Publications by authors named "Christian Milani"

130 Publications

The human gut microbiota during the initial stages of life: insights from bifidobacteria.

Curr Opin Biotechnol 2021 Jul 29;73:81-87. Epub 2021 Jul 29.

APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland. Electronic address:

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.
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http://dx.doi.org/10.1016/j.copbio.2021.07.012DOI Listing
July 2021

Phylogenomic disentangling of the subsp. taxon.

Microb Genom 2021 Jul;7(7)

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

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http://dx.doi.org/10.1099/mgen.0.000609DOI Listing
July 2021

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses.

mSystems 2021 Jun 29:e0058321. Epub 2021 Jun 29.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parmagrid.10383.39, Parma, Italy.

The use of bioinformatic tools for read-based taxonomic and functional analyses of metagenomic data sets, including their assembly and management, is rather fragmentary due to the absence of an accepted gold standard. Moreover, most currently available software tools need input of millions of reads and rely on approximations in data analysis in order to reduce computing times. These issues result in suboptimal results in terms of accuracy, sensitivity, and specificity when used either for the reconstruction of taxonomic or functional profiles through read analysis or analysis of genomes reconstructed by metagenomic assembly. Moreover, the recent introduction of novel DNA sequencing technologies that generate long reads, such as Nanopore and PacBio, represent a valuable data resource that still suffers from a lack of dedicated tools to perform integrated hybrid analysis alongside short read data. In order to overcome these limitations, here we describe a comprehensive bioinformatic platform, METAnnotatorX2, aimed at providing an optimized user-friendly resource which maximizes output quality, while also allowing user-specific adaptation of the pipeline and straightforward integrated analysis of both short and long read data. To further improve performance quality and accuracy of taxonomic assignment of reads and contigs, custom preprocessed and taxonomically revised genomic databases for viruses, prokaryotes, and various eukaryotes were developed. The performance of METAnnotatorX2 was tested by analysis of artificial data sets encompassing viral, archaeal, bacterial, and eukaryotic (fungal) sequence reads that simulate different biological matrices. Moreover, real biological samples were employed to validate results. We developed a novel tool, i.e., METAnnotatorX2, that includes a number of new advanced features for analysis of deep and shallow metagenomic data sets and is accompanied by (regularly updated) customized databases for archaea, bacteria, fungi, protists, and viruses. Both software and databases were developed so as to maximize sensitivity and specificity while including support for shallow metagenomic data sets. Through extensive tests performed on Illumina and Nanopore artificial data sets, we demonstrated the high performance of the software to not only extract taxonomic and functional information from sequence reads but also to assemble and process genomes from metagenomic data. The robustness of these functionalities was validated using "real-life" data sets obtained from Illumina and Nanopore sequencing of biological samples. Furthermore, the performance of METAnnotatorX2 was compared to other available software tools for analysis of shotgun metagenomics data.
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http://dx.doi.org/10.1128/mSystems.00583-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8269244PMC
June 2021

Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire.

Environ Microbiol Rep 2021 Jun 21. Epub 2021 Jun 21.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

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.
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http://dx.doi.org/10.1111/1758-2229.12960DOI Listing
June 2021

Gastric microbiota composition in patients with corpus atrophic gastritis.

Dig Liver Dis 2021 Jun 8. Epub 2021 Jun 8.

Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant'Andrea Hospital, University Sapienza, Rome, Italy. Electronic address:

Background: In corpus atrophic gastritis (CAG), hypochlorhydria makes plausible the overgrowth of intragastric bacteria, whose role in gastric carcinogenesis is under debate.

Aims: To characterize the antrum/corpus composition of the gastric bacterial microbiota in CAG patients compared to controls without CAG.

