico gene evaluation involved in the probiotic potential of Bifidobacterium longum 51A

The Bifidobacterium longum 5^1A strain of isolated from feces of a healthy child, has demonstrated probiotic properties by in vivo and in vitro studies, which may be assigned to its production of metabolites such as acetate. Thus, through the study of comparative genomics, the present work sought to identify unique genes that might be related to the production of acetate. To perform the study, the DNA strain was sequenced using Illumina HiSeq technology, followed by assembly and manual curation of coding sequences. Comparative analysis was performed including 19 complete B. longum genomes available in Genbank/NCBI. In the phylogenetic analysis, the CECT 7210 and 157F strains of B. longum subsp. infantis aggregated within the subsp. longum cluster, suggesting that their taxonomic classification should be reviewed. The strain 5^1A of B. longum has 26 unique genes, six of which are possibly related to carbohydrate metabolism and acetate production. The phosphoketolase pathway from B. longum 5^1A showed a difference in acetyl-phosphate production. This result seems to corroborate the analysis of their unique genes, whose presence suggests the strain may use different sources of carbohydrates that allow a greater production of acetate and consequently offer benefits to the host health.

Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve

Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.

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.

Bifidobacterium Transformation

The protocol presented in this chapter describes a generic method for electrotransformation of Bifidobacterium spp., outlining a technique that is ideal for conferring selective properties onto strains as well as allowing the user to introduce or knock out/in selected genes for phenotypic characterization purposes. We have generalized on the plasmid chosen for transformation and antibiotic selection marker, but the protocol is versatile in this respect and we are able to achieve transformation efficiencies up to 10⁷ transformants/μg of DNA.

A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications

Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.

Site-Directed Mutagenesis of Bifidobacterium Strains

At present, only a limited number of Bifidobacterium species are amenable to genetic manipulation using mutagenesis. This lack of genetic accessibility among the majority of bifidobacterial strains represents a significant roadblock for the study of gene function and expression in these potential probiotics. Genetic tools for generating mutants are difficult to develop for bifidobacteria, as they require workarounds for obstacles such as low transformation efficiencies, and the presence of differing and sometimes multiple restriction modification systems, in different strains. Site-directed mutagenesis is a frequently applied molecular strategy for the generation of targeted mutations, resulting in gene deletion or disruption, or alteration of their expression, thereby revealing information regarding their function. This strategy has been employed as a molecular tool in some Bifidobacterium strains and is typically achieved using a nonreplicating vector, harboring a DNA fragment corresponding to an internal part of the gene to be mutated. This vector is introduced into a bifidobacterial cell of the strain in question by electroporation. Through homologous recombination, this vector is integrated into the genomic DNA of said cell, disrupting the coding region of the targeted gene, thus preventing the expression of a functional protein product. Such mutant versions of Bifidobacterium strains may then be assessed for alterations in their phenotype or gene expression.

Plant Glycan Metabolism by Bifidobacteria

Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.

Generating a fucose permease deletion mutant in Bifidobacterium longum subspecies infantis ATCC 15697

Bifidobacterium longum subsp. infantis ATCC 15697 has emerged as a model for infant gut-associated bifidobacterial strains. Here we present a genetic system for B. longum subsp. infantis ATCC 15697 using its own DNA restriction-modification systems and create a fucose permease deletion mutant lacking the ability to use free fucose as a carbon source.

Altered physiology of gastrointestinal vagal afferents following neurotrauma

The adaptability of the central nervous system has been revealed in several model systems. Of particular interest to central nervous system-injured individuals is the ability for neural components to be modified for regain of function. In both types of neurotrauma, traumatic brain injury and spinal cord injury, the primary parasympathetic control to the gastrointestinal tract, the vagus nerve, remains anatomically intact. However, individuals with traumatic brain injury or spinal cord injury are highly susceptible to gastrointestinal dysfunctions. Such gastrointestinal dysfunctions attribute to higher morbidity and mortality following traumatic brain injury and spinal cord injury. While the vagal efferent output remains capable of eliciting motor responses following injury, evidence suggests impairment of the vagal afferents. Since sensory input drives motor output, this review will discuss the normal and altered anatomy and physiology of the gastrointestinal vagal afferents to better understand the contributions of vagal afferent plasticity following neurotrauma.

Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications

Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance.IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.

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.

Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol

Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.

Interest of bacterial pangenome analyses in clinical microbiology

Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.

Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective

Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

Epigenetics: A New Frontier in Probiotic Research

Research into the benefits of probiotics has progressed beyond interventional studies to identifying the underlying molecular mechanisms. Health-promoting effector molecules produced by probiotics are well documented and have been linked to specific genes and even individual nucleotides. However, the factors controlling the expression of these molecules are poorly understood and we argue that epigenetic influences likely play an important role in mediating the health-promoting attributes of probiotics. Here, we review established epigenetic regulation of important microbial genetic systems involved in health promotion, safety, and industrialization to provide evidence that the same regulation occurs in probiotic organisms. We advocate for studies combining genomic and meta-epigenomic data to better understand the mode of action of probiotics, their associated microbiomes, and their effects on consumers.

Bifidobacterium longum subsp. infantis ATCC 15697 and Goat Milk Oligosaccharides Show Synergism In Vitro as Anti-Infectives against Campylobacter jejuni

Bifidobacteria are known to inhibit, compete with and displace the adhesion of pathogens to human intestinal cells. Previously, we demonstrated that goat milk oligosaccharides (GMO) increased the attachment of Bifidobacterium longum subsp. infantis ATCC 15697 to intestinal cells in vitro. In this study, we aimed to exploit this effect as a mechanism for inhibiting pathogen association with intestinal cells. We examined the synergistic effect of GMO-treated B. infantis on preventing the attachment of a highly invasive strain of Campylobacter jejuni to intestinal HT-29 cells. The combination decreased the adherence of C. jejuni to the HT-29 cells by an average of 42% compared to the control (non-GMO treated B. infantis). Increasing the incubation time of the GMO with the Bifidobacterium strain resulted in the strain metabolizing the GMO, correlating with a subsequent 104% increase in growth over a 24 h period when compared to the control. Metabolite analysis in the 24 h period also revealed increased production of acetate, lactate, formate and ethanol by GMO-treated B. infantis. Statistically significant changes in the GMO profile were also demonstrated over the 24 h period, indicating that the strain was digesting certain structures within the pool such as lactose, lacto-N-neotetraose, lacto-N-neohexaose 3′-sialyllactose, 6′-sialyllactose, sialyllacto-N-neotetraose c and disialyllactose. It may be that early exposure to GMO modulates the adhesion of B. infantis while carbohydrate utilisation becomes more important after the bacteria have transiently colonised the host cells in adequate numbers. This study builds a strong case for the use of synbiotics that incorporate oligosaccharides sourced from goat′s milk and probiotic bifidobacteria in functional foods, particularly considering the growing popularity of formulas based on goat milk.

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum

Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in ≤28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.

Metabolism of biosynthetic oligosaccharides by human-derived Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809

This work aimed to investigate the ability of two human-derived bifidobacterial strains, i.e. Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809, to utilize various oligosaccharides (i.e., 4-galactosyl-kojibiose, lactulosucrose, lactosyl-oligofructosides, raffinosyl-oligofructosides and lactulose-derived galacto-oligosaccharides) synthesized by means of microbial glycoside hydrolases. With the exception of raffinosyl-oligofructosides, these biosynthetic oligosaccharides were shown to support growth acting as a sole carbon and energy source of at least one of the two studied strains. Production of short-chain fatty acids (SCFAs) as detected by HPLC analysis corroborated the suitability of most of the studied novel oligosaccharides as fermentable growth substrates for the two bifidobacterial strains, showing that acetic acid is the main metabolic end product followed by lactic and formic acids. Transcriptomic and functional genomic approaches carried out for B. breve UCC2003 allowed the identification of key genes encoding glycoside hydrolases and carbohydrate transport systems involved in the metabolism of 4-galactosyl-kojibiose and lactulosucrose. In particular, the role of β-galactosidases in the hydrolysis of these particular trisaccharides was demonstrated, highlighting their importance in oligosaccharide metabolism by human bifidobacterial strains.

Milk Glycans and Their Interaction with the Infant-Gut Microbiota

Human milk is a unique and complex fluid that provides infant nutrition and delivers an array of bioactive molecules that serve various functions. Glycans, abundant in milk, can be found as free oligosaccharides or as glycoconjugates. Milk glycans are increasingly linked to beneficial outcomes in neonates through protection from pathogens and modulation of the immune system. Indeed, these glycans influence the development of the infant and the infant-gut microbiota. Bifidobacterium species commonly are enriched in breastfed infants and are among a limited group of bacteria that readily consume human milk oligosaccharides (HMOs) and milk glycoconjugates. Given the importance of bifidobacteria in infant health, numerous studies have examined the molecular mechanisms they employ to consume HMOs and milk glycans, thus providing insight into this unique enrichment and shedding light on a range of translational opportunities to benefit at-risk infants.

Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.

Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

For more than a decade, pan-genome analysis has been applied as an effective method for explaining the genetic contents variation of prokaryotic species. However, genomic characteristics and detailed structures of gene pools have not been fully clarified, because most studies have used a small number of genomes. Here, we constructed pan-genomes of seven species in order to elucidate variations in the genetic contents of >27,000 genomes belonging to Streptococcus pneumoniae, Staphylococcus aureus subsp. aureus, Salmonella enterica subsp. enterica, Escherichia coli and Shigella spp., Mycobacterium tuberculosis complex, Pseudomonas aeruginosa, and Acinetobacter baumannii. This work showed the pan-genomes of all seven species has open property. Additionally, systematic evaluation of the characteristics of their pan-genome revealed that phylogenetic distance provided valuable information for estimating the parameters for pan-genome size among several models including Heaps' law. Our results provide a better understanding of the species and a solution to minimize sampling biases associated with genome-sequencing preferences for pathogenic strains.

Unveiling Genomic Diversity among Members of the Species Bifidobacterium pseudolongum, a Widely Distributed Gut Commensal of the Animal Kingdom

Bifidobacteria are commensals of the animal gut and are commonly found in mammals, birds, and social insects. Specifically, strains of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium longum, and Bifidobacterium pseudolongum are widely distributed in the mammalian gut. In this context, we investigated the genetic variability and metabolic abilities of the B. pseudolongum taxon, whose genomic characterization has so far not received much attention. Phylogenomic analysis of the genome sequences of 60 B. pseudolongum strains revealed that B. pseudolongum subsp. globosum and B. pseudolongum subsp. pseudolongum may actually represent two distinct bifidobacterial species. Furthermore, our analysis highlighted metabolic differences between members of these two subspecies. Moreover, comparative analyses of genetic strategies to prevent invasion of foreign DNA revealed that the B. pseudolongum subsp. globosum group exhibits greater genome plasticity. In fact, the obtained findings indicate that B. pseudolongum subsp. globosum is more adaptable to different ecological niches such as the mammalian and avian gut than is B. pseudolongum subsp. pseudolongumIMPORTANCE Currently, little information exists on the genetics of the B. pseudolongum taxon due to the limited number of sequenced genomes belonging to this species. In order to survey genome variability within this species and explore how members of this taxon evolved as commensals of the animal gut, we isolated and decoded the genomes of 51 newly isolated strains. Comparative genomics coupled with growth profiles on different carbohydrates has further provided insights concerning the genotype and phenotype of members of the B. pseudolongum taxon.

Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses

Bifidobacteria are members of the gut microbiota of animals, including mammals, birds, and social insects. In this study, we analyzed and determined the pangenome of Bifidobacterium animalis species, encompassing B. animalis subsp. animalis and the B. animalis subsp. lactis taxon, which is one of the most intensely exploited probiotic bifidobacterial species. In order to reveal differences within the B. animalis species, detailed comparative genomics and phylogenomics analyses were performed, indicating that these two subspecies recently arose through divergent evolutionary events. A subspecies-specific core genome was identified for both B. animalis subspecies, revealing the existence of subspecies-defining genes involved in carbohydrate metabolism. Notably, these in silico analyses coupled with carbohydrate profiling assays suggest genetic adaptations toward a distinct glycan milieu for each member of the B. animalis subspecies, resulting in a divergent evolutionary development of the two subspecies.IMPORTANCE The majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the gastrointestinal tracts of different animals, including mammals and birds. The present study allowed us to reconstruct the pangenome of this taxon, including the genome contents of 56 B. animalis strains. Through careful assessment of subspecies-specific core genes of the B. animalis subsp. animalis/lactis taxon, we identified genes encoding enzymes involved in carbohydrate transport and metabolism, while unveiling specific gene acquisition and loss events that caused the evolutionary emergence of these two subspecies.

Two Novel α-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan

Arabinose-containing poly- or oligosaccharides are suitable carbohydrate sources for Bifidobacterium longum subsp. longum However, their degradation pathways are poorly understood. In this study, we cloned and characterized the previously uncharacterized glycoside hydrolase family 43 (GH43) enzymes B. longum subsp. longum ArafC (BlArafC; encoded by BLLJ_1852) and B. longum subsp. longum ArafB (BlArafB; encoded by BLLJ_1853) from B. longum subsp. longum JCM 1217. Both enzymes exhibited α-l-arabinofuranosidase activity toward p-nitrophenyl-α-l-arabinofuranoside but no activity toward p-nitrophenyl-β-d-xylopyranoside. The specificities of the two enzymes for l-arabinofuranosyl linkages were different. BlArafC catalyzed the hydrolysis of α1,2- and α1,3-l-arabinofuranosyl linkages found on the side chains of both arabinan and arabinoxylan. It released l-arabinose 100 times faster from arabinan than from arabinoxylan but did not act on arabinogalactan. On the other hand, BlArafB catalyzed the hydrolysis of the α1,5-l-arabinofuranosyl linkage found on the arabinan backbone. It released l-arabinose from arabinan but not from arabinoxylan or arabinogalactan. Coincubation of BlArafC and BlArafB revealed that these two enzymes are able to degrade arabinan in a synergistic manner. Both enzyme activities were suppressed with EDTA treatment, suggesting that they require divalent metal ions. The GH43 domains of BlArafC and BlArafB are classified into GH43 subfamilies 27 and 22, respectively, but show very low similarity (less than 15% identity) with other biochemically characterized members in the corresponding subfamilies. The B. longum subsp. longum strain lacking the GH43 gene cluster that includes BLLJ_1850 to BLLJ_1853 did not grow in arabinan medium, suggesting that BlArafC and BlArafB are important for assimilation of arabinan.IMPORTANCE We identified two novel α-l-arabinofuranosidases, BlArafC and BlArafB, from B. longum subsp. longum JCM 1217, both of which are predicted to be extracellular membrane-bound enzymes. The former specifically acts on α1,2/3-l-arabinofuranosyl linkages, while the latter acts on the α1,5-l-arabinofuranosyl linkage. These enzymes cooperatively degrade arabinan and are required for the efficient growth of bifidobacteria in arabinan-containing medium. The genes encoding these enzymes are located side by side in a gene cluster involved in metabolic pathways for plant-derived polysaccharides, which may confer adaptability in adult intestines.

Bovine colostrum-driven modulation of intestinal epithelial cells for increased commensal colonisation

Nutritional intake may influence the intestinal epithelial glycome and in turn the available attachment sites for bacteria. In this study, we tested the hypothesis that bovine colostrum may influence the intestinal cell surface and in turn the attachment of commensal organisms. Human HT-29 intestinal cells were exposed to a bovine colostrum fraction (BCF) rich in free oligosaccharides. The adherence of several commensal bacteria, comprising mainly bifidobacteria, to the intestinal cells was significantly enhanced (up to 52-fold) for all strains tested which spanned species that are found across the human lifespan. Importantly, the changes to the HT-29 cell surface did not support enhanced adhesion of the enteric pathogens tested. The gene expression profile of the HT-29 cells following treatment with the BCF was evaluated by microarray analysis. Many so called "glyco-genes" (glycosyltransferases and genes involved in the complex biosynthetic pathways of glycans) were found to be differentially regulated suggesting modulation of the enzymatic addition of sugars to glycoconjugate proteins. The microarray data was further validated by means of real-time PCR. The current findings provide an insight into how commensal microorganisms colonise the human gut and highlight the potential of colostrum and milk components as functional ingredients that can potentially increase commensal numbers in individuals with lower counts of health-promoting bacteria.

Implementation of Transposon Mutagenesis in Bifidobacterium

Random transposon mutagenesis allows for relatively rapid, genome-wide surveys to detect genes involved in functional traits, by performing screens of mutant libraries. This approach has been widely applied to identify genes responsible for activities of interest in multiple eukaryote and prokaryote organisms, although most studies on microorganisms have focused on pathogenic and clinically relevant bacteria. In this chapter we describe the implementation of an in vitro Tn5-based transposome strategy to generate a large collection of random mutants in the gut commensal Bifidobacterium breve UCC2003, and discuss considerations when applying this mutagenesis system to other Bifidobacterium species or strains of interest.

Fucosylated Human Milk Oligosaccharides and N-Glycans in the Milk of Chinese Mothers Regulate the Gut Microbiome of Their Breast-Fed Infants during Different Lactation Stages

Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.

