Correction: Aedes albopictus microbiota: Differences between wild and mass-reared immatures do not suggest negative impacts from a diet based on black soldier fly larvae and fish food.

[This corrects the article DOI: 10.1371/journal.pone.0292043.].

Folate-producing bifidobacteria: metabolism, genetics, and relevance.

Folate (the general term for all bioactive forms of vitamin B9) plays a crucial role in the evolutionary highly conserved one-carbon (1C) metabolism, a network including central reactions such as DNA and protein synthesis and methylation of macromolecules. Folate delivers 1C units, such as methyl and formyl, between reactants. Plants, algae, fungi, and many bacteria can naturally produce folate, whereas animals, including humans, must obtain folate from external sources. For humans, folate deficiency is, however, a widespread problem. Bifidobacteria constitute an important component of human and many animal microbiomes, providing various health advantages to the host, such as producing folate. This review focuses on bifidobacteria and folate metabolism and the current knowledge of the distribution of genes needed for complete folate biosynthesis across different bifidobacterial species. Biotechnologies based on folate-trophic probiotics aim to create fermented products enriched with folate or design probiotic supplements that can synthesize folate in the colon, improving overall health. Therefore, bifidobacteria (alone or in association with other microorganisms) may, in the future, contribute to reducing widespread folate deficiencies prevalent among vulnerable human population groups, such as older people, women at child-birth age, and people in low-income countries.

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.

Aedes albopictus microbiota: Differences between wild and mass-reared immatures do not suggest negative impacts from a diet based on black soldier fly larvae and fish food.

The "Sterile Insect Technique" (SIT), a promising method to control Aedes albopictus, the Asian tiger mosquito, is gaining increasing interest. Recently, the role of microbiota in mosquito fitness received attention, but the link between microbiota and larval diet in mass rearing programs for SIT remains largely unexplored. We characterized the microbiota of four larval instars, pupae and eggs of non-wild (NW) lab-reared Ae. albopictus fed with a diet based on Black soldier fly (Hermetia illucens) larvae powder and fish food KOI pellets. We compared it with wild (W) field-collected individuals and the bacterial community occurring in rearing water-diet (DIET). A total of 18 bacterial classes with > 0.10% abundance were found overall in the samples, with seven classes being especially abundant. Overall, the microbiota profile significantly differed among NW, W and DIET. Verrucomicrobiae were significantly more abundant in W and DIET, Bacteroidia were more abundant in NW and DIET, and Gammaproteobacteria were only more abundant in W than in DIET. W-eggs microbiota differed from all the other groups. Large differences also appeared at the bacterial genus-level, with the abundance of 14 genera differing among groups. Three ASVs of Acinetobacter, known to have positive effects on tiger mosquitoes, were more abundant in NW than in W, while Serratia, known to have negative or neutral effects on another Aedes species, was less abundant in NW than in W. The bacterial community of W-eggs was the richest in species, while dominance and diversity did not differ among groups. Our data show that the diet based on Black soldier fly powder and fish food KOI influences the microbiota of NW tiger mosquito immature stages, but not in a way that may suggest a negative impact on their quality in SIT programs.

Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment.

Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3-V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 106 CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 107 CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

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.

Desafios e possibilidades pa ra a implementação de uma educaçãoespecial e inclusiva na rede estadual de ensino de sergipe1 / Challenges and possibilities for implementing a special and inclusive education in the state education network of sergipe

RESUMO Este artigo é fruto de uma pesquisa realizada na Rede Estadual de Ensino de Sergipe acerca da implementação da Educação Especial na Perspectiva da Educação Inclusiva, conforme preconizam a legislação e as políticas públicas brasileiras. Para tanto, teve-se como objetivo apresentar os desafios e as possibilidades que entremeiam a implementação da Educação Especial e Inclusiva no locus supracitado. O estudo, de caráter qualitativo, foi desenvolvido sob a égide da Análise de Conteúdo, e a interpretação dos dados deu-se a partir de seis categorias emergentes: 1) Educação Especial; 2) Educação Inclusiva; 3) Formação Docente; 4) Profissionalidade Docente; 5) Dimensão Coletiva do Trabalho Pedagógico; e 6) Políticas Públicas Educacionais. Os resultados desvelaram que existem indícios de desenvolvimento de uma Educação Especial e Inclusiva, apesar de desafios como falta de investimentos por parte do poder público, sucateamento da educação e falta de formação continuada docente. Todavia, vislumbraram-se possibilidades para que esse contexto possa ser ressignificado na realidade sergipana.

ABSTRACT This article is the result of research carried out in the State Education Network of Sergipe, Brazil, about the implementation of Special Education from the perspective of Inclusive Education, as recommended by Brazilian legislation and public policies. Therefore, the aim was to present the challenges and possibilities that intertwine the implementation of Special and Inclusive Education in the aforementioned locus. The study, of a qualitative nature, was developed under the aegis of the Content Analysis, and the interpretation of the data was based on six emerging categories: 1) Special Education; 2) Inclusive Education; 3) Teacher Training; 4) Teaching Professionality; 5) Collective Dimension of Pedagogical Work; and 6) Education Public Policies. The results revealed that there are signs of development of a Special and Inclusive Education, despite challenges such as lack of investment by the public power, leaving education in ruins and lack of continuing teacher training. However, possibilities were envisioned so that this context may be re-signified in the reality of the state of Sergipe.

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.

Essential Oils and Hydrolates: Potential Tools for Defense against Bacterial Plant Pathogens.

The essential oils (EOs) of Origanum compactum and Satureja montana chemotyped (CT) at carvacrol, two Thymus vulgaris CT at thujanol and thymol, and Hydrolates (Hys) of S. montana and Citrus aurantium var. amara were chosen for studying their bactericidal efficacy against few phytobacterial pathogens. The Minimal Inhibitory Concentration (MIC) and Bactericidal Concentration (MBC) were found by microdilution assay. The essential oils of O. compactum (MBC 0.06% v/v), T. vulgaris CT thymol (MBC 0.06% v/v), and Hy of C. aurantium (MBC 6.25% v/v) resulted in being the most effective against Erwinia amylovora; thus, they were used as starting concentrations for ex vivo assays. Despite the great in vitro effectiveness, the disease incidence and the population dynamic ex vivo assays showed no significant results. On the other hand, EO of O. compactum and Hy of C. aurantium (at 0.03% and 4.5% v/v, respectively) showed resistance induction in tomato plants against Xanthomonas vesicatoria infections; both treatments resulted in approximately 50% protection. In conclusion, EOs and Hys could be promising tools for agricultural defense, but further studies will be necessary to stabilize the EOs emulsions, while Hys application could be an effective method to prevent bacterial diseases when used as resistance inducer by pre-transplantation treatment at roots.

Potential Applications of Essential Oils for Environmental Sanitization and Antimicrobial Treatment of Intensive Livestock Infections.

The extensive use of antibiotics has contributed to the current antibiotic resistance crisis. Livestock infections of Salmonella spp, Clostridium spp. and E. coli antimicrobial-resistant bacteria represent a public threat to human and animal health. To reduce the incidence of these zoonoses, essential oils (EOs) could be effective antibiotic alternatives. This study aims at identifying EOs safe for use, effective both in complementary therapy and in the environmental sanitization of intensive farming. Natural products were chemo-characterized by gas chromatography. Three S. Typhimurium, three C. perfringens and four E. coli strains isolated from poultry and swine farms were used to assess the antimicrobial properties of nine EOs and a modified GR-OLI (mGR-OLI). The toxicity of the most effective ones (Cinnamomum zeylanicum, Cz; Origanum vulgare, Ov) was also evaluated on porcine spermatozoa and Galleria mellonella larvae. Cz, Ov and mGR-OLI showed the strongest antimicrobial activity; their volatile components were also able to significantly inhibit the growth of tested strains. In vitro, Ov toxicity was slightly lower than Cz, while it showed no toxicity on G. mellonella larvae. In conclusion, the study confirms the importance of evaluating natural products to consolidate the idea of safe EO applications in reducing and preventing intensive livestock infections.

Disentangling the Possible Drivers of Indri indri Microbiome: A Threatened Lemur Species of Madagascar.

Research on the gut microbiome may help with increasing our understanding of primate health with species' ecology, evolution, and behavior. In particular, microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar. This species is classified as "critically endangered" by the IUCN Red List of Threatened Species, representing one of the world's 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Indris have never been successfully bred under human care, suggesting that some behavioral and/or ecological factors are still not considered from the ex situ conservation protocols. Here, we explored gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, Synergistetes 16.7 ± 4.5%, and Firmicutes 11.1 ± 1.9%. Further, our results revealed that bacterial alpha and beta diversity were influenced by indri family group and sex. In addition, we investigated the chemical composition of geophagic soil to explore the possible ecological value of soil as a nutrient supply. The quite acidic pH and high levels of secondary oxide-hydroxides of the soils could play a role in the folivorous diet's gut detoxification activity. In addition, the high contents of iron and manganese found the soils could act as micronutrients in the indris' diet. Nevertheless, the concentration of a few elements (i.e., calcium, sulfur, boron, nickel, sodium, and chromium) was higher in non-geophagic than in geophagic soils. In conclusion, the data presented herein provide a baseline for outlining some possible drivers responsible for the gut microbiome diversity in indris, thus laying the foundations for developing further strategies involved in indris' conservation.