Methods: A cross-sectional monocentric study on consecutive patients with known histological diagnosis of CAG undergoing gastroscopy for gastric cancer surveillance and patients without CAG undergoing gastroscopy for dyspepsia or anemia (108 biopsies from 55 patients, median age 61.5). Genomic DNA from one antral and one corpus biopsy from each case (n = 23) and control (n = 32) was extracted. Gastric microbiota was assessed by sequencing hypervariable regions of the 16SrRNA gene.

Results: Bacterial abundance and diversity were significantly lower in CAG cases than in controls (p < 0.001). Firmicutes were more frequent in cases, Bacteroidetes and Fusobacteria in controls (p < 0.0001). Streptococcaceae were more abundant in cases (p < 0.0001), Prevotellaceae in controls (p < 0.0001). The genus Streptococcus was positively correlated with severe OLGA/OLGIM stages linked to a higher risk of gastric cancer.

Conclusion: Gastric bacterial microbiota in CAG showed a reduced abundance and complexity but was characterized by higher colonization of Firmicutes, in particular Streptococcus, increased in subjects with severe atrophy/metaplasia stages at higher risk of gastric cancer.
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http://dx.doi.org/10.1016/j.dld.2021.05.005DOI Listing
June 2021

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

Environ Microbiol 2021 Jun 19;23(6):3294-3305. Epub 2021 May 19.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, 43124, Italy.

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.
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http://dx.doi.org/10.1111/1462-2920.15559DOI Listing
June 2021

Early-Life Development of the Bifidobacterial Community in the Infant Gut.

Int J Mol Sci 2021 Mar 25;22(7). Epub 2021 Mar 25.

Department of Microbiology and Biochemistry of Dairy Products, IPLA-CSIC, 33300 Villaviciosa, Spain.

The establishment of the gut microbiota poses implications for short and long-term health. is an important taxon in early life, being one of the most abundant genera in the infant intestinal microbiota and carrying out key functions for maintaining host-homeostasis. Recent metagenomic studies have shown that different factors, such as gestational age, delivery mode, or feeding habits, affect the gut microbiota establishment at high phylogenetic levels. However, their impact on the specific bifidobacterial populations is not yet well understood. Here we studied the impact of these factors on the different species and subspecies at both the quantitative and qualitative levels. Fecal samples were taken from 85 neonates at 2, 10, 30, 90 days of life, and the relative proportions of the different bifidobacterial populations were assessed by 16S rRNA-23S rRNA internal transcribed spacer (ITS) region sequencing. Absolute levels of the main species were determined by q-PCR. Our results showed that the bifidobacterial population establishment is affected by gestational age, delivery mode, and infant feeding, as it is evidenced by qualitative and quantitative changes. These data underline the need for understanding the impact of perinatal factors on the gut microbiota also at low taxonomic levels, especially in the case of relevant microbial populations such as . The data obtained provide indications for the selection of the species best suited for the development of bifidobacteria-based products for different groups of neonates and will help to develop rational strategies for favoring a healthy early microbiota development when this process is challenged.
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http://dx.doi.org/10.3390/ijms22073382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8036440PMC
March 2021

Metagenomic Analyses of Bifidobacterial Communities.

Authors:
Christian Milani

Methods Mol Biol 2021 ;2278:183-193

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

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.
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http://dx.doi.org/10.1007/978-1-0716-1274-3_15DOI Listing
April 2021

Phageome Analysis of Bifidobacteria-Rich Samples.

Methods Mol Biol 2021 ;2278:71-85

School of Microbiology & APC Microbiome Ireland, Univeristy College Cork, Cork, Ireland.

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.
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http://dx.doi.org/10.1007/978-1-0716-1274-3_7DOI Listing
April 2021

Vaginotypes of the human vaginal microbiome.

Environ Microbiol 2021 Mar 28;23(3):1780-1792. Epub 2021 Feb 28.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

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.
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http://dx.doi.org/10.1111/1462-2920.15441DOI Listing
March 2021

Comparative genome analyses of isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment.