The milk glycobiome has a significant impact on the gut microbiota of infants, which plays a pivotal role in health and development. Fucosylated human milk oligosaccharides (HMOs) and N-glycans on milk proteins are beneficial for the development of healthy gut microbiota, and the fucosylation levels of these glycans can be affected by the maternal fucosyltransferase 2 gene (FUT2). Here, we present results of longitudinal research on paired milk and stool samples from 56 Chinese mothers (CMs) and their breast-fed children. Changes of HMOs and fucosylated N-glycans in milk of CMs at different lactation stages were detected, which allowed characterization of the major differences in milk glycans and consequential effects on the gut microbiome of infants according to maternal FUT2 status. Significant differences in the abundance of total and fucosylated HMOs between secretor and nonsecretor CMs were noted, especially during early lactation. Despite a tendency toward decreasing milk protein concentrations, the fucosylation levels of milk N-glycans increased during late lactation. The changes in the levels of fucosylated HMOs and milk N-glycans were highly correlated with the growth of Bifidobacterium spp. and Lactobacillus spp. in the gut of infants during early and later lactation, respectively. Enriched expression of genes encoding glycoside hydrolases, glycosyl transferases, ATP-binding cassette (ABC) transporters, and permeases in infants fed by secretor CMs contributed to the promotion of these bacteria in infants. Our data highlight the important role of fucosylated milk glycans in shaping the gut microbiome of infants and provide a solid foundation for development of “personalized” nutrition for Chinese infants.

IMPORTANCE Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.

Improvement of electroporation-mediated transformation efficiency for a Bifidobacterium strain to a reproducibly high level

Bifidobacteria are representative probiotics which are defined as live microorganisms that confer a health benefit on the host. Because of their safety and healthfulness when applied to humans, bifidobacteria are suitable as genetically engineered bacteria for applications to benefit human physiology and pathology. However, molecular biological studies of bifidobacteria have been limited due to insufficient genetic tools including effective transformation methods. The aim of this study is to improve the electroporation-mediated transformation efficiency of bifidobacteria to a reproducibly high level. The crucial factors that determine electroporation efficiency are the restriction-modification system, together with the cell wall and cell membrane structure of the bacteria. We optimized the bifidobacterial electroporation conditions by focusing on these factors as well as the amount of plasmid DNA used, the electrical parameters and the bacterial growth phase. As a result, the electroporation efficiency of B. bifidum BGN4 drastically and consistently increased from 10³ to 10⁵ CFU / μg DNA. The most significant factor for increasing the electroporation efficiency was the cell wall weakening mediated by NaCl, which improved the electroporation frequency by 20 times. Because the optimized electrotransformation conditions reported here should be widely applicable to other Bifidobacterium species, these could promote the extensive genetic manipulation of the various Bifidobacterium species in future studies.

Characterisation of a Hydroxycinnamic Acid Esterase From the Bifidobacterium longum subsp. longum Taxon

Bifidobacterium longum subsp. longum, a common member of the human gut microbiota with perceived positive health effects, is capable of metabolising certain complex, plant-derived carbohydrates which are commonly found in the (adult) human diet. These plant glycans may be employed to favourably modulate the microbial communities in the intestine. Hydroxycinnamic acids (HCAs) are plant phenolic compounds, which are attached to glycans, and which are associated with anti-oxidant and other beneficial properties. However, very little information is available regarding metabolism of HCA-containing glycans by bifidobacteria. In the current study, a gene encoding a hydroxycinnamic acid esterase was found to be conserved across the B. longum subsp. longum taxon and was present in a conserved locus associated with plant carbohydrate utilisation. The esterase was shown to be active against various HCA-containing substrates and was biochemically characterised in terms of substrate preference, and pH and temperature optima of the enzyme. This novel hydroxycinnamic acid esterase is presumed to be responsible for the release of HCAs from plant-based dietary sources, a process that may have benefits for the gut environment and thus host health.

Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions

Members of the Bifidobacterium genus are widely used as probiotics in fermented milk products. Bifidobacterium animalis subsp. animalis CNCM I-4602 grows and survives poorly in reconstituted skimmed milk (RSM). Availing of genome and transcriptome information, this poor growth and survival phenotype in milk was substantially improved by the addition of certain compounds, such as yeast extract, uric acid, glutathione, cysteine, ferrous sulfate, and a combination of magnesium sulfate and manganese sulfate. Carbohydrate utilization of CNCM I-4602 was also investigated, allowing the identification of several carbohydrate utilization gene clusters, and highlighting this strain's inability to utilize lactose, unlike the type strain of this subspecies, B. animalis subsp. animalis ATCC25527 and the B. animalis subsp. lactis subspecies. In addition, the ability of B. animalis subsp. animalis CNCM I-4602 to colonize a murine model was investigated, which showed that this strain persists in the murine gut for a period of at least 4 weeks. Associated in vivo transcriptome analysis revealed that, among other genes, a gene cluster encoding a predicted type IVb tight adherence (Tad) pilus was upregulated, indicating that this extracellular structure plays a role in the colonization/adaptation of the murine gastrointestinal tract by this strain.