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The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.

Recent pandemic infection caused by SARS-CoV-2 (COVID-19) led the scientific community to investigate the possible causes contributing to the physiopathology of this disease. In this context, analyses of the intestinal microbiota highlighted possible correlation between host-associated bacterial communities and development of the COVID-19. Nevertheless, a detailed investigation of the role of the human microbiota in the severity of the symptoms of this disease is still lacking. This study performed a comprehensive meta-analysis of 323 faecal samples from public and novel Italian data sets based on the shotgun metagenomic approach. In detail, the comparative analyses revealed possible differences in the microbial biodiversity related to the individual health status, highlighting a species richness decrease in COVID-19 patients with a severe prognosis. Moreover, healthy subjects resulted characterized by a higher abundance of protective and health-supporting bacterial species, while patients affected by COVID-19 disease displayed a significant increase of opportunistic pathogen bacteria involved in developing putrefactive dysbiosis. Furthermore, prediction of the microbiome functional capabilities suggested that individuals affected by COVID-19 subsist in an unbalanced metabolism characterized by an overrepresentation of enzymes involved in the protein metabolism at the expense of carbohydrates oriented pathways, which can impact on disease severity and in excessive systemic inflammation.

During infancy, gut microbiota development is a crucial process involved in the establishment of microbe–host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.

BackgroundInfants are frequently exposed to antibiotics (AB) in the first week of life for suspected bacterial infections. Little is known about the effect of AB on the developing intestinal microbiota. Therefore, we studied intestinal microbiota development with and without AB exposure in the first week of life in term born infants.MethodsWe analysed the faecal microbiota from birth until 2.5 years of age by 16S rRNA gene amplicon sequencing in a cohort with 56 term born infants, exposed to AB in the first week of life (AB+) (AB for 2–3 days (AB2, n=20), AB for 7 days (AB7, n=36)), compared with 126 healthy controls (AB-). The effects of AB and duration were examined in relation to delivery and feeding mode.ResultsAB+ was associated with significantly increased relative abundance ofEnterobacteriaceaeat 3 weeks and 1 year and a decrease ofBifidobacteriaceae, from 1 week until 3 months of age only in vaginally delivered, but not in C-section born infants. Similar deviations were noted in AB7, but not in AB2. After AB, breastfed infants had lower relative abundance of potentially pathogenicEnterobacteriaceaecompared with formula fed infants and recovered 2 weeks faster towards controls.ConclusionsAB exposure in the first week of life alters faecal microbiota development with deviations in the relative abundance of individual taxa until 1 year of age. These alterations can have long-term health consequences, which emphasises the need for future studies aiming at restoring intestinal microbiota after AB administration.

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.

Bifidobacteria have been shown to produce exopolysaccharides (EPS), which are polymeric structures composed of various carbohydrates, commonly containing glucose, galactose, and rhamnose. EPS are produced by different bifidobacterial taxa commonly identified in the human gut, such as Bifidobacterium breve and Bifidobacterium longum subsp. longum, and have been suggested to modulate the interaction of bifidobacterial cells with other members of the human gut microbiota as well as with their host. In this study, we evaluated if bifidobacterial EPS production of four selected EPS-producing strains is associated with enhanced resistance to antibiotic treatments through MIC analysis when compared to bacterial cultures that do not produce exopolysaccharides. Our results showed that an increase in EPS production by modifying the growth medium with different carbon sources, i.e. glucose, galactose or lactose and/or by applying stressful conditions, such as bile salts and acidity, is associated with a tolerance enhancement of bifidobacterial cells toward various beta-lactam antibiotics. In addition, after analyzing the production of EPS at the phenotypic level, we explored the genes involved in the production of these structures and evaluated their expression, in presence of various carbon sources, using RNAseq. Overall, this study provides preliminary experimental evidence showing how bifidobacterial EPS modifies the level of susceptibility of these bacteria towards antibiotics.

The Protected Designation of Origin (PDO) guarantees the traceability of food production processes, and that the production takes place in a well-defined restricted geographical area. Nevertheless, the organoleptic qualities of the same dairy products, i.e., cheeses under the same PDO denomination, differ between manufacturers.

