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microorganisms Article Environmental Impact on Differential Composition of Gut Microbiota in Indoor Chickens in Commercial Production and Outdoor, Backyard Chickens Zuzana Seidlerova, Tereza Kubasova, Marcela Faldynova, Magdalena Crhanova, Daniela Karasova, Vladimir Babak and Ivan Rychlik * Veterinary Research Institute, 62100 Brno, Czech Republic; [email protected] (Z.S.); [email protected] (T.K.); [email protected] (M.F.); [email protected] (M.C.); [email protected] (D.K.); [email protected] (V.B.) * Correspondence: [email protected]; Tel.: +420-533331201 Received: 8 April 2020; Accepted: 18 May 2020; Published: 20 May 2020 Abstract: In this study, we compared the caecal microbiota composition of egg-laying hens from commercial production that are kept indoors throughout their whole life with microbiota of hens kept outdoors. The microbiota of outdoor hens consisted of lower numbers of bacterial species than the microbiota of indoor hens. At the phylum level, microbiota of outdoor hens was enriched for Bacteroidetes (62.41 4.47% of total microbiota in outdoor hens and 52.01 6.27% in indoor ± ± hens) and Proteobacteria (9.33 4.99% in outdoor and 5.47 2.24% in indoor hens). On the other ± ± hand, Firmicutes were more abundant in the microbiota of indoor hens (33.28 5.11% in indoor ± and 20.66 4.41% in outdoor hens). Horizontally transferrable antibiotic resistance genes tetO, ± tet(32), tet(44), and tetW were also less abundant in the microbiota of outdoor hens than indoor hens. A comparison of the microbiota composition at the genus and species levels pointed toward isolates specifically adapted to the two extreme environments. However, genera and species recorded as being similarly abundant in the microbiota of indoor and outdoor hens are equally as noteworthy because these represent microbiota members that are highly adapted to chickens, irrespective of their genetics, feed composition, and living environment. Keywords: chicken microbiota; microbiome; caecum; environment; backyard chicken 1. Introduction Chickens in commercial production are hatched without any contact with adult birds, and colonization of their intestinal tract is dependent on environmental sources only. The development of their microbiota is therefore slower than in chicks that have any form of contact with adult hen microbiota [1,2]. The speed of microbiota development is quite important since the level of microbiota development correlates with the chicken’s natural resistance to infection with pathogens like Salmonella or Clostridium perfringens [3–5]. Both the speed and quality of microbiota establishment is therefore key for the production of healthy chickens and, consequently, for improved productivity, reduced need for antibiotic therapy, and increased animal welfare [6,7]. Attempts with administration of microbiota from healthy adults to newly hatched chicks in intensive production systems date back to the 1970s [2]. The concept, termed competitive exclusion due to the exclusion of enteric pathogens from gut colonization, is known in poultry production. Products containing complex gut microbiota obtained by anaerobic culture of fecal microbiota from adult hens, e.g., Aviguard or Broilact, are commercially available. However, hens used as donors of fecal microbiota for the fermentation of competitive exclusion products are hatched in hatcheries, without any contact with microbiota from healthy adult hens. Moreover, to minimize the risk of Microorganisms 2020, 8, 767; doi:10.3390/microorganisms8050767 www.mdpi.com/journal/microorganisms Microorganisms 2020, 8, 767 2 of 11 uncontrolled infection of the donor hens, these hens are kept under highly contained conditions. Microorganisms 2020, 8, x FOR PEER REVIEW 2 of 10 However, this style of raising chickens is quite different from the conditions to which chickens have adaptedHowever, during this style millions of raising of years chickens of evolution. is quite different While a from contained the conditions environment to which is necessary chickens for have the productionadapted during of safe millions products, of years this measureof evolution. may While exclude a contained some beneficial environment microbes is necessary from entering for the the intestinalproduction tract of safe of these products, donor this hens. measure This may is why exclude we have some become beneficial interested microbes in from the dienteringfferences the in microbiotaintestinal tract of indoor of these hens donor in intensive hens. This commercial is why productionwe have become and outdoor interested chickens in the kept differences in backyards in ofmicrobiota private owners of indoor for their hens own in eggintensive production. commercial production and outdoor chickens kept in backyardsIn this of study, private we owners therefore for their compared own egg the production. caecal microbiota composition in chickens from commercialIn this production, study, we kepttherefore indoors compared throughout the theircaecal whole microbiota life and withcomposition microbiota in ofchickens chickens from kept outdoorscommercial throughout production, their kept whole indoors life. Caecalthroughout microbiota their whole was selected life and due with to microbiota its high complexity of chickens and alsokept importance outdoors throughout for natural their resistance whole life. of chickens Caecal mi tocrobiota the colonization was selected of pathogensdue to its high like complexity Salmonella. Privateand also owners importance in village for areas natural of the resistance Czech Republic of chickens keep small to the