Appl Environ Microbiol 2021 Feb 12. Epub 2021 Feb 12.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

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 genus, whose relative abundance and microbial taxa composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of 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 was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated fifteen strains from different environments in which this species is abounding, 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 and combined with those decoded in this study, revealed a genetic adaptation of strains to their ecological niche. In addition, growth experiments involving all isolated strains together with a synthetic vaginal microbiota reveal how this species is able to modulate the composition of the vaginal microbial consortia at strain level. Overall, our findings suggest that plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. 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 species 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 was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genome of new 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 in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.
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http://dx.doi.org/10.1128/AEM.02899-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091109PMC
February 2021

Amoxicillin-Clavulanic Acid Resistance in the Genus .

Appl Environ Microbiol 2021 03 11;87(7). Epub 2021 Mar 11.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy

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 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 batch cultures. Based on our results, we observed a drastic reduction in gut microbiota diversity of children treated with antibiotics, which also affected the abundance of , 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 experiments revealed that one strain, i.e., PRL2020, is able to persist in the presence of a complex microbiota combined with AMC antibiotic.
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http://dx.doi.org/10.1128/AEM.03137-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091617PMC
March 2021

Probiogenomics Analysis of 97 Strains as a Tool for the Identification of Promising Next-Generation Probiotics.

Microorganisms 2020 Dec 30;9(1). Epub 2020 Dec 30.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.

Members of the genus 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 in the vaginal environment has been linked to vaginal health, leading to the widespread use of many strains as probiotics. Nevertheless, despite the scientific and industrial relevance of this species, a comprehensive investigation of the genomics of taxon is still missing. For this reason, we have performed a comparative genomics analysis of 97 strains, encompassing 16 strains sequenced in the framework of this study alongside 81 additional publicly available genome sequences. Thus, allowing the dissection of the 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 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.
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http://dx.doi.org/10.3390/microorganisms9010073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824148PMC
December 2020

The Gut-Muscle Axis in Older Subjects with Low Muscle Mass and Performance: A Proof of Concept Study Exploring Fecal Microbiota Composition and Function with Shotgun Metagenomics Sequencing.

Int J Mol Sci 2020 Nov 25;21(23). Epub 2020 Nov 25.

Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Via Antonio Gramsci 14, 43126 Parma, Italy.

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), and , and of . 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.
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http://dx.doi.org/10.3390/ijms21238946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728056PMC
November 2020

Decoding the Genomic Variability among Members of the Species.

Microorganisms 2020 Nov 3;8(11). Epub 2020 Nov 3.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124 Parma, Italy.

Members of the 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 strains collected from fecal samples of several primate species and an . Thus, we investigated the genomic variability and metabolic abilities of the new 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 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.
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http://dx.doi.org/10.3390/microorganisms8111720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693768PMC
November 2020

Special Issue "Bifidobacteria: Insights from Ecology to Genomics of a Key Microbial Group of the Mammalian Gut Microbiota".

Microorganisms 2020 Oct 27;8(11). Epub 2020 Oct 27.

APC Microbiome Ireland and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.

In recent years, substantial efforts have been made to dissect the composition of microbial communities that are present in the human gut, and to investigate their interactions with their host [...].
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http://dx.doi.org/10.3390/microorganisms8111660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7693948PMC
October 2020

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

Appl Environ Microbiol 2020 12 17;87(1). Epub 2020 Dec 17.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

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 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 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 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 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. The identification of nine different genotypes among members of 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 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 genotypes.
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http://dx.doi.org/10.1128/AEM.02188-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755242PMC
December 2020

Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs).

Comput Struct Biotechnol J 2020 15;18:2480-2493. Epub 2020 Sep 15.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.