Background The correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut microbiota as a main driver of the health status of athletes. In addition, it has been postulated that the metabolic activity of the microbial population harbored by the large intestine of athletes might influence their physical performances. Here, we analyzed 418 publicly available shotgun metagenomics datasets obtained from fecal samples of healthy athletes and healthy sedentary adults. Results This study evidenced how agonistic physical activity and related lifestyle can be associated with the modulation of the gut microbiota composition, inducing modifications of the taxonomic profiles with an enhancement of gut microbes able to produce short-fatty acid (SCFAs). In addition, our analyses revealed a correlation between specific bacterial species and high impact biological synthases (HIBSs) responsible for the generation of a range of microbially driven compounds such vitamin B12, amino acidic derivatives, and other molecules linked to cardiovascular and age-related health-risk reduction. Conclusions Notably, our findings show how subsist an association between competitive athletes, and modulation of the gut microbiota, and how this modulation is reflected in the potential production of microbial metabolites that can lead to beneficial effects on human physical performance and health conditions.

Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.

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., We thank GenProbio srl for the financial support of the Laboratory of Probiogenomics. Part of this research is conducted using the High Performance Computing (HPC) facility of the University of Parma. D.v.S. is a member of The APC Microbiome Institute funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan (Grant numbers SFI/12/RC/2273a and SFI/12/RC/2273b). This work was financially supported by a PostDoc fellowship (Bando Ricerca Finalizzata) to G.A. F.T. is funded by Italian Ministry of Health through the Bando Ricerca Finalizzata (Grant Number GR-2018-12365988).

The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.

From birth to adulthood, the human gut-associated microbial communities experience profound changes in their structure. However, while the taxonomical composition has been extensively explored, temporal shifts in the microbial metabolic functionalities related to the metabolism of bioactive small molecules are still largely unexplored. Here, we collected a total of 6,617 publicly available human fecal shotgun metagenomes and 42 metatranscriptomes from infants and adults to explore the dynamic changes of the microbial-derived small molecule metabolisms according to the age-related development of the human gut microbiome. Moreover, by selecting metagenomic data from 250 breastfed and 217 formula-fed infants, we also investigated how feeding types can shape the metabolic functionality of the incipient gut microbiome. From the small molecule metabolism perspective, our findings suggested that the human gut microbial communities are genetically equipped and prepared to metabolically evolve toward the adult state as early as 1 month after birth, although at the age of 4 years, it still appeared functionally underdeveloped compared to adults. Furthermore, in respect of formula-fed newborns, breastfed infants showed enrichment in microbial metabolic functions related to specific amino acids present at low concentrations in human milk, highlighting that the infant gut microbiome has specifically evolved to synthesize bioactive molecules that can complement the human breast milk composition contributing to complete nutritional supply of infant.

The recent COVID-19 pandemic prompted a rapid-growing interest in the investigation of the human microbiota of the upper airways. In fact, the resident microbial community of this body district may have an influence on the onset of SARS-CoV-2 infection and its clinical course in terms of presence, symptom severity, and outcomes. However, several microbiological methodologies are available to study the human microbiota, reflecting the extensive fragmentation of methodological approaches. We investigate the impact of two critical steps that can induce biases in the downstream analyses, i.e. sampling method and microbial DNA extraction kit employed. We observed major discrepancies regarding the total amount of prokaryotic DNA that could be retrieved from a biological sample and the proportion between bacterial DNA and human host DNA. Moreover, shotgun DNA sequencing and taxonomic profile reconstruction also revealed correlations between sampling methods and the procedures applied for microbial DNA extraction. Based on all the data collected in this study, we formulate indications regarding the most efficient and reliable methodological procedures for the metagenomic analyses of the upper airways' microbiota to maximize accuracy and reproducibility.

Bifidobacterium asteroides is considered the ancestor of the genus Bifidobacterium, which has evolved in close touch with the hindgut of social insects. However, recent studies revealed high intraspecies biodiversity within this taxon, uncovering the putative existence of multiple bifidobacterial species, thus, suggesting its reclassification. Here, a genomic investigation of 98 B. asteroides-related genomes retrieved from public repositories and reconstructed from metagenomes of the hindgut of Apis mellifera and Apis cerana was performed to shed light on the genetic variability of this taxon. Phylogenetic and genomic analyses revealed the existence of eight clusters, of which five have been recently characterized with a representative type strain of the genus and three were represented by putative novel bifidobacterial species inhabiting the honeybee gut. Then, the dissection of 366 shotgun metagenomes of honeybee guts revealed a pattern of seven B. asteroides-related taxa within A. mellifera that co-exist with the host, while A. cerana microbiome was characterized by the predominance of one of the novel species erroneously classified as B. asteroides. A further glycobiome analysis unveiled a conserved repertoire of glycosyl hydrolases (GHs) reflecting degradative abilities towards a broad range of simple carbohydrates together with genes encoding specific GHs of each B. asteroides-related taxa.

