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

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

Bifidobacterium mellis sp. nov., isolated from the honey stomach of the honey bee Apis mellifera.

A novel Bifidobacterium strain, Bin7NT, was isolated from the honey stomach of the honey bee Apis mellifera. Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Their optimal growth is at 37 °C in anaerobiosis in MRS (De Man, Rogosa and Sharpe) added with cysteine. The honey bee microbiota was composed of several phylotypes of Bifidobacterium and Lactobacillus. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain Bin7NT grouped with Bifidobacterium species originating from honey bees and was closely related to Bifidobacterium asteroides DSM 20089T (99.67 % similarity). However, the highest average nucleotide identity and digital DNA-DNA hybridization values of 94.88 and 60.6 %, respectively, were obtained with Bifidobacterium choladohabitans JCM 34586T. The DNA G+C content of the type strain is 60.8 mol%. The cell-wall peptidoglycan is of the A4ß l-Orn-d-Asp type. The main cellular fatty acids of strain Bin7NT are C18 : 1 ω9c, C16 : 0, C18 : 1 ω7c and C18 : 0. Phenotypic characterization and genotyping based on the genome sequences clearly show that this strain is distinct from the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium mellis sp. nov. (Bin7NT=DSM 29108T=CCUG 66113T) is proposed as novel Bifidobacterium species.

Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.

AIMS: Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris. METHODS AND RESULTS: Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype. CONCLUSIONS: Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.

The "right" side of sleeping: laterality in resting behaviour of Aldabra giant tortoises (Aldabrachelys gigantea).

Although some studies investigated lateralization in reptiles, little research has been done on chelonians, focusing only on few behaviours such as righting response and escape preference. The aim of this study was to investigate lateralization in Aldabra giant tortoises (Aldabrachelys gigantea), focusing on asymmetrical positioning of the limbs and the head during resting behaviour, called sleep-like behaviour, involving both wild tortoises and individuals under human care. Subjects of the study were 67 adult Aldabra tortoises (54 free ranging on Curieuse, 13 under human care in Mahè Botanical Garden). For each tortoise observed during sleep-like behaviour, we recorded the position of the head (on the left, on the right or in line with the body midline) and we collected which forelimb and hindlimb were kept forward. Moreover, the number of subjects in which limbs were in a symmetrical position during the sleep-like behaviour was recorded. Based on our results, the number of tortoises with asymmetrical position of head and limb was higher (head: 63%; forelimbs: 88%; hindlimbs: 70%) than the number of tortoises with symmetrical position of the head and the limb. Regarding the head, throughout the subjects found with the asymmetrical position of the head during sleep-like behaviour, tortoises positioning the head on the right (42%) were more than those sleeping with the head on the left (21%). We found a relationship between the position of the forelimbs and hindlimbs during sleep-like behaviour. We reported no differences between Mahè (under human care) and Curieuse (wild) tortoises. Findings of this preliminary study underlined traces of group-level lateralization in head positioning during the sleep-like behaviour, possibly due to a left-eye/right-hemisphere involvement in anti-predatory responses and threatening stimuli as reported in reptiles and other vertebrates. This study aims at adding data on brain lateralization, often linked to lateralized behaviours, in reptiles, especially in chelonians.

I Like the Way You Eat It: Lemur (Indri indri) Gut Mycobiome and Geophagy.

Here, we investigated the possible linkages among geophagy, soil characteristics, and gut mycobiome of indri (Indri indri), an endangered lemur species able to survive only in wild conditions. The soil eaten by indri resulted in enriched secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Besides, we found that soil subject to geophagy and indris' faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) commonly associated with soil and plant material were found in both geophagic soil and indri samples. On the contrary, some taxa with pathogenic potentials, such as Cryptococcus, were only found in indri samples. Further, many saprotrophs and plant-associated fungal taxa were detected in the indri faeces. These fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. In conclusion, we found an intimate connection between gut mycobiome and soil, highlighting, once again, the potential consequent impacts on the wider habitat.

Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients.

Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: • Comparison of gut microbiota and mycobiota between IBS and healthy subjects • Investigation of cultivable fungi in IBS and healthy subjects • Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.

Is aromatherapy effective in obstetrics? A systematic review and meta-analysis.

The aim of this systematic review is to collect clinical trials conducted using essential oils (EOs) in obstetric symptoms by evaluating if and in which context the aromatherapy practice is effective in obstetrics. The research was conducted by using the databases of EMBASE, Medline, Biosis and Toxcenter, PubMed, and Google Scholar search engine, selecting articles from January 2004 to July 2020. This study was performed according to the MOOSE and PRISMA guidelines. Only the randomized clinical trials were considered, and in cases of multiple publications, it was considered the most up to date information. Biases were highlighted. In the presence of homogeneous data, pooling statistics and meta-analysis were applied. The research led to 71 articles, 17 of which were eligible. Among the trials selected, eight investigated the effectiveness of EOs on anxiety, depression, and stress. Two concerned the treatment of nausea and vomiting, six evaluated the application of EOs on labor for pain treatment, and two showed the effectiveness in the treatment of episiotomy. The heterogeneity of works carried out so far has made it possible to develop a meta-analysis only in the field of pain treatment during childbirth, identifying the effectiveness of the EOs Lavandula spp. and Rosa damascena.

