Study On The Gut Microbiota Of Rhesus Macaques Under Captive And Free-ranging Conditions

The gut of animals is a complex ecosystem,containing abundant and diverse microbiome.More and more studies have shown that gut microbiota play crucial role on nutrient absorption,energy metabolic balance,immune function,and behaviors.Gut microbiota may be also one of the adaptive features in animals,and could be affected by habitat,food resources.Gut microbiota is considered as ‘the second genomes’ of animal.However,human-dominant global and reginal changes not only can directly / indirectly influence animal’s habitat,food resources,physiological ecology and behaviors,but also could affect the above-mentioned aspects through altering the gut microbiota.Therefore,it is important to investigate the gut microbiota in animals,especially in wildlife,under different environmental conditions.These will be helpful for understanding the responses of animals to changing environment,and also be useful for the conservation and management of wildlife,especially for rare / endangered species.Rhesus macaque(Macaca mulatta)is the most world-widely distributed non-human primate species.It has many similarities with humans in the aspects of physiology,biochemistry,and behaviors.It is not only a key laboratory animal,butalso a star species for zoo,safari park,and ecotourism area.In order to investigate the effects of environmental differences on the gut microbiota in rhesus macaques,fecal samples of captive and free-ranging individuals were freshly collected through non-invasive sampling methods between June 2016 and October 2017.Next generation sequencing platform were adopted,and the technology and platform of bioinformatics were adopted to analyze the data.Then the gut microbiota were analyzed and compared.The major contents and results are as follows:1)Study of gut microbiota in captive rhesus macaquesIn January 2017,20 fecal samples of rhesus macaques were freshly collected in the morning(AM group)and afternoon(PM group)respectively from captive environment,the Zhengzhou Zoo.The fecal genomic DNAs were extracted with commercial DNA extraction kits,and the quality was assessed.Then 10 samples for each group were randomly selected for sequencing.The results showed that: 1)gut microbiota: there were totally 741 OTUs,belong to 160 genera,57 families,13 phyla,including 28 OTUs and 2 genera unique to AM group,while only 6 OTUs unique to PM group;2)alpha diversity: the indices of abundance(Sobs),richness(Shannon)and evenness(Shannon even)of gut microbiota in the AM group were significantly higher than that of the PM group;3)sample grouping: the analyses of ANOSIM showed there were no significant differences between AM group and PM group at the levels of OTU,genus,family and phylum;4)core gut microbiota: the abundance of Firmicutes and Bacteroidetes took up 86 % in phylum level,and Ruminococcaceae and Prevotellaceae were the major groups at the level of family,and Prevotella were the dominant genus and therefore the gut microbiota of captive rhesus macaque could be assigned as ‘Prevotella enterotype’;5)differences between groups: the abundance of OTU299,OTU691 and OTU705 in AM group were significantly higher than that in the PM group,but the OTU177 was opposite;the abundances of Lactobacillus at genus level and Lactobacillaceae at family level in PM group were significantly higher than that in AM group;at phylum level,the abundance of Tenericutes in the AM group was significantly higher than that in the PM group.2)Study of gut microbiota in free-ranging rhesus macaquesDuring January 11 th and 15 th,2017,fecal samples of rhesus macaques for adult females(AF group)and adult males(AM group)were freshly collected from free-ranging WLK-1 group inhabiting in the Jiyuan Wulongkou Scenic Area.The fecal genomic DNAs were extracted with commercial DNA extraction kits,and the quality was assessed.Then 10 samples for each group were randomly selected for sequencing.The results showed that: 1)gut microbiota: there were totally 845 OTUs,belong to 185 genera,62 families,14 phyla,including 11 OTUs,1 genus,1 family,and 1 phylum unique to AF group,while 37 OTUs and 1 genus unique to AM group;2)alpha diversity: there were no significant differences between AF and AM groups in the indices of abundance(Sobs),richness(Shannon)and evenness(Shannon even)of gut microbiota at the levels of OTU,genus,family and phylum;3)sample grouping: the analyses of ANOSIM showed there were no significant differences between AF group and AM group at the levels of OTU,genus,family and phylum;4)core gut microbiota: the abundance of Firmicutes and Bacteroidetes took up 84 % in phylum level,and Ruminococcaceae and Prevotellaceae took up ca.43%,and Prevotella were the dominant genus and therefore the gut microbiota of free-ranging rhesus macaque could be assigned as ‘Prevotella enterotype’;5)differences between groups: the abundance of Bacteroidales_S24-7_group at family level in AF group was significantly higher than that in AM group;at phylum level,Cyanobacteria was only detected in AF group rather than the AM group.3)Comparison of gut microbiota in captive and free-ranging rhesus macaquesBased on the two studies,the analyses of the gut microbiota in captive and free-ranging rhesus macaques have shown there were no significant intragroup differences.Therefore,further comparison was performed between captive(C group)and free-ranging(F group)groups.The results showed that: 1)gut microbiota: there were totally 1064 OTUs,belong to 191 genera,66 families,14 phyla,including 60 OTUs,3 genera and 2 families,unique to C group,while 95 OTUs and 7 genera and1 family unique to F group;2)alpha diversity: abundance of gut microbiota at genus level in F group was higher than that of the C group,but there were no furthersignificant differences between C and F groups in the indices of abundance(Sobs),richness(Shannon)and evenness(Shannon even)of gut microbiota at the levels of OTU,genus,family and phylum;3)sample grouping: the analyses of ANOSIM showed there were significant differences between C group and F group at the levels of OTU,genus and family,but no difference was detected in the ANOSIM analysis,rather than Adonis analysis,at phylum level;4)core gut microbiota: the abundance of Firmicutes and Bacteroidetes took up 85 % in phylum level,and Ruminococcaceae and Prevotellaceae took up ca.44%,and Prevotella were the dominant genus and therefore the gut microbiota of both captive and free-ranging rhesus macaque could be assigned as ‘Prevotella enterotype’;5)differences between groups: the abundance of OTU669,OTU957,OTU1034,OTU668,OTU1003,and OTU361 in the C group was significantly higher than that of the F group,but the abundance of OTU2877,OTU958,OTU806,OTU181,OTU92 and OTU809 were opposite;at the genus level,the abundances of Succunivibrio and Megasphaera in the F group were significantly higher than that of the C group;at the family level,the abundances of Lachnospiraceae,Veillonellaceae,Succinivibrionaceae in the F group were significantly higher than that of the C group,rather than the Peptostreptococcaceae;at the phylum level,the abundances of Bacteroidetes,Tenericutes,Verrucomicrobia and Lentisphaerae in C group were significantly higher than that of the F group.In summary,the results of the study showed that the gut microbiota of rhesus macaques was characterized as high conservation but also relative plasticity.The gut microbiota could show slight differences under captive and free-ranging environments.This study primarily analyzed the effects of environmental difference on the gut microbiota of rhesus macaques.However,whether these effects will influence the sustainability of rhesus macaques,especially the impact on wild populations,remains to be further studied.