Department of Livestock Microbial Ecology

Research Projects

Current Research Projects

LiMBiom-S - Development of methodological standards for meaningful, reproducible and application driven microbiome research in livestock

LiMBiom-S - Development of methodological standards for meaningful, reproducible and application driven microbiome research in livestock

Status: ongoing


Project start: 01.03.2023
Project end: 28.02.2026

Funding code: 28N-2-051-01 (Federal Ministry of Food and Agriculture)

Description

The LiMBiom-S aims to establish for the first time a standardised working protocol and open-source references for microbiome research on farm animals using the example of pigs. Together with standardised documentation guidelines, this should make it possible to compare microbiome data and results from a wide range of laboratories, generate statistics and thus reach conclusions more quickly on their practical relevance and application, e.g. for improved animal welfare, health and performance of farm animals as well as for sustainable animal production and agricultural practice. To this end, about 650 pig microbiome studies will first be analysed to identify relevant protocols from sampling to bioinformatics analysis that are currently in use. Based on this, a template for the collection of metadata will be created to enable a standardised, accurate and comparable collection of animal and experiment-relevant data and factors (e.g. feeding, housing conditions, etc.) in the future. A pilot study will also compare different approaches to microbiome characterisation (target amplicon sequencing and shotgun metagenomics) and analysis (bioinformatics pipelines and reference databases) and compile their advantages and disadvantages and recommendations and references for different aspects of use. A statistically significant ring trial will be initiated at six designated livestock research sites to demonstrate the reproducibility and added value of a standardised protocol. The project partners will validate the manageability and advantages of the protocol and references, integrate data and propose standards and references for good scientific practice after evaluation.

 

 

Project Coordination:

Jun. Prof. Amélia Camarinha Silva

Microbial Ecology of Livestock, Institute of Animal Sciences

Hohenheim Center for Livestock Microbiome Research (HoLMiR), University of Hohenheim

 

Project Partners

Prof. Jürgen Zentek

Institute of Animal Nutrition, Freie Universität Berlin

 

Jun. Prof. Stéphanie Céline Hornburg

Institute for Animal Nutrition and Metabolic Physiology, Christian-Albrechts-Universität zu Kiel

 

Prof. Angelika Schniecke and Dr. habil. Krzysztof Flisikowski

Livestock Biotechnology, Technical University of Munich

 

Prof. Jens Tetens

Functional Breeding, Georg-August-University, Göttingen

 

Prof. Klaus Wimmers und Dr. Henry Reyer

Research Institute for Farm Animal Biology, Dummerstorf

 

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New strategies for reducing diseases on organic broiler farms with particular regard to the gut microbiome

New strategies for reducing diseases on organic broiler farms with particular regard to the gut microbiome

Status: ongoing


Project start: 01.10.2022
Project end: 30.09.2025

Funding code: 2821OE034 (Federal Ministry of Food and Agriculture)

Description

The overall objective of the ProBioHuhn project is a fundamental contribution to the development of new strategies for the reduction of disease on organic broiler farms with special consideration of the gut microbiome. In more detail, the project pursues the following work objectives:

(1) To increase knowledge on disease and therapy frequencies as well as antibiotic resistance in organic chicken flocks for meat production with respect to three fattening types, i.e. slower growing meat hybrids, and young cockerels of dual and single purpose lines.

(2) To elucidate the relationship between fattening type and gut microbiome, disease rates and antibiotic resistance, taking into account animal age, fattening performance, housing environment and management including feeding, e.g. regarding dietary fibre content.

(3) Derive and evaluate innovative strategies to reduce disease on organic broiler farms, taking into account on-farm factors as well as factors across farms and stages (feeding, health management, fattening types, etc.).

 

Persons involved

University of Hohenheim
Jun.-Prof. Dr. Amélia Camarinha Silva

University of Kassel
Prof. Dr. Ute Knierim
Dr. Margret Krieger

Federal Institute for Risk Assessment
PD Dr. Bernd-Alois Tenhagen

Thuringian Animal Diseases Fund
PD Dr Karsten Donat

 

The influence of the microbiome and their metabolites towards epithelial functions and smooth muscle contractility in regards to InsP6 degradation

Inositol phosphates and myo-inositol in poultry: studies at the interfaces of genetics, physiology, microbiome and nutrition

Improvement of protein utilization efficiency in pigs

Status: laufend

Projektbeginn: 01.08.2018
Projektende: 30.12.2021

Beschreibung
The overall goal of this project is to identify the impact of, microbiome, animal genetics, nutrition and protein metabolism on protein utilization efficiency. This project combines the expertise of five research groups that will further study protein utilization efficiency in pigs and ow to improve it.

The department Livestock Microbial Ecology is responsible to characterize the composition of the microbiota on a case-by-case basis and to reveal relationships with the proteome and protein turnover.

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This is a collaborative project with the departments of Prof. Jana Seifert (Feed-Gut Microbiota Interaction), Prof. Markus Rodehutscord (Animal Nutrition) and Prof. Jörn Bennewitz (Animal Genetics and Breeding).

Förderer

 

Publication:

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency

 

 

Dietary modulation of intestinal microbiota as trigger of liver health: role of bile acids (Di-Mi-Liv)

Status: laufend

Projektbeginn: 01.09.2018
Projektende: 31.9.2021

Förderkennzeichen: 01EA1804B

Description
The overall aim of the Di-Mi-Liv project is to determine whether the interaction of intestinal microbiota and bile acids is critical for the initiating and progressing stages of NAFLD. The project is part of the HDHL-INTIMIC Cofunded Call "Interrelation of the Intestinal Microbiome, Diet and Health".