This manuscript provides a general overview about the future avenues of research in the field of microbiota., Summary The human gut microbiota is involved in multiple health‐influencing host interactions during the host’s entire life span. Microbes colonize the infant gut instantaneously after birth and subsequently the founding and interactive progress of this early gut microbiota is considered to be driven and modulated by different host‐ and microbe‐associated forces. A rising number of studies propose that the composition of the human gut microbiota in the early stages of life impact on the human health conditions at later stages of life. This notion has powered research aimed at detailed investigations of the infant gut microbiota composition. Nevertheless, the molecular mechanisms supporting the gut microbiome functionality and the interaction of the early gut microbes with the human host remain largely unknown.

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., Joint Programming Initiative A healthy diet for a healthy life. Grant Number: 15/JP‐HDHL/3280. Science Foundation Ireland. Grant Numbers: SFI/12/RC/2273a, SFI/12/RC/2273b

TwoBifidobacteriumstrains, i.e., 2176BTand 2177BT, 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 andd-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (includinghsp60,rpoB,dnaJ,dnaG andclpC genes) and the core genome revealed that bifidobacterial strains 2176BTand 2177BTexhibit close phylogenetic relatedness toBifidobacterium felsineumDSM 103139TandBifidobacterium bifidumLMG 11041T, 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 recognizedBifidobacteriumspecies. Thus,Bifidobacterium cebidarumsp. nov. (2176BT=LMG 31469T=CCUG 73785T) andBifidobacterium leontopithecisp. nov. (2177BT=LMG 31471T=CCUG 73786Tare proposed as novelBifidobacteriumspecies.

Emerging evidence has shown an association between the composition of intestinal microbial communities and host physical activity, suggesting that modifications of the gut microbiota composition may support training, performance, and post-exercise recovery of the host. Nevertheless, investigation of differences in the gut microbiota between athletes and individuals with reduced physical activity is still lacking. In this study, we performed a meta-analysis of 207 publicly available shotgun metagenomics sequencing data of fecal samples from athletes and healthy non-athletes. Accordingly, analysis of species-level fecal microbial profiles revealed three recurring compositional patterns, named HPC1 to 3, that characterize the host based on their commitment to physical activity. Interestingly, the gut microbiome of athletes showed a higher abundance of anti-inflammatory, health-promoting bacteria than that of non-athletic individuals. Moreover, the bacterial species profiled in the gut of professional athletes are short-fatty acid producers, which potentially improve energy production, and therefore sports performances. Intriguingly, microbial interaction network analyses suggested that exercise-induced microbiota adaptation involves the whole microbial community structure, resulting in a complex microbe-microbe interplay driven by positive relationships among the predicted butyrate-producing community members.

The Human Respiratory Tract (HRT) is colonized by various microbial taxa, known as HRT microbiota, in a manner that is indicative of mutualistic interaction between such microorganisms and their host.To investigate the microbial composition of the HRT and its possible correlation with the different compartments of the respiratory tract.In the current study, we performed an in-depth meta-analysis of 849 HRT samples from public shotgun metagenomic datasets obtained through several distinct collection methods.The statistical robustness provided by this meta-analysis allowed the identification of 13 possible HRT-specific Community State Types (CSTs), which appear to be specific to each anatomical region of the respiratory tract. Furthermore, functional characterization of the metagenomic datasets revealed specific microbial metabolic features correlating with the different compartments of the respiratory tract.The meta-analysis here performed suggested that the variable presence of certain bacterial species seems to be linked to a location-related abundance gradient in the HRT and seems to be characterized by a specific microbial metabolic capability.

In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the “infant-like” gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.

Background: The World Health Organization defines probiotics as “live microorganisms, which when administered in adequate amounts confer a health benefit on the host”. In this framework, probiotic strains should be regarded as safe for human and animal consumption, i.e., they should possess the GRAS (generally recognized as safe) status, notified by the local authorities. Consistently, strains of selected Bifidobacterium species are extensively used as probiotic agents to prevent and ameliorate a broad spectrum of human and/or animal gastrointestinal disorders. Even though probiotic properties are often genus- or species-associated, strain-level differences in the genetic features conferring individual probiotic properties to commercialized bifidobacterial strains have not been investigated in detail. Methods: In this study, we built a genomic database named Integrated Probiotic DataBase (IPDB), whose first iteration consists of common bifidobacterial strains used in probiotic products for which public genome sequences were available, such as members of B. longum subsp. longum, B. longum subsp. infantis, B. bifidum, B. breve, and B. animalis subsp. lactis taxa. Furthermore, the IPDB was exploited to perform comparative genome analyses focused on genetic factors conferring structural, functional, and chemical features predicted to be involved in microbe-host and microbe-microbe interactions. Results and conclusion: Our analyses revealed strain-level genetic differences, underlining the importance of inspecting the strain-specific and outcome-specific efficacy of probiotics. In this context, IPDB represents a valuable resource for obtaining genetic information of well-established bifidobacterial probiotic strains.

The reconstruction of microbial genome sequences by bioinformatic pipelines and the consequent functional annotation of their genes’ repertoire are fundamental activities aiming at unveiling their biological mechanisms, such as metabolism, virulence factors, and antimicrobial resistances. Here, we describe the development of the MEGAnnotator2 pipeline able to manage all next-generation sequencing methodologies producing short- and long-read DNA sequences. Starting from raw sequencing data, the updated pipeline can manage multiple analyses leading to the assembly of high-quality genome sequences and the functional classification of their genetic repertoire, providing the user with a useful report constituting features and statistics related to the microbial genome. The updated pipeline is fully automated from the installation to the delivery of the output, thus requiring minimal bioinformatics knowledge to be executed.

Probiotic bacteria are widely administered as dietary supplements and incorporated as active ingredients in a variety of functional foods due to their purported health-promoting features. Currently available probiotic products may have issues with regards to their formulation, such as insufficient levels of viable probiotic bacteria, complete lack of probiotic strains that are stated to be present in the product, and the presence of microbial contaminants. To avoid the distribution of such unsuitable or misleading products, we propose here a novel approach named Probiotic Identity Card (PIC), involving a combination of shotgun metagenomic sequencing and bacterial cell enumeration by flow cytometry. PIC was tested on 12 commercial probiotic supplements revealing several inconsistencies in the formulation of five such products based on their stated microbial composition and viability.

Culture-independent approaches now represent the gold standard for the investigation of both environmental and host-associated complex microbial communities. Nevertheless, despite the great advantages offered by these novel methodologies based on the use of next-generation DNA sequencing approaches, a number of bias sources have been identified. Among the latter, free DNA contained in biological matrices is one of the main sources of inaccuracy in reconstructing the resident microbial population of viable cells. For this reason, the photoreactive DNA-binding dye propidium monoazide (PMAxx™) has been developed by improving standard PMA. This compound binds and inactivates free DNA, thus preventing its amplification and sequencing. While the performances of PMA have been previously investigated, the efficiency with PMAxx™ has been tested mainly for amplicon-based profiling approaches on a limited number of biological matrices. In this study, we validated the performance of PMAxx™ for shotgun metagenomics approaches employing various human-associated matrices. Notably, results revealed that the effectiveness of PMAxx™ in inactivating free DNA of prokaryotes and eukaryotes tends to vary significantly based on the biological matrices analyzed.

Bifidobacterium bifidum is reported to be among the first colonizers of the newborn's gastrointestinal tract due to its ability to metabolize human milk oligosaccharides (HMOs). In order to investigate biological features that allow this bifidobacterial species to colonize a newborn, bifidobacterial internally transcribed spacer profiling of stool samples of 50 mother-infant dyads, as well as corresponding breastmilk samples, was performed. Hierarchical clustering based on bifidobacterial population profiles found in infant faecal samples revealed the presence of four bifidobacterial clusters or the so-called bifidotypes. Bifidobacterium bifidum was shown to be a key member among bifidotypes, in which its presence correlate with several different bifidobacterial species retrieved in infant faecal samples. For this reason, we investigated cross-feeding behaviour facilitated by B. bifidum on a bioreactor model using human milk as growth substrate. Transcriptional profiles of this strain were evaluated when grown on nine specific glycans typically constituting HMOs. Remarkably, these analyses suggest extensive co-evolution with the host and other bifidobacterial species in terms of resource provision and sharing, respectively, activities that appear to support a bifidobacteria-dominant microbiome.

Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, 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 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, 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. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.

Health promoting or probiotic bacteria are commonly incorporated into a variety of functional foods and drug formulations, due to their purported ability to confer benefit to host health. Despite the extensive commercial exploitation of probiotic formulations there are still major knowledge gaps regarding the precise molecular mechanism of action and corresponding genetic/genomic properties of probiotic bacteria. In the current study, we describe a metagenomic approach which allows determination of the composition of probiotic supplements through next-generation sequencing analyses based on rRNA-associated sequences to assess bacterial composition of the product combined with a shotgun metagenomics approach directed to decode the genome sequences of the probiotic strains for each product assayed. The here developed approach has been tested for 10 probiotic supplements, revealing inconsistencies between the identified probiotic strains and the declared strains as indicated by the producers. Furthermore, the decoded bacterial genome sequence of Bifidobacterium animalis subsp. lactis BB-12 from a 1995 frozen dried stock revealed genetic evidence for genome evolution and stability of this microorganism when compared with the re-constructed genome of the identical strain from a probiotic supplement of 2017.

Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.

Members of the Bifidobacterium longum species have been shown to possess adaptive abilities to allow colonization of different mammalian hosts, including humans, primates and domesticated mammalian species, such as dogs, horses, cattle and pigs. To date, three subspecies have formally been recognized to belong to this bifidobacterial taxon, i.e. B. longum subsp. longum , B. longum subsp. infantis and B. longum subsp. suis . Although B. longum subsp. longum is widely distributed in the human gut irrespective of host age, B. longum subsp. infantis appears to play a significant role as a prominent member of the gut microbiota of breast-fed infants. Nevertheless, despite the considerable scientific relevance of these taxa and the vast body of genomic data now available, an accurate dissection of the genetic features that comprehensively characterize the B. longum species and its subspecies is still missing. In the current study, we employed 261 publicly available B. longum genome sequences, combined with those of 11 new isolates, to investigate genomic diversity of this taxon through comparative genomic and phylogenomic approaches. These analyses allowed us to highlight a remarkable intra-species genetic and physiological diversity. Notably, characterization of the genome content of members of B. longum subsp. infantis subspecies suggested that this taxon may have acquired genetic features for increased competitiveness in the gut environment of suckling hosts. Furthermore, specific B. longum subsp. infantis genomic features appear to be responsible for enhanced horizontal gene transfer (HGT) occurrences, underpinning an intriguing dedication toward acquisition of foreign DNA by HGT events.

Current scientific literature has identified the infant gut microbiota as a multifaceted organ influencing a range of aspects of host-health and development. Many scientific studies have focused on characterizing the main microbial taxa that constitute the resident bacterial population of the infant gut. This has generated a wealth of information on the bacterial composition of the infant gut microbiota, and on the functional role/s exerted by their key microbial members. In this context, one of the most prevalent, abundant and investigated microbial taxon in the human infant gut is the genus Bifidobacterium, due to the purported beneficial activities is bestows upon its host. This review discusses the most recent findings regarding the infant gut microbiota with a particular focus on the molecular mechanisms by which bifidobacteria impact on host health and well-being.

In recent decades, infants' gut microbiota has aroused constant scientific interest, primarily due to early‐ and long‐term repercussions on the host health. In this context, nutritional challenges such as those found in less developed countries can influence infants' gut microbiota development, thus generating potentially critical health outcomes. However, comprehensive investigations regarding species‐level differences in the infant gut microbiota's composition between urbanized and rural countries are still missing. In this study, 16S rRNA and Shallow Shotgun metagenomics sequencing were exploited to dissect the microbial community's species‐level composition of 11 faecal samples collected from infants living in a semi‐urban area of Sub‐Saharan Africa, i.e. Côte d'Ivoire. Moreover, the generated data were coupled with those retrieved from public available metagenomic repositories, including two rural communities and 13 urban communities of industrialized countries. The meta‐analysis led to the identification of Infant Species Community States Type (ISCSTs) and microbial species covariances, which were exploited to reveal key signatures of infants living in rural and semi‐urban societies. Remarkably, analysis of rural and semi‐urban datasets revealed shifts from ISCSTs prevalent in urbanized populations with putative health implications. Thus, indicating the need for population‐wide investigations aimed to define the factors determining such potentially harmful gut microbial communities' signatures.