Effect of bioactive compounds released from Brassicaceae defatted seed meals on bacterial load in pig manure.

Animal manure application to soils is considered to be one of the main cause of antibiotic and bacterial pathogen spread in the environment. Pig livestock, which is the source of one of the most used fertilizer for cultivated land, is also a hotspot for antibiotics and antibiotic-resistant bacteria. Besides harsh chemical and physical sanitization treatments for the abatement of antibiotics and bacterial load in livestock waste, more sustainable and environmentally friendly strategies need to be considered. In this context, the use of natural substances which are proved useful for pest and disease control is currently under exploration for their role in the reduction of bacterial pathogen population. Among these, plants and derived products from the Brassicaceae family, characterized by the presence of a defensive glucosinolate-myrosinase enzymatic system, have been successfully exploited for years in agriculture using the so-called biofumigation technique against crop diseases. Although the application of biofumigation to suppress a range of soil borne pests has been well documented, no studies have been examined to reduce bacterial population in animal waste. In the present study, the release and the antibacterial activity of bioactive compounds deriving from different Brassicaceae defatted seed meals against pathogens and bacterial population in pig manure is addressed. Rapistrum rugosum and Brassica nigra defatted seed meals were found to be the most active products against tested pathogens and able to significantly reduce the bacterial load in the manure.

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.

Host-Diet Effect on the Metabolism of Bifidobacterium.

Bifidobacterium has a diverse host range and shows several beneficial properties to the hosts. Many species should have co-evolved with their hosts, but the phylogeny of Bifidobacterium is dissimilar to that of host animals. The discrepancy could be linked to the niche-specific evolution due to hosts' dietary carbohydrates. We investigated the relationship between bifidobacteria and their host diet using a comparative genomics approach. Since carbohydrates are the main class of nutrients for bifidobacterial growth, we examined the distribution of carbohydrate-active enzymes, in particular glycoside hydrolases (GHs) that metabolize unique oligosaccharides. When bifidobacterial species are classified by their distribution of GH genes, five groups arose according to their hosts' feeding behavior. The distribution of GH genes was only weakly associated with the phylogeny of the host animals or with genomic features such as genome size. Thus, the hosts' dietary pattern is the key determinant of the distribution and evolution of GH genes.

Identification of Bifidobacteria by the Phosphoketolase Assay.

Bifidobacteria are commensal bacteria, which naturally colonize the gastrointestinal tract of a large number of animals, including humans, contributing to their health and well-being. An important taxonomic marker for the identification of members of the bifidobacterial group is the presence of the fructose-6-phosphate phosphoketolase (F6PPK) activity. The F6PPK enzyme is involved in the bifidus shunt based on the ability of F6PPK to split fructose-6-phosphate into erythrose-4-phosphate and acetyl phosphate. Here, we describe the two main methods utilized to detect the presence of F6PPK activity, that is, the enzymatic assay and the presence of the D-xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene.

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.

Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments.

A microbiome is defined as a complex collection of microorganisms and their genetic material. Studies regarding gut microbiomes of different animals have provided ecological and evolutionary information showing a strong link between health and disease. Very few studies have compared the gut microbiota of animals housed under controlled conditions and those in wild habitats. Little research has been performed on the reptile gut microbiota, and what studies do exist are mainly focused on carnivorous reptiles. The aim of this study was first to describe the overall microbiota structure of Aldabra giant tortoises (Aldabrachelys gigantea) and, second, to compare the microbiota of tortoises living under natural conditions and tortoises living in controlled environments, such as zoological and botanical parks, in Italy and in the Seychelles. Seventeen fecal samples were collected from giant tortoises located on Curieuse Island (CI, n = 8), at the Botanical Garden (BG, n = 3) in Mahé (Seychelles Islands) and at Parco Natura Viva-Garda Zoological Park (PNV, n = 6) in Verona (Italy). The V3-V4 region of the 16S rRNA gene was amplified in order to characterize the gut microbiota profile. Overall, the major phyla identified were Bacteroidetes 42%, Firmicutes 32%, and Spirochaetes 9%. A higher microbial diversity (alpha indices) was observed for the BG samples as compared to the PNV samples (Shannon: 5.39 vs. 4.43; InvSimpson: 80.7 vs. 25; Chao1: 584 vs. 377 p < 0.05). The results in the present study showed a significant difference in beta diversity between the samples from CI, BG, and PNV (p = 0.001), suggesting a different bacterial fecal profile of giant tortoises at the different habitats. This study provided novel insights into the effects of different environmental conditions on the gut microbial communities of giant tortoises. In particular, differences were reported regarding the bacterial gut community structure between tortoises in natural and in controlled environments. These results could help to improve the management of giant tortoises under human care, thus enhancing ex-situ conservation efforts far from the species geographic range.

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.