Di-Mi-Liv combines the expertise of five research groups that will further study the effect of prebiotics in disease progression, gut microbiome and overall health. At Hohenheim the microbiome analyses will be based on metagenomics and metabolomics data.

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Completed Research Projects

Changes in broiler gastrointestinal bacterial community: response to different experimental diets

Status: completed

Projektbeginn: 01.01.2015
Projektende: 01.01.2018

Förderkennzeichen: HU 838/12-2, SE 20592/2

Schlagworte: Broiler, Gastrointestinaltract, microbial community, phosphorus, phytase

Beschreibung
Animal welfare is a public concern and all conditions must be provided in order to supply all animal needs. One of the most important needs is an appropriate diet, being this the reason why nutritionists develop adequate diets for broilers. Every change in the diet has an implication on the gut microbial community, which would affect the health status and growth rate. High-throughput techniques have shown to be useful for the identification of phylogenetic and functional composition of communities in diverse microbial ecosystems. On this project, high throughput sequencing will allow us to detect which are the microorganisms involved, and the metabolic mechanisms used to carry out feed digestion. It is important to gain a deep understanding of the microbial community and its interaction with the host, particularly in the gut where it occurs the breakdown of proteins and nutrient absorption. This is a collaborative project with the Animal Nutrition group.

Beteiligte Personen

Beteiligte Einrichtungen

Publikationen im Rahmen des Projekts

  • Borda-Molina D, Seifert J and Camarinha-Silva A (2018): Current perspectives of the chicken gastrointestinal tract and its microbiome
    DOI 10.1016/j.csbj.2018.03.002
  • Borda-Molina D, Vital M, Sommerfeld V, Rodehutscord M and Camarinha-Silva (2016:): AInsights into broilers’ gut microbiota fed with phosphorus, calcium, and phytase supplemented diets
    DOI 10.3389/fmicb.2016.02033

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract

Status: completed

Projektbeginn: 01.08.2014
Projektende: 31.12.2015

Schlagworte: Gastrointestinaltract, microbial community, pig

Beschreibung
A crucial step in the analyses of the microbial community of the porcine gastrointestinal tract is the extraction of DNA from the different section. The chosen method should allow to the identification of the majority of microorganisms present. Due to sample heterogeneity it is complicated to equally lyse cells of all species present, so it is important to investigate the best method to cover the highest number of microorganisms. Several methods use mechanical lysis that may increase the DNA degradation, while others have a gentle approach that may underestimate the existent species. There is a huge offer in the market regarding DNA extraction kits and several robust methods for DNA extraction were used in the literature. Standardization of methods is important to gain reliable knowledge on bacterial community profiles and to make porcine studies more comparable. The aim of this project is to test different DNA extraction methods and analyze the bacterial community composition with terminal restriction fragment length polymorphism (T-RFLP) and Illumina amplicon sequencing in order to identify the most suitable method for a comprehensive investigation of the porcine gastrointestinal microbiota.

Beteiligte Personen

Weitere Beteiligte Einrichtungen

Publikationen im Rahmen des Projekts

  • Burbach K, Seifert J, Pieper DH, Camarinha-Silva A (2016): Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
    DOI: 10.1002/mbo3.312

The effect of host genetics factors on shaping porcine gut microbiota

Status: completed

Projektbeginn: 01.08.2014
Projektende: 01.08.2016

Schlagworte: Genetics, microbial community, pig

Beschreibung
Data from United Nations Food and Agriculture Organization have shown that pork is the most consumed meat in Germany. Thus, it is an important concern in pork industry to maintain meat quality and food safety while improving growth performance. The microbiota of the gastrointestinal tract of the porcine has a tremendous impact on these traits. Besides studies about the influence of nutrition and medication on the microbiota, not much is known until date about how the quantitative genetic background of the host affects the porcine gut microbiota. To better understand this question, we study the microbial community composition using Illumina amplicon and sequencing genotype data obtained from Porcine SNP60 Bead Chip from Illumina.

Beteiligte Personen

Beteiligte Einrichtungen

Publikationen im Rahmen des Projekts

  • Camarinha-Silva A, Maushammer M, Wellmann R, Vital M, Preuss S and Bennewitz J (2017): Host genome influence on gut microbial composition and microbial prediction of complex traits in pigs
    DOI 10.1534/genetics.117.200782

Mitochondrial functionality in the dairy cow

Aging-associated modification of intestinal homeostasis and barrier function: Role of microbiota, iNOS and innate immunity - DFG SPP 1656

Status: laufend

Projektbeginn: 01.06.2016
Projektende:2020

Förderkennzeichen: DFG SPP 1656 (CA 1708/1-1)

Schlagworte: mice, aging, microbial community, sequenzierung

Beschreibung
Intestinal microbiota is known as a key component of gastrointestinal homeostasis and maintenance of intestinal barrier function. Thus, playing an important role in human health.

This project aims to understand the interaction of intestinal microbiota and intestine during aging with a particular focus on the impact of diet and energy bioavailability as factors contributing to aging-associated alterations of intestinal microbiota and intestinal barrier function.

Beteiligte Personen

Beteiligte Einrichtungen

Förderer

 

Projektwebsite:
www.intestinal-microbiota.de