flocks colonization of 5–10 hens of forpathogens their own like egg consumption,Salmonella. Private i.e., not owners for global in village market areas distribution of the Czech (Figure Republic1). This keep comparison small flocks allowed of 5–10 us to hens address for thetheir importance own egg ofconsumption, the external environmenti.e., not for inglobal shaping market chicken distribution gut microbiota. (Figure Due 1). toThis access comparison to a wide varietyallowed of us feed, to address we expected the importance that the microbiota of the extern ofal outdoor environment chickens in wouldshaping be chicken more complex gut microbiota. than the microbiotaDue to access of commercial to a wide variety indoor of chickens. feed, we However,expected that what the if themicrobiota feed of commercialof outdoor chickens indoor chickens would enrichedbe more forcomplex vitamins, than trace the microbiota elements, specificof commercia feed additivesl indoor etc.chickens. may allowHowever, for a what broader if the microbiota feed of tocommercial colonize their indoor intestinal chickens tract? enriched Could for the vitamins, outdoor trace chicken’s elements, specific specific microbiota feed additives members etc. be may used asallow probiotics for a broader for indoor microbiota chickens, to colonize or do they their represent intestinal microbiota tract? Could members the outdoor too adapted chicken’s to specific outdoor chickens?microbiota Or members are the microbiota be used as members probiotics present for indoor in both chickens, indoor andor do outdoor they represent chickens microbiota those of the highestmembers probiotic too adapted potential to outdoor since these chickens? are always Or are present, the microbiota irrespective members of chicken present genetic in line,both diindoorfferent feed,and andoutdoor habitat chickens occupied? those Though of the not highest all these probio questionstic potential could besince ultimately these are answered always inpresent, a single study,irrespective a comparison of chicken of microbiota genetic line, of outdoor different and feed, indoor and chickens habitat isoccupied? the first necessary Though stepnot towardsall these a betterquestions understanding could be ultimately of chicken answered core microbiota in a single and study, microbiota a comparison members of microbiota specifically of selected outdoor under and twoindoor extreme chickens environmental is the first necessary ecosystems. step towards a better understanding of chicken core microbiota and microbiota members specifically selected under two extreme environmental ecosystems. Figure 1. Living environment of indoor and outdoor chickens. Raising of egg layers in commercial Figure 1. Living environment of indoor and outdoor chickens. Raising of egg layers in commercial production in an indoor environment (panel (a)) and egg laying hens in an outdoor, backyard production in an indoor environment (panel (a)) and egg laying hens in an outdoor, backyard environment (panels (b–e)). environment (panels (b–e)). 2. Materials and Methods 2. Materials and Methods 2.1. Experimental Animals 2.1. Experimental Animals Twenty 30–50-week-old hens were obtained from three different egg producing farms using enrichedTwenty battery 30–50-week-old cages for egg hens production. were obtained At any from time three of rearingdifferent or egg egg producing production, farms these using hens hadenriched no access battery to thecages outdoor for egg environment production. andAt any were time kept of inrearing a strictly or egg controlled production, indoor these environment. hens had Anno additionalaccess to the 17 outdoor hens were environment obtained from and sixwere diff kepterent in backyard a strictly poultrycontrolled flocks indoor with environment. the agreement An of additional 17 hens were obtained from six different backyard poultry flocks with the agreement of the owners. These hens were 2–4 years old and were reared
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  • Genetics of Human Gut Microbiome Composition

    Genetics of Human Gut Microbiome Composition

    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.26.173724; this version posted June 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Genetics of human gut microbiome composition Authors: Alexander Kurilshikov1,†, Carolina Medina-Gomez2,3,†, Rodrigo Bacigalupe4,5,†, Djawad Radjabzadeh2,†, Jun Wang4,5,6,†, Ayse Demirkan1,7§, Caroline I. Le Roy8,§, Juan Antonio 5 Raygoza Garay9,10,§, Casey T. Finnicum11,§, Xingrong Liu12,§, Daria V. Zhernakova1,§, Marc Jan Bonder1,§, Tue H. Hansen13, Fabian Frost14, Malte C. Rühlemann15, Williams Turpin9,10, Jee- Young Moon16, Han-Na Kim17,18, Kreete Lüll19, Elad Barkan20, Shiraz A. Shah21, Myriam Fornage22,23, Joanna Szopinska-Tokov24, Zachary D. Wallen25, Dmitrii Borisevich13, Lars Agreus26, Anna Andreasson27, Corinna Bang15, Larbi Bedrani9, Jordana T. Bell8, Hans 10 Bisgaard21, Michael Boehnke28, Dorret I. Boomsma29, Robert D. Burk16,30,31, Annique Claringbould1, Kenneth Croitoru9,10, Gareth E. Davies11,29, Cornelia M. van Duijn32,33, Liesbeth Duijts3,34, Gwen Falony4,5, Jingyuan Fu1,35, Adriaan van der Graaf1, Torben Hansen13, Georg Homuth36, David A. Hughes37,38, Richard G. Ijzerman39, Matthew A. Jackson7,40, Vincent W.V. Jaddoe3,32, Marie Joossens4,5, Torben Jørgensen41, Daniel Keszthelyi42,43, Rob Knight44,45,46, 15 Markku Laakso47, Matthias Laudes48, Lenore J. Launer49, Wolfgang Lieb50, Aldons J. Lusis51,52, Ad A.M. Masclee42,43, Henriette A. Moll34, Zlatan Mujagic42,43, Qi Qibin16, Daphna Rothschild20, Hocheol Shin53,54, Søren J. Sørensen55, Claire J.