Appropriate development of the intestinal microbiota during infancy is known to be important for human health. In fact, aberrant alterations of the microbial composition during childhood may cause short- and/or long-term negative health effects. Many factors influence the initial assembly and subsequent progression of the gut microbiota of a neonate, such as feeding type, delivery mode, gestational age, maternal metabolic status and antibiotic exposure. In the current study, the composition of the infant gut core-microbiota was explored, revealing particular variations of this core-microbiota during the first three years as influenced by delivery mode and feeding type. A multi-population cohort meta-analysis was performed by selecting 15 publicly available datasets pertaining to taxonomic profiles of 1035 fecal samples of healthy infants, as obtained by means of a 16S rRNA gene-based profiling approach. Interestingly, this multi-population cohort meta-analysis revealed great microbial complexity and specific taxonomic shifts in children older than six months, suggesting a major impact by the introduction of solid foods which prompts progression of infant gut microbiota towards that typical of adults. The taxonomic data sets employed in this multi-population cohort meta-analysis possess the statistical robustness to allow the identification of infant community state types (ICSTs). Our analysis therefore reveals the existence of specific taxonomic patterns that correspond to particular nutritional and developmental stages of early life, and that had previously been obscured by the high variability typical of such infant gut microbiota.
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http://dx.doi.org/10.1016/j.csbj.2020.08.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516180PMC
September 2020

Envisioning emerging frontiers on human gut microbiota and its applications.

Microb Biotechnol 2021 01 24;14(1):12-17. Epub 2020 Sep 24.

APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland.

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.
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http://dx.doi.org/10.1111/1751-7915.13671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7888449PMC
January 2021

Multi-omics Approaches To Decipher the Impact of Diet and Host Physiology on the Mammalian Gut Microbiome.

Appl Environ Microbiol 2020 11 10;86(23). Epub 2020 Nov 10.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

In recent years, various studies have demonstrated that the gut microbiota influences host metabolism. However, these studies were focused primarily on a single or a limited range of host species, thus preventing a full exploration of possible taxonomic and functional adaptations by gut microbiota members as a result of host-microbe coevolution events. In the current study, the microbial taxonomic profiles of 250 fecal samples, corresponding to 77 host species that cover the mammalian branch of the tree of life, were reconstructed by 16S rRNA gene-based sequence analysis. Moreover, shotgun metagenomics was employed to investigate the metabolic potential of the fecal microbiomes of 24 mammals, and subsequent statistical analyses were performed to assess the impact of host diet and corresponding physiology of the digestive system on gut microbiota composition and functionality. Functional data were confirmed and extended through metatranscriptome assessment of gut microbial populations of eight animals, thus providing insights into the transcriptional response of gut microbiota to specific dietary lifestyles. Therefore, the analyses performed in this study support the notion that the metabolic features of the mammalian gut microbiota have adapted to maximize energy extraction from the host's diet. Diet and host physiology have been recognized as main factors affecting both taxonomic composition and functional features of the mammalian gut microbiota. However, very few studies have investigated the bacterial biodiversity of mammals by using large sample numbers that correspond to multiple mammalian species, thus resulting in an incomplete understanding of the functional aspects of their microbiome. Therefore, we investigated the bacterial taxonomic composition of 250 fecal samples belonging to 77 host species distributed along the tree of life in order to assess how diet and host physiology impact the intestinal microbial community by selecting specific microbial players. Conversely, the application of shotgun metagenomics and metatranscriptomics approaches to a group of selected fecal samples allowed us to shed light on both metabolic features and transcriptional responses of the intestinal bacterial community based on different diets.
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http://dx.doi.org/10.1128/AEM.01864-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7657629PMC
November 2020

Catching a glimpse of the bacterial gut community of companion animals: a canine and feline perspective.