Bifidobacteria in two-toed sloths (Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov.

Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6T), whereas the type strain of Bifidobacterium dentium DSM 20436T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6T combined with phenotypic analyses clearly revealed that the strain BRDM 6T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6T=NBRC 114053T=BCRC 81222T) is proposed.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Proposal to reclassify four Lactobacillus species as Apilactobacillus bombintestini, Companilactobacillus suantsaicola, Lactiplantibacillus garii and Levilactobacillus suantsaiihabitans.

The taxonomy of the genus Lactobacillus was revised in April 2020 to reclassify species that were originally described as Lactobacillus species into 25 genera that comprise phylogenetically related micro-organisms. The species in these 25 genera also share major metabolic traits and generally have a shared ecology. A total of four comb. nov. names, however, were not considered validly published because the valid publication of the corresponding basonyms was published in later issues of the International Journal of Systematic and Evolutionary Microbiology. This communication aims to validly publish the names Apilactobacillus bombintestini, Companilactobacillus suantsaicola, Lactiplantibacillus garii and Levilactobacillus suantsaiihabitans.

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of closed and open meetings, 3 September 2018, Berlin, Germany.

The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium,Lactobacillus and related organisms was held within the frame of the FoodMicro 2018 Congress (FoodMicro 2018, 3-6 September 2018, Berlin, Germany). The meeting comprised an open session with a workshop entitled 'Modern approaches of LAB identification and conservation' and a closed session on issues related to ICSP Subcommittee activities.

International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of open and closed meetings, 19 July 2016, Dublin, Ireland.

The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms was held within the frame of the FoodMicro 2016 Congress in Dublin (FoodMicro 2016, 19-22 July 2016, Dublin, Ireland). The meeting comprised an open session with a workshop entitled 'Research and networking taxonomy in food with an emphasis on LAB' and a closed session on issues related to ICSP Subcommittee activities.

Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada).

A novel irregularly shaped and slightly curved rod bacterial strain, GLDI4/2T, showing activity of fructose 6-phosphate phosphoketolase was isolated from a faecal sample of an adult gelada baboon (Theropithecus gelada). Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing fusA, gyrB and xfp genes) and the core genome revealed that GLDI4/2T exhibited phylogenetic relatedness to Alloscardovia omnicolens DSM 21503T and to Alloscardovia macacae DSM 24762T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain A. omnicolens DSM 21503T (96.0 %). Activities of α- and ß-gluco(galacto)sidases were detected in strain GLDI4/2T, which is characteristic for almost all members of the family Bifidobacteriaceae. Compared to other Alloscardovia species its DNA G+C content (43.8 mol%) was very low. Phylogenetic studies and the evaluation of phenotypic characteristics, including the results of biochemical, physiological and chemotaxonomic analyses, confirmed the novel species status for strain GLDI4/2T, for which the name Alloscardoviatheropitheci sp. nov. is proposed. The type strain is GLDI4/2T (=DSM 106019T=JCM 32430T).

Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus).

A novel Bifidobacterium strain, MRM 9.3T, was isolated from a faecal sample of a baby common marmoset (Callithrixjacchus). Cells were Gram-stain-positive, non-motile, non-sporulating, non-haemolytic, facultatively anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, clpC, dnaJ and dnaG genes) and the core genomes revealed that strain MRM 9.3T exhibited phylogenetic relatedness to Bifidobacterium myosotis DSM 100196T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B.ifidobacterium myosotis DSM 100196T (95.6 %). The average nucleotide identity, amino acid average identity and in silico DNA-DNA hybridization values between MRM 9.3T and DSM 100196T were 79.9, 72.1 and 28.5 %, respectively. Phenotypic and genotypic features clearly showed that the strain MRM 9.3T represents a novel species, for which the name Bifidobacterium jacchi sp. nov. is proposed. The type strain is MRM 9.3T (=DSM 103362T =JCM 31788T).

Bifidobacterium catulorum sp. nov., a novel taxon from the faeces of the baby common marmoset (Callithrix jacchus).

