Background: Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism.Results: Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid relatedCandidatusMycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence ofCandidatusMycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites.Conclusion: Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments.

Bacteria of the avian [Pasteurella haemolytica]–‘Actinobacillus salpingitidis’ complex have been associated with different pathological conditions in birds, among which salpingitis and peritonitis in chickens of layer type seem to dominate. The aim of this study was to classify these bacteria by comparison of 37 strains tentatively classified as biovars of the avian [P. haemolytica]–‘A. salpingitidis’ complex or as Pasteurella anatis. PFGE, AFLP and plasmid profiling showed that strains representing different biovars were genotypically different. Phylogenetic analysis of 22 strains characterized by 16S rRNA gene sequence comparison showed that strains classified as biovars 5, 8 and 9 were closely related to the suggested type strain of ‘A. salpingitidis’ (98·4–99·9 % similarity), whereas the remaining strains classified in 12 biovars or as P. anatis were closely related to the type strain of P. anatis (98·1–100 % similarity). The two groups were related at 95·7–97·1 % similarity. The closest similarity outside this group was 94·6 %, between biovar 15 and Bisgaard taxon 3. DNA–DNA hybridization was performed with 34 strains and showed binding above 85 % for strains of biovars 5 and 8, including the suggested type strain of ‘A. salpingitidis’. Two strains of P. anatis (F 149^T and F 279) were closely related at 79 % DNA binding to 27 strains of biovars 1, 3, 4, 11, 12, 17–20, 22 and 24. A new genus, Gallibacterium gen. nov., is proposed to include the avian [P. haemolytica]–‘A. salpingitidis’–P. anatis complex, since these taxa form a monophyletic unit with similarities above 95 % on the basis of 16S rRNA sequence comparison and they are unrelated to other genera of the family Pasteurellaceae Pohl 1981. The new genus consists of Gram-negative, non-motile, rod-shaped or pleomorphic bacteria. The bacteria are catalase-, oxidase- and phosphatase-positive. Nitrate is reduced and acid is produced without gas formation from glycerol, (−)d-ribose, (+)d-xylose, (−)d-mannitol, (−)d-fructose, (+)d-galactose, (+)d-glucose, (+)d-mannose, sucrose and raffinose. The genus Gallibacterium can be separated from other genera of Pasteurellaceae by differences in catalase, symbiotic growth, haemolysis, urease, indole, acid production from (+)d-xylose, (−)d-mannitol, (−)d-sorbitol, (+)d-mannose, maltose, raffinose and dextrin and ONPG and PNPG tests. Pasteurella anatis Mutters et al. 1985 is transferred to the new genus as Gallibacterium anatis gen. nov., comb. nov. Genomospecies 1 of Gallibacterium is proposed to include the former biovars 5 and 8 of the avian [P. haemolytica]–‘A. salpingitidis’ complex. The type strain of Gallibacterium anatis is F 149^T (=ATCC 43329^T=NCTC 11413^T) and the reference strain of Gallibacterium genomospecies 1 is CCM 5974.

Gram-negative bacteria include a number of pathogens that cause disease in humans and animals. Although antibiotics are still effective in treating a considerable range of infections caused by Gram-negative bacteria, the alarming increase of antimicrobial resistance (AMR) induced by excessive use of antibiotics has raised global concerns.

A stratified cross-sectional study consisting of four strata of biosecurity based on production system type, including organic/free-range layer, battery-cage layer, layer parent, broiler parent and broiler grandparentflocks, was performed to estimate the prevalence of haemolytic Gallibacterium spp. Thirty birds were sampled by tracheal and cloacal swabs in each flock. A flock was considered infected when just one bird tested positive. A total of 27 flocks was included in the study. All chickens from the broiler grandparent flocks sampled negative, whereas 28% of the broiler parents, 40% of the layer parents, 67% of the battery-cage layers and 96% of the organic/free-range chickens sampled positive. A total of 95.9% (standard deviation ± 7.6%) of birds from infected flocks was colonized by haemolytic Gallibacterium species. A significantly higher number of tracheal swabs was positive compared with cloacal swabs. The probability of vertical transfer was investigated by sampling offspring from an infected as well as a non-infected parent flock. None of the samples were found positive. In conclusion, we showed that haemolytic Gallibacterium spp. were widely distributed within the Danish commercial chicken production systems. However, prevalence proportions were highly influenced by the production system and found to be significantly associated with the biosecurity level observed in the flocks. In general, flock infections resembled an 'all or none' type of colonization as practically all of the chickens in infected flocks sampled positive. There was no evidence of vertical transmission of Gallibacterium.

Gallibacterium anatis biovar haemolytica has been suggested to have a causal role in peritonitis and salpingitis in chickens. Therefore, the aim of this study was to investigate the occurrence of G. anatis biovar haemolytica in chickens with reproductive disorders. One hundred and forty one birds from 31 layer flocks were submitted for necropsy and the following organs were examined for bacteria: choana, trachea, lung, heart, liver, spleen, ovary, oviduct, duodenum and cloaca. Examination for Escherichia coli was included as it can induce reproductive disorders. G. anatis was isolated in pure culture from the reproductive tract of affected birds in six of the 31 flocks while E. coli was obtained in pure culture from 10 of them. Both G. anatis and E. coli were isolated from the reproductive tract of 14 of the 31 flocks. The genetic diversity of the Gallibacterium isolates was assessed by amplified fragment length polymorphism on a subset of 83 isolates. Generally, each flock was infected with a single clone, which could be isolated from various sites in the birds. However, in two flocks, the majority of birds yielded positive samples from the internal organs, indicating that these particular clones may be more invasive. The findings support previous suggestions that G. anatis biovar haemolytica is associated with infection of the reproductive tract of chickens, making it a likely cause of lowered productivity and an animal welfare concern.

[Pasteurella]trehalosiis an important pathogen of sheep, being primarily associated with serious systemic infections in lambs but also having an association with pneumonia. The aim of the present investigation was to characterize a broad collection of strains tentatively identified as [P.]trehalosiin order to reclassify and rename this taxon to support improvements in our understanding of the pathogenesis and epidemiology of this important organism. The type strain for [P.]trehalosi, strain NCTC 10370^T, was included along with 42 field isolates from sheep (21), cattle (14), goats (1), roe deer (3) and unknown sources (3). An extended phenotypic characterization was performed on all 43 strains. Amplified fragment length polymorphism (AFLP) was also performed on the isolates. Two of the field isolates were subjected to 16S rRNA gene sequencing. These sequences, along with five existing sequences for [P.]trehalosistrains and 12 sequences for other taxa in the familyPasteurellaceae, were subjected to a phylogenetic analysis. All the isolates and the reference strains were identified as [P.]trehalosi. A total of 17 out of 22 ovine isolates produced acid from all glycosides, while only four out of 14 bovine isolates produced acid from all glycosides. All 22 ovine isolates were haemolytic and CAMP-positive, while no other isolate was haemolytic and only two bovine isolates were CAMP-positive. Nineteen AFLP types were found within the [P.]trehalosiisolates. All [P.]trehalosiisolates shared at least 70 % similarity in AFLP patterns. The largest AFLP type included the type strain and 7 ovine field isolates. Phylogenetic analysis indicated that the seven strains studied (two field isolates and the five serovar reference strains) are closely related, with 98.6 % or higher 16S rRNA gene sequence similarity. As both genotypic and phenotypic testing support the separate and distinct nature of these organisms, we propose the transfer of [P.]trehalosito a new genus,Bibersteinia, asBibersteinia trehalosicomb. nov. The type strain is NCTC 10370^T(=ATCC 29703^T).Bibersteinia trehalosican be distinguished from the existing genera of the family by the observation of only nine characteristics; catalase, porphyrin, urease, indole, phosphatase, acid from dulcitol, (+)-d-galactose, (+)-d-mannose and (+)-d-trehalose.