The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxon composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results, we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated 15 L. crispatus strains from different environments in which this species abounds, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study revealed a genetic adaptation of strains to their respective ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains, together with a synthetic vaginal microbiota, reveal how this species is able to modulate the composition of the vaginal microbial consortia at the strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. IMPORTANCE The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus strains is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genomes of new L. crispatus strains from different environments, and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.

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.

Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.

Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.

Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.

Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.

Members of the genus Lactobacillus represent the most common colonizers of the human vagina and are well-known for preserving vaginal health and contrasting the colonization of opportunistic pathogens. Remarkably, high abundance of Lactobacillus crispatus in the vaginal environment has been linked to vaginal health, leading to the widespread use of many L. crispatus strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of L. crispatus taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 L. crispatus strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the L. crispatus pan-genome and core-genome followed by a comprehensive phylogenetic analysis based on the predicted core genes that revealed clustering based on ecological origin. Subsequently, a genomics-targeted approach, i.e., probiogenomics analysis, was applied for in-depth analysis of the eight L. crispatus strains of human origin sequenced in this study. In detail their genetic repertoire was screened for strain-specific genes responsible for phenotypic features that may guide the identification of optimal candidates for next-generation probiotics. The latter includes bacteriocin production, carbohydrates transport and metabolism, as well as a range of features that may be responsible for improved ecological fitness. In silico results regarding the genetic repertoire involved in carbohydrate metabolism were also validated by growth assays on a range of sugars, leading to the selection of putative novel probiotic strains.

The gut microbiota could influence the pathophysiology of age-related sarcopenia through multiple mechanisms implying modulation of chronic inflammation and anabolic resistance. The aim of this study was to compare the fecal microbiota composition and functionality, assessed by shotgun metagenomics sequencing, between two groups of elderly outpatients, differing only for the presence of primary sarcopenia. Five sarcopenic elderly subjects and twelve non-sarcopenic controls, classified according to lower limb function and bioimpedance-derived skeletal muscle index, provided a stool sample, which was analyzed with shotgun metagenomics approaches, to determine the overall microbiota composition, the representation of bacteria at the species level, and the prediction of bacterial genes involved in functional metabolic pathways. Sarcopenic subjects displayed different fecal microbiota compositions at the species level, with significant depletion of two species known for their metabolic capacity of producing short-chain fatty acids (SCFAs), Faecalibacterium prausnitzii and Roseburia inulinivorans, and of Alistipes shahii. Additionally, their fecal metagenome had different representation of genes belonging to 108 metabolic pathways, namely, depletion of genes involved in SCFA synthesis, carotenoid and isoflavone biotransformation, and amino acid interconversion. These results support the hypothesis of an association between microbiota and sarcopenia, indicating novel possible mediators, whose clinical relevance should be investigated in future studies.

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.

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.

Two

This work was supported by EU/EFPIA/Innovative Medicines Initiative Joint Undertaking PRECISESADS grant No. 115565.

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 32224T = DSM 112544T), B. pongonis sp. nov. (64T4 = LMG 32281T = DSM 112547T), B. saguinibicoloris sp. nov. (79T10 = LMG 32232T = DSM 112543T), B. colobi sp. nov. (80T4 = LMG 32225T = DSM 112552T), B. simiiventris sp. nov. (81T8 = LMG 32226T = DSM 112549T), B. santillanense sp. nov. (82T1 = LMG 32284T = DSM 112550T), B. miconis sp. nov. (82T10 = LMG 32282T = DSM 112551T), B. amazonense sp. nov. (82T18 = LMG 32297T = DSM 112548T), pluvialisilvae sp. nov. (82T24 = LMG 32229T = DSM 112545T), and B. miconisargentati sp. nov. (82T25 = LMG 32283T = DSM 112546T) are proposed as novel Bifidobacterium species.

