Identification of horizontally transmissible genes including those responsible for antibiotic resistance is apparently a single task. However, immediately after it turns out that this task is not that simple. In our new paper in the Microbiology Spectrum focused on this issue and proposed a functional pipeline. Our conclusions can be founded in this pdf file.
A new paper from our production has been accepted for publication in the Poultry Science. This paper introduces microbial composition of skin and tracheal microbiota and further develops importance of contact between a hen and newly hatched chicks for the development of skin and respiratory tract microbiota of chickens. Many bacteria of gut origin were detected as a part of skin and trachea microbiota but since we used DNA sequencing to determine microbiota composition, this was likely only a DNA from no longer viable gut anaerobes. On the other hand, Lactobacilli and Streptococci belonged among likely vital bacteria which were common in skin and tracheal microbiota of chicks in contact with adult hens. Cutibacterium acnes represented another taxon common in skin and respiratory tract microbiota. Finally, Clostridium disporicum and Clostridium perfringens were common in skin microbiota but only rarely entered respiratory tract.
Our new paper on the relationship of gut microbiota and presence of low molecular weight compounds in caecal digesta of one-week-old chickens has been just published in the Poultry Science. A general conclusion is that colonisation of the chicken caecum with Bacteroides, Megamonas, Megasphaera, Phascolarctobacterium, Succinatimonas or Sutterella (gut anaerobes) leads to release of additional molecules of plant origin from the feed into digesta. Digesta of chicks colonised by gut anaerobes was enriched for derivates of nucleotides and amino acids, and products of their fermentation. Digesta of chicks colonised by gut anaerobes was enriched also for biologically active molecules like daidzein, genistein, glycitein, nicotinamide, feruloyl putrescine or feruloyl agmatine. There were also some exceptions confirming this rule, e.g. glutamate and tyramine were more abundant in caecal digesta of control chickens. Similarly, betaine or soyasaponin I dominated in digesta of control chickens in comparison to those colonised by gut anaerobe mixture.
We are still considering placement of this knowledge since increased abundance of a given metabolite is a compromise between degradative function of gut microbiota of feed ingredients associated with release of additional molecules, metabolic function of gut microbiota and their ability to ferment just released amino acids or nucleotides, ability of chickens to resorb newly available nutrients and ability of chickens to secrete their own metabolites in caecal digesta. Increased abundance of daidzein, genistein or glycitein, all soya flavonoids, therefore indicates inability of chickens to resorb them in such an amount. On the other hand, disappearance of betaine in digesta of chicks colonised by gut anaerobe mixture indicates that at least one of them can utilise and degrade betaine. Despite such uncertainties, a mere fact that the composition of gut microbiota extensively modifies composition of low molecular weight compounds means that it is possible to enrich digesta for biologically active molecules by a combination of feed formula modification and administration of defined mixtures of selected gut microbiota members.
We have updated our file on the occurrence of different bacteria in different hosts. This file was enriched for new data on the distribution of bacterial genera and species along chicken production. Once you find out how to work with this file, you will see that Anaerostipes is tightly associated with humans, Succinatimonas with chickens and Phascolarctobacterium represent genus representatives of which can be found in intestinal tract of different hosts. In chicken production, Brevibacterium and Brachybacterium are associated with litter, Acinetobacter with eggshell waste and Cutibacterium with skin and trachea. However, you can find out much more information, e.g. on the distribution of Lactobacilli in humans or dogs. Download our file for more information here.
A new review paper from our production has been accepted for publication in the Avian Diseases. This review introduces bacterial flora in different chicken organs as well as in their environment. As is the case in our reviews, we have decided for less standard and rather challenging review in which we mention alternative views and challenging associations. The challenging approach is not a purpose for itself. Instead, reason for such style is to force readers to think, to agree (better possibility) or to disagree, to get readers out of their daily comfort of routine way of thinking. One example of alternative idea presented in the review is the information that E. coli is not a species adapted to intestinal tract. Instead, E. coli dominates in chicken environment from where it enters intestinal tract. There are more alternative ideas in this review. If you are ready to think differently, find the original paper here.
New paper on the protection of chickens by defined probiotic mixtures consisting of strict gut anaerobes against pathogenic E. coli has been just accepted for publication in the Poultry Science. Although we successfully test different defined mixtures of strict gut anaerobes in a protection of chickens against Salmonella, the first published paper reports on the viability of such concept in a protection of chickens against pathogenic E. coli. Currently we prepare the first product of this type for registration in the Czech Republic in 2023, and this will be followed by its commercial distribution immediately after. Information on the ability to suppress infection by pathogenic E. coli can be found here.
A new paper on the development of litter microbiota in chicken production has been accepted in the Applied and Environmental Microbiology in which we describe a time-dependent development. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei and Lactobacilli dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Identification of the species present in the litter opens the possibility for active manipulation of litter microbiota, something what we are already working on.
We have published a new paper comparing chicken, pig, human and even Antarctic penguin microbiota in the Microorganisms journal. Apparently strange idea has brought interesting findings. We have found out that bacteria belonging to phylum Bacteroidetes exhibit host adaptation while representatives of phylum Firmicutes were usually broadly distributed among different hosts. Host adaptation is not directly associated with taxonomic classification but correlates with the ability of gut anaerobes to survive in external environment. Bacterial species exhibiting some form of their existence resistant to aerobic environment may survive outside eukaryotic host and easily spread to another host. Since Firmicutes include spore forming Clostridiales and aerotolerant Bacillales, global distribution among different hosts is typical for them. On the other hand, anaerobic bacteria from phylum Bacteroidetes usually do not exhibit any form of their existence in aerobic environment and therefor spread only over a short distance, usually by contact among individuals of the same host species. This favours host adaptation and speciation what is indeed observed in these bacteria. Such findings may be important for the development of novel types of probiotics. In host adapted gut microbiota species it is recommended to consider their host preference. On the other hand, origin of probiotic strain is less important in the host non-adapted specie. However, to respect natural ecology of host non-adapted species, i.e. their permanent supply from environment, such probiotics should be provided for prolonged period of time, either via drinking water or feed.
For more information, click here.
A miniconference presenting final results achieved during INPOMED project was arranged on May 23, 2022 at the Veterinary Research Institute, Brno, Czech Republic. Recordings of all presentations can be seen here.
on March 22, 2022, as a part of Interreg supported INPOMED project we organised an on-line webinar. The first presentation was given by Prof. Bernd Kaspers from Ludwig-Maximilians University Munich and was be focused on the importance of gut microbiota on the development of gut immune system. Second invited presentation was delivered by prof. Silke Rautenschlein from University of Veterinary Medicine Hannover covering a topic of Campylobacter interactions with chicken host. Following invited speaker’s presentations, results of INPOMED project partners were introduced in a form of four brief presentations. We hope that you have learnt at least something new and inspirative for you.
For the full recording of the whole webinar, click here.