Paola Mattarelli

Probiotics and prebiotics in animal feeding for safe food production

Recent outbreaks of food-borne diseases highlight the need for reducing bacterial pathogens in foods of animal origin. Animal enteric pathogens are a direct source for food contamination. The ban of antibiotics as growth promoters (AGPs) has been a challenge for animal nutrition increasing the need to find alternative methods to control and prevent pathogenic bacterial colonization. The modulation of the gut microbiota with new feed additives, such as probiotics and prebiotics, towards host-protecting functions to support animal health, is a topical issue in animal breeding and creates fascinating possibilities. Although the knowledge on the effects of such feed additives has increased, essential information concerning their impact on the host are, to date, incomplete. For the future, the most important target, within probiotic and prebiotic research, is a demonstrated health-promoting benefit supported by knowledge on the mechanistic actions. Genomic-based knowledge on the composition and functions of the gut microbiota, as well as its deviations, will advance the selection of new and specific probiotics. Potential combinations of suitable probiotics and prebiotics may prove to be the next step to reduce the risk of intestinal diseases and remove specific microbial disorders. In this review we discuss the current knowledge on the contribution of the gut microbiota to host well-being. Moreover, we review available information on probiotics and prebiotics and their application in animal feeding.

Bifidobacterium ruminantium sp. nov. and Bifidobacterium merycicum sp. nov. from the rumens of cattle

Among several hundred bifidobacteria isolated from bovine rumens, eight strains were recognized primarily on the basis of DNA-DNA hybridization results as members of two new distinct DNA homology groups. We studied the morphology, oxygen, carbon dioxide, temperature, and pH requirements, fermentation patterns, end products of glucose fermentation, biochemical reactions, protein electrophoretic patterns, isozyme patterns, DNA homology relationships, and guanine-plus-cytosine contents of these organisms, and we propose that these two groups of strains should be considered new species, Bifidobacterium ruminantium (type strain, strain ATCC 49390) and Bifidobacterium merycicum (type strain, strain ATCC 49391).

The potential of bifidobacteria as a source of natural folate

Aims:  To screen 19 strains of bifidobacteria for main folate forms composition in synthetic folate‐free and complex folate‐containing media.

Urease-Positive Bacteria Other than Helicobacter pylori in Human Gastric Juice and Mucosa

BACKGROUND AND AIM:Many bacteria carry the urease enzyme in different human ecosystems, but Helicobacter pylori is the only known bacterium showing urease activity in gastric ecosystems. For this reason, the rapid urease test (RUT) on gastric biopsies and urea breath test (C-UBT) are used to detect H. pylori infection.The aim of this study was to evaluate the presence of urease-positive bacteria other than H. pylori in gastric juice and mucosa in hypochlorhydric subjects.METHODS:Twenty-five hypochlorhydric and 10 normochlorhydric patients were analyzed for the presence of H. pylori and bacterial overgrowth both in gastric juice and on the mucosa. During upper gastrointestinal endoscopy at 8.00 a.m. gastric juice samples and biopsy specimens were taken from the antrum and corpus. All samples were analyzed using standard microbiological procedures like aerobic/anaerobic growth, gram-staining, gas chromatography, API test, 96-clone method, and selective medium to search for specific bacteria. In addition, all strains isolated were screened for urease activity using the CP-test. Urease positive strains were tested for the capacity to survive in an acid environment with or without urea (10 mM/L), at pH 7, 4, 3, and 2, respectively, at different times (0, 20, 30, and 60 min).RESULTS:Six hypochlorhydric patients had 10 strains of urease-positive non-H. pylori bacteria among which Staphylococcus capitis urealiticum showed the strongest urease activity.CONCLUSIONS:Hypochlorhydric patients present many urease-positive bacteria other than H. pylori. The strong urease activity may be responsible for false positive results at RUT or UBT test in patients with suspected H. pylori infection.

Occurrence of the Family Bifidobacteriaceae in Human Dental Caries and Plaque

Despite the constant presence of members of Bifidobacteriaceae in the human oral cavity, few studies of their occurrence in this habitat have been made. The presence and the distribution in human plaque and dental caries of Bifidobacterium dentium, Scardovia inopinata and Parascardovia denticolens, all belonging to the family Bifidobacteriaceae, were studied. The identification to species level was based on morphological and growth type features, fermentation tests, polyacrylamide gel electrophoresis of the soluble proteins and DNA-DNA homology. The three species, isolated on propionic acid trypticase phytone yeast extract medium, were present in 13 out of 19 and in 11 out of 15 subjects examined for dental caries and plaque, respectively. S. inopinata was the species most frequently isolated in dental caries, whereas B. dentium was more numerous in dental plaque.The prevalence of P. denticolens was similar in the two habitats. In conclusion, the prevalence of bifidobacteria species (B. dentium, P. denticolens, S. inopinata) in relation to non-bifidobacteria isolates was significantly different in caries versus plaque samples (p < 0.0001; χ2 test).

Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera.

Minimal standards for the description of new cultivable strains that represent novel genera and species belonging to the genera Bifidobacterium, Lactobacillus and related genera are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision): the description of novel species should be based on phenotypic, genotypic and ecological characteristics to ensure a rich polyphasic characterization. Concerning genotypic characterization, in addition to DNA G+C content (mol%) data, the description should be based on DNA-DNA hybridization (DDH), 16S rRNA gene sequence similarities and at least two housekeeping gene (e.g. hsp60 and recA) sequence similarities. DDH might not be needed if the 16S rRNA gene sequence similarity to the closest known species is lower than 97 %. This proposal has been endorsed by members of the Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms of the International Committee on the Systematics of Prokaryotes.

Bifidobacterium saeculare : a new species isolated from feces of rabbit

Summary In a previous investigation, some bifidobacteria isolated from rabbit feces were characterized as “unassigned homology group I”. New evidence derived from studies on DNA-DNA homology, phenotypic characters and electrophoretic patterns of proteins and of isozymes suggests that “unassigned homology group I” represents a new species of the genus Bifidobacterium, described in this paper as Bifidobacterium saeculare (type strain ATCC 49392).

Effect of growth temperature on the biosynthesis of cell wall proteins from Bifidobacterium globosum

Seventy strains of Bifidobacterium globosum isolated from gastrointestinal tracts of different animals were studied. Strains were grown at temperatures ranging from 25 to 46.5 degrees C in order to examine changes both in the expression of bifidobacterial outer proteins (BIFOPs) and in their hydrophobic properties. It was observed that the expression of BIFOPs found on the cell-surface changes according to growth temperature, with quantitative and/or qualitative variations. Generally speaking, it was observed that BIFOP expression at low-growth temperature was considerably attenuated, while at medium- and high-growth temperature it increased. Furthermore, at high-growth temperatures, the presence of a new common protein was detected in all the strains studied. Cells from B. globosum strains grown under different temperature conditions were studied in terms of their cellular hydrophobicity properties. At medium-growth temperature, the cell hydrophobicity was strictly correlated with BIFOP expression, while at low and high-growth temperatures, the presence of BIFOP only partially influenced the hydrophobic features.

Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

BackgroundMembers 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.ResultsPhylogenomics-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.ConclusionsWithin 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.