Summary Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors, and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was employed here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens. In silico analysis revealed the presence of a core microbiota that is typical of those animals that live in different geographical areas and that have limited contact with humans. Anthropic influences guide the metabolic potential and the presence of antibiotic resistance genes of these different bacterial communities. Culturomics attempts, based on different cultivation conditions, were applied to reconstruct in vitro the microbiota of feral chickens. A unique strain collection representing members of the four major phyla of the poultry microbiota was assembled, including bacterial strains that are not typically retrieved from the chicken gut. This article is protected by copyright. All rights reserved.

A novel Bifidobacterium strain, Tam10BT, i.e. LMG 30126T, was isolated from emperor tamarin (Saguinus imperator). Cells were Gram-positive, non-motile, non-sporulating, non-haemolytic, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that Bifidobacterium Tam10BT exhibited close phylogenetic relatedness to Bifidobacterium tissieri DSM 100201T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B. tissieri DSM 100201T (96.5 %). Furthermore, genotyping based on the genome sequence of Tam 10B, in combination with phenotypic analyses, clearly showed that strain Tam10BT is distinct from each of the type strains of the so far recognized Bifidobacterium species. The type strain Tam10BT (=LMG 30126T=CCUG 70655T) represents a novel species, for which the name Bifidobacterium vansinderenii sp. nov is proposed.

Contamination of food by chemicals or pathogenic bacteria may cause particular illnesses that are linked to food consumption, commonly referred to as foodborne diseases. Bacteria are present in/on various foods products, such as fruits, vegetables and ready-to-eat products. Bacteria that cause foodborne diseases are known as foodborne pathogens (FBPs). Accurate detection methods that are able to reveal the presence of FBPs in food matrices are in constant demand, in order to ensure safe foods with a minimal risk of causing foodborne diseases. Here, a multiplex PCR-based Illumina sequencing method for FBP detection in food matrices was developed. Starting from 25 bacterial targets and 49 selected PCR primer pairs, a primer collection called foodborne pathogen - panel (FPP) consisting of 12 oligonucleotide pairs was developed. The FPP allows a more rapid and reliable identification of FBPs compared to classical cultivation methods. Furthermore, FPP permits sensitive and specific FBP detection in about two days from food sample acquisition to bioinformatics-based identification. The FPP is able to simultaneously identify eight different bacterial pathogens, i.e. Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Salmonella enterica subsp. enterica serovar enteritidis, Escherichia coli, Shigella sonnei, Staphylococcus aureus and Yersinia enterocolitica, in a given food matrix at a threshold contamination level of 101cell/g. Moreover, this novel detection method may represent an alternative and/or a complementary approach to PCR-based techniques, which are routinely used for FBP detection, and could be implemented in (parts of) the food chain as a quality check.

Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species. The collected profiles revealed the presence of 89 putative novel bifidobacterial taxa in addition to 45 previously described species. Remarkably, in contrast to what is currently known for many gut commensals, we did not observe host-specialization among bifidobacterial species but rather their widespread distribution across mammals. Moreover, ITS rRNA profiling of wild relatives of domesticated dogs, rabbits and pigs clearly indicates that domestication and close contact with humans have impacted on the composition of the fecal bifidobacterial population. These data were complemented by analysis of bifidobacterial communities in milk of eight mammalian families, showing that bifidobacteria represent prototypical early gut microbiota members which are inherited by newborns from their lactating mother. Thus this study highlights the role of bifidobacteria as pioneering gut colonizers of a wide range of mammals.

Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals). Assessment of the retrieved taxonomic profiles allowed the most updated reconstruction of the global core-microbiome as based on currently available data, as well as the identification and targeted genome reconstruction of bacterial taxa that appear to have been lost and/or acquired during urbanization/industrialization. Functional characterization of these metagenomic datasets indicates that the urbanization/industrialization process which occurred in recent human history has shaped the gut microbiota through the acquisition and/or loss of specific gut microbes, thereby potentially impacting on the overall functionality of the gut microbiome.

Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut., This work was primarily funded by the EU Joint Programming Initiative – A Healthy Diet for a Healthy Life (JPI HDHL, http://www.healthydietforhealthylife.eu/) to DvS (in conjunction with Science Foundation Ireland [SFI], Grant number 15/JP-HDHL/3280) and to MV (in conjunction with MIUR, Italy). D.v.S. is member of APC microbiome Ireland which is funded by SFI through the Irish Government’s National Development Plan (Grant Numbers SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2). The study is supported by Fondazione Cariparma, under TeachInParma Project (DV).