Microb Biotechnol 2020 11 30;13(6):1708-1732. Epub 2020 Aug 30.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Dogs and cats have gained a special position in human society by becoming our principal companion animals. In this context, efforts to ensure their health and welfare have increased exponentially, with in recent times a growing interest in assessing the impact of the gut microbiota on canine and feline health. Recent technological advances have generated new tools to not only examine the intestinal microbial composition of dogs and cats, but also to scrutinize the genetic repertoire and associated metabolic functions of this microbial community. The application of high-throughput sequencing techniques to canine and feline faecal samples revealed similarities in their bacterial composition, with Fusobacteria, Firmicutes and Bacteroidetes as the most prevalent and abundant phyla, followed by Proteobacteria and Actinobacteria. Although key bacterial members were consistently present in their gut microbiota, the taxonomic composition and the metabolic repertoire of the intestinal microbial population may be influenced by several factors, including diet, age and anthropogenic aspects, as well as intestinal dysbiosis. The current review aims to provide a comprehensive overview of the multitude of factors which play a role in the modulation of the canine and feline gut microbiota and that of their human owners with whom they share the same environment.
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http://dx.doi.org/10.1111/1751-7915.13656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7533323PMC
November 2020

Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA.

Sci Rep 2020 08 24;10(1):14112. Epub 2020 Aug 24.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.

Gamma aminobutyric acid (GABA) is the principal inhibitory neurotransmitter playing a key role in anxiety and depression disorders in mammals. Recent studies revealed that members of the gut microbiota are able to produce GABA modulating the gut-brain axis response. Among members of the human gut microbiota, bifidobacteria are well known to establish many metabolic and physiologic interactions with the host. In this study, we performed genome analyses of more than 1,000 bifidobacterial strains publicly available revealing that Bifidobacterium adolescentis taxon might represent a model GABA producer in human gastrointestinal tract. Moreover, the in silico screening of human/animal metagenomic datasets showed an intriguing association/correlation between B. adolescentis load and mental disorders such as depression and anxiety. Interestingly, in vitro screening of 82 B. adolescentis strains allowed identifying two high GABA producers, i.e. B. adolescentis PRL2019 and B. adolescentis HD17T2H, which were employed in an in vivo trial in rats. Feeding Groningen rats with a supplementation of B. adolescentis strains, confirmed the ability of these microorganisms to stimulate the in vivo production of GABA highlighting their potential implication in gut-brain axis interactions.
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http://dx.doi.org/10.1038/s41598-020-70986-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445748PMC
August 2020

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach.

mSystems 2020 Jul 28;5(4). Epub 2020 Jul 28.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings. We developed a novel method for accurate cataloguing of bacterial communities at (sub)species level involving amplification of the internal transcribed spacer (ITS) region through optimized primers, followed by next-generation sequencing and taxonomic classification of amplicons by means of a comprehensive database of bacterial ITS sequences. Host-associated, food, and environmental matrices were employed to test the performance of the microbial ITS profiling pipeline. Moreover, mucosal biopsy samples from colorectal cancer patients were analyzed to demonstrate the scientific relevance of this profiling approach in a clinical setting through identification of putative novel biomarkers. The results indicate that the ITS-based profiling pipeline proposed here represents a key metagenomic tool with major relevance for research, industrial, and clinical settings.
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http://dx.doi.org/10.1128/mSystems.00404-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394355PMC
July 2020

Evolutionary development and co-phylogeny of primate-associated bifidobacteria.

Environ Microbiol 2020 08 24;22(8):3375-3393. Epub 2020 Jun 24.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, 43124, Italy.

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.
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http://dx.doi.org/10.1111/1462-2920.15108DOI Listing
August 2020

Bifidobacterium mongoliense genome seems particularly adapted to milk oligosaccharide digestion leading to production of antivirulent metabolites.

BMC Microbiol 2020 05 7;20(1):111. Epub 2020 May 7.

Department of Food Science, Fundamental and Applied Research for Animal and Health, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.

Background: Human milk oligosaccharides (HMO) could promote the growth of bifidobacteria, improving young children's health. In addition, fermentation of carbohydrates by bifidobacteria can result in the production of metabolites presenting an antivirulent activity against intestinal pathogens. Bovine milk oligosaccharides (BMO), structurally similar to HMO, are found at high concentration in cow whey. This is particularly observed for 3'-sialyllactose (3'SL). This study focused on enzymes and transport systems involved in HMO/BMO metabolism contained in B. crudilactis and B. mongoliense genomes, two species from bovine milk origin. The ability of B. mongoliense to grow in media supplemented with whey or 3'SL was assessed. Next, the effects of cell-free spent media (CFSM) were tested against the virulence expression of Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium.

