Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets

Background

Evidence is accumulating that perturbation of early life microbial colonization of the gut induces long-lasting adverse health effects in individuals. Understanding the mechanisms behind these effects will facilitate modulation of intestinal health. The objective of this study was to identify biological processes involved in these long lasting effects and the (molecular) factors that regulate them. We used an antibiotic and the same antibiotic in combination with stress on piglets as an early life perturbation. Then we used host gene expression data from the gut (jejunum) tissue and community-scale analysis of gut microbiota from the same location of the gut, at three different time-points to gauge the reaction to the perturbation. We analysed the data by a new combination of existing tools. First, we analysed the data in two dimensions, treatment and time, with quadratic regression analysis. Then we applied network-based data integration approaches to find correlations between host gene expression and the resident microbial species.

Results

The use of a new combination of data analysis tools allowed us to identify significant long-lasting differences in jejunal gene expression patterns resulting from the early life perturbations. In addition, we were able to identify potential key gene regulators (hubs) for these long-lasting effects. Furthermore, data integration also showed that there are a handful of bacterial groups that were associated with temporal changes in gene expression.

Conclusion

The applied systems-biology approach allowed us to take the first steps in unravelling biological processes involved in long lasting effects in the gut due to early life perturbations. The observed data are consistent with the hypothesis that these long lasting effects are due to differences in the programming of the gut immune system as induced by the temporary early life changes in the composition and/or diversity of microbiota in the gut.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1733-8) contains supplementary material, which is available to authorized users.     

Better off dead: assessment of aquatic disinfectants and thermal shock treatments to prevent the spread of invasive freshwater bivalves

Wetlands Ecology and Management - Biosecurity protocols designed to prevent further spread of invasive alien species have become a key component of invader management strategies. Yet, the...     

The Control of Precancerous Conditions of the Colon and Rectum

The early diagnosis and treatment of precancerous lesions is an important means of control of intestinal cancer. The precancerous tendency is relatively slight with solitary colo-rectal polyps, ulcerative colitis and bilharzial infestation, but it is exceptionally severe in familial colonic polyposis.For more than 30 years, research into the inheritance and treatment of familial polyposis has been continued at St. Mark''s Hospital, London, England, and more than 90 families have been investigated and family pedigrees prepared. These now include 1050 “members”, of whom 343 have had either polyposis or intestinal cancer, or both, the number with cancer being 243. One hundred and one of these 343 patients have been operated on at St. Mark''s, 61 undergoing colectomy and ileorectal anastomosis.Cancer control is achieved by keeping under supervision all members of a family who have already developed polyposis or who may do so later.     

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Duckweeds, such as Lemna minor Linnaeus (Alismatales: Lemnaceae), are common in aquatic habitats and have been suggested to reduce larval mosquito survivorship via mechanical and chemical effects. Furthermore, pond dyes are used increasingly in aquatic habitats to enhance their aesthetics, although they have been shown to attract mosquito oviposition. The present study examined the coupled effects of L. minor and black pond dye on the oviposition selectivity of Culex pipiens Linnaeus (Diptera: Culicidae) mosquitoes in a series of laboratory choice tests. Subsequently, using outdoor mesocosms, the combined influence of duckweed and pond dye on mosquito abundances in aquatic habitats was quantified. Mosquitoes were strongly attracted to duckweed, and oviposited significantly greater numbers of egg rafts in duckweed-treated water compared with untreated controls, even when the duckweed was ground. The presence of pond dye interacted with the duckweed and further enhanced positive selectivity towards duckweed-treated water. The presence of duckweed caused significant and sustained reductions in larval mosquito numbers, whereas the relative effects of dye were not evident. The use of floating aquatic plants such as duckweed, combined with dye, may help reduce mosquito populations via the establishment of population sinks, characterized by high rates of oviposition coupled with high levels of larval mortality.     

Touch too much: aquatic disinfectant and steam exposure treatments can inhibit further spread of invasive bloody-red mysid shrimp Hemimysis anomala

Wetlands Ecology and Management - Biosecurity protocols designed to prevent further spread of invasive alien species have become a key component of invader management strategies. However,...     

The Population Decline of Gyps Vultures in India and Nepal Has Slowed since Veterinary Use of Diclofenac was Banned

Populations of oriental white-backed vulture (Gyps bengalensis), long-billed vulture (Gyps indicus) and slender-billed vulture (Gyps tenuirostris) crashed during the mid-1990s throughout the Indian subcontinent. Surveys in India, initially conducted in 1991–1993 and repeated in 2000, 2002, 2003 and 2007, revealed that the population of Gyps bengalensis had fallen by 2007 to 0.1% of its numbers in the early 1990s, with the population of Gyps indicus and G. tenuirostris combined having fallen to 3.2% of its earlier level. A survey of G. bengalensis in western Nepal indicated that the size of the population in 2009 was 25% of that in 2002. In this paper, repeat surveys conducted in 2011 were analysed to estimate recent population trends. Populations of all three species of vulture remained at a low level, but the decline had slowed and may even have reversed for G. bengalensis, both in India and Nepal. However, estimates of the most recent population trends are imprecise, so it is possible that declines may be continuing, though at a significantly slower rate. The degree to which the decline of G. bengalensis in India has slowed is consistent with the expected effects on population trend of a measured change in the level of contamination of ungulate carcasses with the drug diclofenac, which is toxic to vultures, following a ban on its veterinary use in 2006. The most recent available information indicates that the elimination of diclofenac from the vultures’ food supply is incomplete, so further efforts are required to fully implement the ban.