Identification of gut bacteria such as Lactobacillus johnsonii that disseminate to systemic tissues of wild type and MyD88-/- mice

In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD8

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Nutrient management planning on Irish dairy farms

End of Project ReportThe objective of the work undertaken was to investigate nutrient use on intensive dairy farms. A survey of 12 dairy farms was undertaken in 1997 to determine nutrient management practices. These were compared with current nutrient advice and recommended practices. Data recording was completed by the farmer and supplemented by regular farm visits to assist with and validate the process. The mean farm size was 64.8 ha with an average of 128 cows and an annual milk yield per cow of 5594 kg. The mean stocking rate was 2.58 Livestock Units/ha. Dairy cows accounted for highest proportion of the total livestock with most of the younger stock consisting of dairy replacements. Approximately 80% of soil P levels were greater than 6 mg/l while 67% of soils had soil K levels in excess of 100 mg/l. The mean soil P and K levels on the grazing and silage areas were 11 and 128 mg/l, 12 and 117 mg/l, respectively. The mean farm nutrient balance (inputs - outputs) established an annual surplus of N, P and K of 304, 18 and 53 kg/ha, respectively. The adoption of nutrient management plans instead of current practice would reduce N, P and K inputs on average by 44, 13 and 24 kg/ha, respectively. The use of the Teagasc revised P nutrient advice would further reduce the P input requirements by 2 kg/ha. On average the farms had 90% of the 16 week slurry storage capacity. Approximately 14, 42, 14 and 31% of the slurry was applied in spring, summer, autumn and winter, respectively. In all cases there was significant between farm variability. The soil P fertility on the survey farms is skewed towards index 3 and 4 when compared with the average for all samples received at Johnstown Castle. There is no agronomic advantage in terms of crop or animal production for soils to have P levels in excess 10 mg/l. This result indicates that P inputs to farms of this type can be reduced in many cases without prejudicing production potential. The nutrient balance conducted highlighted the extent of the nutrient surpluses and the between farm variability. The data suggest that there is not a serious nutrient surplus on the survey farms, which would require the use of additional off-farm land for slurry recycling, as obtains on pig and poultry farms. The study also indicates that although farm unit cost savings may be small in adopting nutrient management planning, overall farm savings may be significant. For example on the survey farms, savings of up to £2,000 can be achieved apart from the obvious positive environmental impact

Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals

In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.Science Foundation Irelan

A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome

Background: The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). Methods: The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP). Results: Of the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus. Conclusions: These findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date

Aspects of slurry management on pig farms.

End of Project ReportThe objectives of manure or slurry management on intensive pig farms are the provision of adequate slurry storage capacity and the efficient recycling of the slurry nutrients for crop production. However, recent surveys of pig slurry dry matter suggest there is excessive dilution of raw pig slurry with water. This has two important implications for management. The first is greater storage capacity will be required due to the increased volume of slurry generated. Slurry storage is expensive. For example, a 350 sow unit adding 10 weeks storage needs to invest £50,000. Secondly, evidence from the literature indicates an improved slurry nitrogen efficiency with the more dilute manure. The results of field trials showed that higher dry matter pig slurries reduced the relative efficiency of pig slurry nitrogen for second cut silage production. This is probably linked to reduced ammonia volatilisation losses, consequent to the less viscous nature of dilute slurry which permits a more rapid infiltration of the ammonium nitrogen into the soil. The use of a band spreader or shallow injection rather than the conventional splash plate were shown to increase the efficiency of pig slurry nitrogen for grass silage production. Therefore, the potential for the higher pig slurry dry matter, required for cost effective storage/ handling costs, to reduce the efficiency of its nitrogen for grass silage production can be partially offset by using band spreaders or shallow injection spreading systems. These have the added advantage of reducing odour emissions from the land spreading operation.Teagasc Walsh Fellowship Programm

Draft genome sequence of Lactobacillus crispatus EM-LC1, an isolate with antimicrobial activity cultured from an elderly subject

Here we report the 1.86-Mb draft genome sequence of Lactobacillus crispatus EM-LC1, a fecal isolate with antimicrobial activity. This genome sequence is expected to provide insights into the antimicrobial activity of L. crispatus and improve our knowledge of its potential probiotic traits

Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli

Lactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate) and ATCC27782 (bovine isolate), but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to PWOT. BAN was the recipient of an Embark studentship from the Irish Research Council for Science Engineering and Technology. TD and KN were supported by the Alimentary Pharmabiotic Centre, funded by Science Foundation Ireland

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. Highthroughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genuslevel with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult.MJC, OOS, RPR and PWOT are members of the ELDERMET consortium (http://eldermet.ucc.ie), whose work is supported in part by the (Govt. of Ireland) Dept. Agriculture Fisheries and Food/Health Research Board FHRI award to the ELDERMET project, as well as the Alimentary Pharmabiotic Centre. JN and WMdV are supported by the Finnish Funding Agency for Technology and Innovation (TEKES grant 40274/06) and was performed in the Centre of Excellence on Microbial Food Safety of the Academy of Finlan

The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study

Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine