Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

The aim of this study was to evaluate the influence of simultaneous, long-term exposure to increasing concentrations of three classes of antimicrobials (β-lactams, fluoroquinolones and nitroimidazoles) on: (1) the efficiency of anaerobic digestion of sewage sludge, (2) qualitative and quantitative changes in microbial consortia that participate in methane fermentation, and (3) fate of antibiotic resistance genes (ARGs). Long-term supplementation of sewage sludge with a combination of metronidazole, amoxicillin and ciprofloxacin applied at different doses did not induce significant changes in process parameters, including the concentrations of volatile fatty acids (VFAs), or the total abundance of ARGs. Exposure to antibiotics significantly decreased methane production and modified microbial composition. The sequencing analysis revealed that the abundance of OTUs characteristic of Archaea was not correlated with the biogas production efficiency. The study also demonstrated that the hydrogen-dependent pathway of methylotrophic methanogenesis could significantly contribute to the stability of anaerobic digestion in the presence of antimicrobials. The greatest changes in microbial biodiversity were noted in substrate samples exposed to the highest dose of the tested antibiotics, relative to control. The widespread use of antimicrobials increases antibiotic concentrations in sewage sludge, which may decrease the efficiency of anaerobic digestion, and contribute to the spread of antibiotic resistance (AR).

Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov

Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224^T = DSM 112544^T), B. pongonis sp. nov. (64T4 = LMG 32281^T = DSM 112547^T), B. saguinibicoloris sp. nov. (79T10 = LMG 32232^T = DSM 112543^T), B. colobi sp. nov. (80T4 = LMG 32225^T = DSM 112552^T), B. simiiventris sp. nov. (81T8 = LMG 32226^T = DSM 112549^T), B. santillanense sp. nov. (82T1 = LMG 32284^T = DSM 112550^T), B. miconis sp. nov. (82T10 = LMG 32282^T = DSM 112551^T), B. amazonense sp. nov. (82T18 = LMG 32297^T = DSM 112548^T), pluvialisilvae sp. nov. (82T24 = LMG 32229^T = DSM 112545^T), and B. miconisargentati sp. nov. (82T25 = LMG 32283^T = DSM 112546^T) are proposed as novel Bifidobacterium species.

Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non‐human primates.

Assembly, Annotation, and Comparative Analysis of Bifidobacterial Genomes

Genome assembly and annotation are two of the key actions that must be undertaken in order to explore the genomic repertoire of (bifido)bacteria. The gathered information can be employed to genomically characterize a given microorganism, and can also be used to perform comparative genome analysis by including other sequenced (bifido)bacterial strains. Here, we highlight various bioinformatic programs able to manage next generation sequencing data starting from the assembly of a genome to the comparative analyses between strains.

Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut

The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host–microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.

Five novel bifidobacterial species isolated from faeces of primates in two Czech zoos: Bifidobacterium erythrocebi sp. nov., Bifidobacterium moraviense sp. nov., Bifidobacterium oedipodis sp. nov., Bifidobacterium olomucense sp. nov. and Bifidobacterium panos sp. nov

Five Bifidobacterium strains, VB23^T, VB24^T, VB25^T, VB26^T and VB31^T, were isolated from chimpanzee (Pan troglodytes), cotton-top tamarin (Saguinus oedipus), Goeldi's marmoset (Callimico goeldii), moustached tamarin (Saguinus mystax) and patas monkey (Erythrocebus patas), respectively, which were kept in two Czech zoos. These strains were isolated from faecal samples and were Gram-positive, non-motile, non-sporulating, anaerobic and fructose-6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA revealed close relatedness between VB23^T and Bifidobacterium angulatum LMG 11039^T (96.0 %), VB24^T and Bifidobacterium pullorum subsp. pullorum DSM 20433^T (96.1 %), VB25^T and Bifidobacterium goeldii LMG 30939^T (96.5 %), VB26^T and Bifidobacterium imperatoris LMG 30297^T (98.1 %), and VB31^T and B. angulatum LMG 11039^T (99.40 %). Internal transcribed spacer profiling revealed that VB23^T, VB24^T, VB25^T, VB26^T and VB31^T had highest similarity to Bifidobacterium breve LMG 13208^T (77.2 %), Bifidobacterium longum subsp. infantis ATCC 15697^T (85.8 %), Bifidobacterium biavatii DSM 23969^T (76.9 %), B. breve LMG 13208^T (81.2 %) and B. angulatum LMG 11039^T (88.2 %), respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses with their closest neighbours supported the independent phylogenetic positions of the strains with values between 86.3 and 94.3 % for ANI and 25.8 and 54.9 % for dDDH. These genomic and phylogenetic analyses suggested that the evaluated strains were novel Bifidobacterium species named Bifidobacterium erythrocebi sp. nov. (VB31^T=DSM 109960^T=CCUG 73843^T), Bifidobacterium moraviense sp. nov. (VB25^T=DSM 109958^T=CCUG 73842^T), Bifidobacterium oedipodis sp. nov. (VB24^T=DSM 109957^T=CCUG 73932^T), Bifidobacterium olomucense sp. nov. (VB26^T=DSM 109959^T=CCUG 73845^T) and Bifidobacterium panos sp. nov. (VB23^T=DSM 109963^T=CCUG 73840^T).

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.

Proposal of Bifidobacterium saeculare Biavati et al. 1992 as a later heterotypic synonym of Bifidobacterium gallinarum Watabe et al. 1983 and Bifidobacterium gallinarum subsp. saeculare subsp. nov

In 2018, Nouioui et al. transferred Bifidobacterium gallinarum and Bifidobacterium saeculare to Bifidobacterium pullorum as B. pullorum subsp. gallinarum and B. pullorum subsp. saeculare on the basis of digital DNA–DNA hybridization (dDDH) values. These two new subspecies were validated in the same year. However, we found that the genome (GenBank/ENA/DDBJ accession number JGZJ01000000) of B. pullorum used by Nouioui et al. in the dDDH analysis cannot represent B. pullorum . So, the taxonomic relationship between B. gallinarum , B. saeculare and B. pullorum should be re-examined. B. pullorum DSM 20433T had 88.7–89.0 % average nucleotide identity (ANI) values and 37.5–38.0 % dDDH values to the type strains of B. gallinarum and B. saeculare , respectively, less than the threshold for species demarcation, confirming that B. pullorum represents a different species from B. gallinarum and B. saeculare . The ANI values and dDDH values between the type strains of B. gallinarum and B. saeculare were 96.7–96.9 % and 73.0–73.3 %, respectively, greater than the threshold for species demarcation, confirming that they represent the same species. Relatively low dDDH values (less than the 79–80 % threshold for subspecies demarcation) between the type strains of B. gallinarum and B. saeculare indicated that B. saeculare can be considered as a subspecies of B. gallinarum . On the basis of the results presented here, (i) B. gallinarum and B. saeculare should not be transferred to B. pullorum ; (ii) we propose B. saeculare Biavati et al. 1992 as a later heterotypic synonym of B. gallinarum Watabe et al. 1983 and as a new subspecies of B. gallinarum , for which the name B. gallinarum subsp. saeculare subsp. nov. is proposed.

Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov

Three bifidobacterial Gram-stain-positive, non-spore forming and fructose-6-phosphate phosphoketolase-positive strains, SMA1^T, SMB2 and SMA15^T were isolated from the faeces of two adult males of the squirrel monkey (Saimiri sciureus). On the basis of 16S rRNA gene sequence similarities, the type strain of Bifidobacterium primatium DSM 100687^T (99.3%; similarity) was the closest neighbour to strains SMA1^T and SMB2, whereas the type strain of Bifidobacterium stellenboschense DSM 23968^T (96.5%) was the closest neighbour to strain SMA15^T. The average nucleotide identity (ANI) values of SMA1^T and SAM15^T with the closely related type strains were 93.7% and 88.1%, respectively. The in silico DNA‒DNA hybridization values with the closest neighbours were 53.1% and 36.9%, respectively. GC contents of strains SMA1^T and SMA15^T were 63.6 and 66.4 mol%, respectively. Based on the phylogenetic, genotypic and phenotypic data obtained, the strains SMA1^T and SMA15^T clearly represent two novel taxa within the genus Bifidobacterium for which the names Bifidobacterium saimiriisciurei sp. nov. (type strain SMA1^T = BCRC 81223^T = NBRC 114049^T = DSM 106020^T) and Bifidobacterium platyrrhinorum sp. nov. (type strain SMA15^T = BCRC 81224^T = NBRC 114051^T = DSM 106029^T) are proposed.

Evolutionary development and co-phylogeny of primate-associated bifidobacteria

In recent years, bifidobacterial populations in the gut of various monkey species have been assessed in several ecological surveys, unveiling a diverse, yet unexplored ecosystem harbouring novel species. In the current study, we investigated the species distribution of bifidobacteria present in 23 different species of primates, including human samples, by means of 16S rRNA microbial profiling and internal transcribed spacer bifidobacterial profiling. Based on the observed bifidobacterial-host co-phylogeny, we found a statistically significant correlation between the Hominidae family and particular bifidobacterial species isolated from humans, indicating phylosymbiosis between these lineages. Furthermore, phylogenetic and glycobiome analyses, based on 40 bifidobacterial species isolated from primates, revealed that members of the Bifidobacterium tissieri phylogenetic group, which are typical gut inhabitants of members of the Cebidae family, descend from an ancient ancestor with respect to other bifidobacterial taxa isolated from primates.

Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov

Two Bifidobacterium strains, i.e., 2176B^T and 2177B^T, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176B^T and 2177B^T exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139^T and Bifidobacterium bifidum LMG 11041^T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176B^T=LMG 31469^T=CCUG 73785^T) and Bifidobacterium leontopitheci sp. nov. (2177B^T=LMG 31471^T=CCUG 73786^T are proposed as novel Bifidobacterium species.

Bifidobacteria cell wall-derived exo-polysaccharides, lipoteichoic acids, peptidoglycans, polar lipids and proteins - their chemical structure and biological attributes

A variety of health benefits has been documented to be associated with the consumption of probiotic bacteria, namely bifidobacteria and lactobacilli. Thanks to the scientific advances in recent years we are beginning to understand the molecular mechanisms by which bacteria in general and probiotic bacteria in particular act as host physiology and immune system modulators. More recently, the focus has shifted from live bacteria towards bacteria-derived defined molecules, so called postbiotics. These molecules may represent safer alternative compared to the live bacteria while retaining the desired effects on the host. The excellent source of effector macromolecules is the bacterial envelope. It contains compounds that are pivotal in the adhesion phenomenon, provide direct bacteria-to-host signaling capacity and the associated physiological impact and immunomodulatory properties of bacteria. Here we comprehensively review the structure and biological role of Bifidobacterium surface and cell wall molecules: exopolysaccharides, cell wall polysaccharides, lipoteichoic acids, polar lipids, peptidoglycans and proteins. We discuss their involvement in direct signaling to the host cells and their described immunomodulatory effects.

Varied Pathways of Infant Gut-Associated Bifidobacterium to Assimilate Human Milk Oligosaccharides: Prevalence of the Gene Set and Its Correlation with Bifidobacteria-Rich Microbiota Formation

The infant's gut microbiome is generally rich in the Bifidobacterium genus. The mother's milk contains natural prebiotics, called human milk oligosaccharides (HMOs), as the third most abundant solid component after lactose and lipids, and of the different gut microbes, infant gut-associated bifidobacteria are the most efficient in assimilating HMOs. Indeed, the fecal concentration of HMOs was found to be negatively correlated with the fecal abundance of Bifidobacterium in infants. Given these results, two HMO molecules, 2'-fucosyllactose and lacto-N-neotetraose, have recently been industrialized to fortify formula milk. As of now, however, our knowledge about the HMO consumption pathways in infant gut-associated bifidobacteria is still incomplete. The recent studies indicate that HMO assimilation abilities significantly vary among different Bifidobacterium species and strains. Therefore, to truly maximize the effects of prebiotic and probiotic supplementation in commercialized formula, we need to understand HMO consumption behaviors of bifidobacteria in more detail. In this review, we summarized how different Bifidobacterium species/strains are equipped with varied gene sets required for HMO assimilation. We then examined the correlation between the abundance of the HMO-related genes and bifidobacteria-rich microbiota formation in the infant gut through data mining analysis of a deposited fecal microbiome shotgun sequencing dataset. Finally, we shortly described future perspectives on HMO-related studies.

Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches

Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples. A combination of in silico analyses based on nucleotide and protein sequences facilitate the identification of genetic material belonging to putative novel species. Consequently, the prediction of metabolic properties by in silico analyses permits the identification of specific substrates that are then employed to isolate these species through a cultivation method.

A comparative study of gut microbiomes in captive nocturnal strepsirrhines

Feeding strategy and diet are increasingly recognized for their roles in governing primate gut microbiome (GMB) composition. Whereas feeding strategy reflects evolutionary adaptations to a host's environment, diet is a more proximate measure of food intake. Host phylogeny, which is intertwined with feeding strategy, is an additional, and often confounding factor that shapes GMBs across host lineages. Nocturnal strepsirrhines are an intriguing and underutilized group in which to examine the links between these three factors and GMB composition. Here, we compare GMB composition in four species of captive, nocturnal strepsirrhines with varying feeding strategies and phylogenetic relationships, but nearly identical diets. We use 16S rRNA sequences to determine gut bacterial composition. Despite similar husbandry conditions, including diet, we find that GMB composition varies significantly across host species and is linked to host feeding strategy and phylogeny. The GMBs of the omnivorous and the frugivorous species were significantly more diverse than were those of the insectivorous and exudativorous species. Across all hosts, GMBs were enriched for bacterial taxa associated with the macronutrient resources linked to the host's respective feeding strategy. Ultimately, the reported variation in microbiome composition suggests that the impacts of captivity and concurrent diet do not overshadow patterns of feeding strategy and phylogeny. As our understanding of primate GMBs progresses, populations of captive primates can provide insight into the evolution of host-microbe relationships, as well as inform future captive management protocols that enhance primate health and conservation.

Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera

The family Bifidobacteriaceae constitutes an important phylogenetic group that particularly includes bifidobacterial taxa demonstrating proven or debated positive effects on host health. The increasingly widespread application of probiotic cultures in the twenty-first century requires detailed classification to the level of particular strains. This study aimed to apply the glutamine synthetase class I (glnAI) gene region (717 bp representing approximately 50% of the entire gene sequence) using specific PCR primers for the classification, typing, and phylogenetic analysis of bifidobacteria and closely related scardovial genera. In the family Bifidobacteriaceae, this is the first report on the use of this gene for such purposes. To achieve high-value results, almost all valid Bifidobacteriaceae type strains (75) and 15 strains isolated from various environments were evaluated. The threshold value of the glnAI gene identity among Bifidobacterium species (86.9%) was comparable to that of other phylogenetic/identification markers proposed for bifidobacteria and was much lower compared to the 16S rRNA gene. Further statistical and phylogenetic analyses suggest that the glnAI gene can be applied as a novel genetic marker in the classification, genotyping, and phylogenetic analysis of isolates belonging to the family Bifidobacteriaceae.

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.

Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov

Five Bifidobacterium strains, i.e. 2020B^T, 2028B^T, 2033B^T, 2034B^T and 2036B^T, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020B^T, 2028B^T, 2033B^T, 2034B^T and 2036B^T exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969^T, Bifidobacterium bifidum LMG 11041^T, Bifidobacterium choerinum LMG 10510^T, Bifidobacterium gallicum LMG 11596^T, Bifidobacterium imperatoris LMG 30297^T, Bifidobacterium italicum LMG 30187^T and Bifidobacterium vansinderenii LMG 30126^T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020B^T=LMG 30937^T=CCUG 72816^T), Bifidobacterium callimiconis sp. nov. (2028B^T=LMG 30938^T=CCUG 72814^T), Bifidobacterium samirii sp. nov. (2033B^T=LMG 30940^T=CCUG 72817^T), Bifidobacterium goeldii sp. nov. (2034B^T=LMG 30939^T=CCUG 72815^T) and Bifidobacterium dolichotidis sp. nov. (2036B^T=LMG 30941^T=CCUG 72818^T) are proposed as novel Bifidobacterium species.

Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov

Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189^T=CCUG 70960^T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188^T=CCUG 70962^T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297^T=CCUG 70961^T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187^T=CCUG 70963^T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296^T=CCUG 70959^T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295^T=CCUG 70964^T) are proposed as novel Bifidobacterium species.

Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach

For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus Bifidobacterium by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria.IMPORTANCE Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.

Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species

Bifidobacterium sp. strains TRE 1, TRE D, TRE H, and TRI 7 were isolated from two tamarins housed in Parco Natura Viva, Garda Zoological Park S.r.l. (Bussolengo, Verona, Italy). These strains belong to four putative novel species of the genus Bifidobacterium. The genome sizes were 2.7 Mb for TRE 1, 2.7 Mb for TRE D, 2.4 Mb for TRE H, and 2.7 Mb for TRI 7. The average GC contents were 63.18% for TRE 1, 58.27% for TRE D, 57.11% for TRE H, and 63.79% for TRI 7.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.

Assessment of Bifidobacterium Species Using groEL Gene on the Basis of Illumina MiSeq High-Throughput Sequencing

The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut’s microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far. The results showed that the novel designed primer set can specifically differentiate Bifidobacterium species from non-bifidobacteria, and as low as 10⁴ cells of Bifidobacterium species can be detected using the novel designed primer set on the basis of Illumina Miseq high-throughput sequencing. We also developed a novel protocol to assess the diversity of Bifidobacterium species in both human and rat feces through high-throughput sequencing technologies using groEL gene as a discriminative marker.

Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator)

Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5^T was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5^T was closely related to Bifidobacterium saguini DSM 23967^T (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213^T (hsp60 94.1 %), Bifidobacterium saguini DSM 23967^T (clpC 91 %), Bifidobacterium avesanii DSM 100685^T (dnaG 80.3 %), Bifidobacterium longumsubsp. infantis ATCC 15697^T (dnaJ 85.3 %) and Bifidobacterium longumsubsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising l-Orn (Lys) - l-Ser - l-Ala - l-Thr - l-Ala. The DNA G+C content of strain TRI 5^T was 60.9 mol%. Based on the data provided, strain TRI 5^T represents a novel species of the genus Bifidobacterium for which the name Bifidobacteriumcallitrichidarum sp. nov. is proposed. The type strain is TRI 5^T (=DSM 103152^T=JCM 31790^T).