Results: Due to the presence of genes encoding β-galactosidases, β-hexosaminidases, α-sialidases and α-fucosidases, B. mongoliense presents a genome more sophisticated and more adapted to the digestion of BMO/HMO than B. crudilactis (which contains only β-galactosidases). In addition, HMO/BMO digestion involves genes encoding oligosaccharide transport systems found in B. mongoliense but not in B. crudilactis. B. mongoliense seemed able to grow on media supplemented with whey or 3'SL as main source of carbon (8.3 ± 1.0 and 6.7 ± 0.3 log cfu/mL, respectively). CFSM obtained from whey resulted in a significant under-expression of ler, fliC, luxS, stx1 and qseA genes (- 2.2, - 5.3, - 2.4, - 2.5 and - 4.8, respectively; P < 0.05) of E. coli O157:H7. CFSM from 3'SL resulted in a significant up-regulation of luxS (2.0; P < 0.05) gene and a down-regulation of fliC (- 5.0; P < 0.05) gene. CFSM obtained from whey resulted in significant up-regulations of sopD and hil genes (2.9 and 3.5, respectively; P < 0.05) of S. Typhimurium, while CFSM obtained from 3'SL fermentation down-regulated hil and sopD genes (- 2.7 and - 4.2, respectively; P < 0.05).

Conclusion: From enzymes and transporters highlighted in the genome of B. mongoliense and its potential ability to metabolise 3'SL and whey, B. mongoliense seems well able to digest HMO/BMO. The exact nature of the metabolites contained in CFSM has to be identified still. These results suggest that BMO associated with B. mongoliense could be an interesting synbiotic formulation to maintain or restore intestinal health of young children.
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http://dx.doi.org/10.1186/s12866-020-01804-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206731PMC
May 2020

Ecology of Lactobacilli Present in Italian Cheeses Produced from Raw Milk.

Appl Environ Microbiol 2020 06 2;86(12). Epub 2020 Jun 2.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

Among the bacterial genera that are used for cheese production, is a key taxon of high industrial relevance that is commonly present in commercial starter cultures for dairy fermentations. Certain lactobacilli play a defining role in the development of the organoleptic features during the ripening stages of particular cheeses. We performed an in-depth 16S rRNA gene-based microbiota analysis coupled with internally transcribed spacer-mediated compositional profiling of 21 common Italian cheeses produced from raw milk in order to evaluate the ecological distribution of lactobacilli associated with this food matrix. Statistical analysis of the collected data revealed the existence of putative community state types (LCSTs), which consist of clusters of (sub)species. Each LCST is dominated by one or two taxa that appear to represent keystone elements of an elaborate network of positive and negative interactions with minor components of the cheese microbiota. The results obtained in this study reveal the existence of peculiar cheese microbiota assemblies that represent intriguing targets for further functional studies aimed at dissecting the species-specific role of bacteria in cheese manufacturing. The microbiota is known to play a key role in the development of the organoleptic features of dairy products. Lactobacilli have been reported to represent one of the main components of the nonstarter bacterial population, i.e., bacteria that are not deliberately added to the milk, harbored by cheese, although the species-level composition of this microbial population has never been assessed in detail. In the present study, we applied a recently developed metagenomic approach that employs an internally transcribed spacer to profile the population harbored by cheese produced from raw milk at the (sub)species level. The obtained data revealed the existence of particular community state types consisting of clusters of (sub)species that tend to cooccur in the screened cheeses. Moreover, analysis of covariances between members of this genus indicate that these taxa form an elaborate network of positive and negative interactions that define specific clusters of covariant lactobacilli.
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http://dx.doi.org/10.1128/AEM.00139-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267208PMC
June 2020

Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers.