In our previous study based on hsp60 PCR-restriction fragment length polymorphism and 16S rRNA gene sequencing, we stated that the bifidobacterial strains isolated from the individual faecal samples of five baby common marmosets constituted different phylogenetically isolated groups of the genus Bifidobacterium. In that study, we also proposed that these isolated groups potentially represented novel species of the genus Bifidobacterium. Out of them, Bifidobacterium aesculapii, Bifidobacterium myosotis, Bifidobacterium tissieri and Bifidobacterium hapali, have been described recently. Another strain, designated MRM 8.19T, has been classified as member of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA, hsp60, clpC, dnaJ, dnaG and rpoB gene sequences. Analysis of 16S rRNA and hsp60 gene sequences revealed that strain MRM 8.19T was related to B. tissieri DSM 100201T (95.8 %) and to Bifidobacterium bifidum ATCC 29521T (93.7 %), respectively. The DNA G+C composition was 63.7 mol% and the peptidoglycan structure was l-Orn(Lys)-l-Ser. Based on the phylogenetic, genotypic and phenotypic data reported, strain MRM 8.19T represents a novel taxon within the genus Bifidobacterium for which the name Bifidobacterium catulorum sp. nov. (type strain MRM 8.19T=DSM 103154T=JCM 31794T) is proposed.

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

Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5T was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5T was closely related to Bifidobacterium saguini DSM 23967T (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213T (hsp60 94.1 %), Bifidobacterium saguini DSM 23967T (clpC 91 %), Bifidobacterium avesanii DSM 100685T (dnaG 80.3 %), Bifidobacterium longumsubsp. infantis ATCC 15697T (dnaJ 85.3 %) and Bifidobacterium longumsubsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3ß, with an interpeptide bridge comprising l-Orn (Lys) - l-Ser - l-Ala - l-Thr - l-Ala. The DNA G+C content of strain TRI 5T was 60.9 mol%. Based on the data provided, strain TRI 5T represents a novel species of the genus Bifidobacterium for which the name Bifidobacteriumcallitrichidarum sp. nov. is proposed. The type strain is TRI 5T (=DSM 103152T=JCM 31790T).

Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.

BACKGROUND: Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.e., Aeriscardovia, Alloscardovia, Bifidobacterium, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia, was performed. Furthermore, in order to include a representative of each of the 67 (currently recognized) (sub) species belonging to the Bifidobacteriaceae family, we sequenced the genomes of an additional 11 species from this family, accomplishing the most extensive comparative genomic analysis performed within this family so far. RESULTS: Phylogenomics-based analyses revealed the deduced evolutionary pathway followed by each member of the Bifidobacteriaceae family, highlighting Aeriscardovia aeriphila LMG 21773 as the deepest branch in the evolutionary tree of this family. Furthermore, functional analyses based on genome content unveil connections between a given member of the family, its carbohydrate utilization abilities and its corresponding host. In this context, bifidobacterial (sub) species isolated from humans and monkeys possess the highest relative number of acquired glycosyl hydrolase-encoding genes, probably in order to enhance their metabolic ability to utilize different carbon sources consumed by the host. CONCLUSIONS: Within the Bifidobacteriaceae family, genomics of the genus Bifidobacterium has been extensively investigated. In contrast, very little is known about the genomics of members of the other eight genera of this family. In this study, we decoded the genome sequences of each member of the Bifidobacteriaceae family. Thanks to subsequent comparative genomic and phylogenetic analyses, the deduced pan-genome of this family, as well as the predicted evolutionary development of each taxon belonging to this family was assessed.

Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.).

In a previous study on bifidobacterial distribution in New World monkeys, six strains belonging to the Bifidobacteriaceae were isolated from faecal samples of baby common marmosets (Callithrix jacchus L.). All the isolates were Gram-positive-staining, anaerobic, asporogenous and fructose-6-phosphate phosphoketolase-positive. Comparative analysis of 16S rRNA gene sequences revealed relatively low levels of similarity (maximum identity 96 %) to members of the genus Bifidobacterium, and placed the isolates in three independent clusters: strains of cluster I (MRM_5.9T and MRM_5.10) and cluster III (MRM_5.18T and MRM_9.02) respectively showed 96.4 and 96.7 % 16S rRNA gene sequence similarity to Bifidobacterium callitrichos DSM 23973T, while strains of cluster II (MRM_8.14T and MRM_9.14) showed 95.4 % similarity to Bifidobacterium stellenboschense DSM 23968T. Phylogenetic analysis of partial hsp60 and clpC gene sequences supported an independent phylogenetic position of each cluster from each other and from the related type strains B. callitrichos DSM 23973T and B. stellenboschense DSM 23968T. Clusters I, II and III respectively showed DNA G+C contents of 64.9-65.1, 56.4-56.7 and 63.1-63.7 mol%. The major cellular fatty acids of MRM_5.9T were C14 : 0, C16 : 0 and C18 : 1ω9c dimethylacetal, while C16 : 0 was prominent in strains MRM_5.18T and MRM_8.14T, followed by C18 : 1ω9c and C14 : 0. Biochemical profiles and growth parameters were recorded for all the isolates. Based on the data provided, the clusters represent three novel species, for which the names Bifidobacterium myosotis sp. nov. (type strain MRM_5.9T = DSM 100196T = JCM 30796T), Bifidobacterium hapali sp. nov. (type strain MRM_8.14T = DSM 100202T = JCM 30799T) and Bifidobacterium tissieri sp. nov. (type strain MRM_5.18T = DSM 100201T = JCM 30798T) are proposed.