FEMS Microbiol Ecol 2020 May;96(5)

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Human milk is known to carry its own microbiota, of which the precise origin remains obscure. Breastfeeding allows mother-to-baby transmission of microorganisms as well as the transfer of many other milk components, such as human milk oligosaccharides (HMOs), which act as metabolizable substrates for particular bacteria, such as bifidobacteria, residing in infant intestinal tract. In the current study, we report the HMO composition of 249 human milk samples, in 163 of which we quantified the abundance of members of the Bifidobacterium genus using a combination of metagenomic and flow cytometric approaches. Metagenomic data allowed us to identify four clusters dominated by Bifidobacterium adolescentis and Bifidobacterium pseudolongum, Bifidobacterium crudilactis or Bifidobacterium dentium, as well as a cluster represented by a heterogeneous mix of bifidobacterial species such as Bifidobacterium breve and Bifidobacterium longum. Furthermore, in vitro growth assays on HMOs coupled with in silico glycobiome analyses allowed us to elucidate that members of the Bifidobacterium bifidum and B. breve species exhibit the greatest ability to degrade and grow on HMOs. Altogether, these findings indicate that the bifidobacterial component of the human milk microbiota is not strictly correlated with their ability to metabolize HMOs.
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http://dx.doi.org/10.1093/femsec/fiaa049DOI Listing
May 2020

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

Int J Syst Evol Microbiol 2020 Apr 17;70(4):2288-2297. Epub 2020 Feb 17.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

Two strains, i.e., 2176B and 2177B, were isolated from Golden-Headed Lion Tamarin () and Goeldi's monkey (). 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 60, B, J, G and C genes) and the core genome revealed that bifidobacterial strains 2176B and 2177B exhibit close phylogenetic relatedness to DSM 103139 and LMG 11041, 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 species. Thus, sp. nov. (2176B=LMG 31469=CCUG 73785) and sp. nov. (2177B=LMG 31471=CCUG 73786 are proposed as novel species.
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http://dx.doi.org/10.1099/ijsem.0.004032DOI Listing
April 2020

The infant gut microbiome as a microbial organ influencing host well-being.

Ital J Pediatr 2020 Feb 5;46(1):16. Epub 2020 Feb 5.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.

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.
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http://dx.doi.org/10.1186/s13052-020-0781-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003403PMC
February 2020

Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota.

Appl Environ Microbiol 2020 03 18;86(7). Epub 2020 Mar 18.

Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy

During the course of evolution, dogs and cats have been subjected to extensive domestication, becoming the principal companion animals for humans. For this reason, their health care, including their intestinal microbiota, is considered of considerable importance. However, the canine and feline gut microbiota still represent a largely unexplored research area. In the present work, we profiled the microbiota of 23 feline fecal samples by 16S rRNA gene and bifidobacterial internally transcribed spacer (ITS) approaches and compared this information with previously reported data from 138 canine fecal samples. The obtained data allowed the reconstruction of the core gut microbiota of the above-mentioned samples coupled with their classification into distinct community state types at both genus and species levels, identifying , , and 9 as the main bacterial components of the canine and feline gut microbiota. At the species level, the intestinal bifidobacterial gut communities of dogs and cats differed in terms of both species number and composition, as emphasized by a covariance analysis. Together, our findings show that the intestinal populations of cats and dogs are similar in terms of genus-level taxonomical composition, while at the bifidobacterial species level, clear differences were observed, indicative of host-specific colonization behavior by particular bifidobacterial taxa. Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus and bifidobacterial species levels, allowing classification of these microbial populations into distinct gut community state types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with covariance network analysis based on bifidobacterial internally transcribed spacer (ITS) profiling revealed differences in the bifidobacterial compositions of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host.
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http://dx.doi.org/10.1128/AEM.02875-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082561PMC
March 2020
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