Additional file 3: Figure S1. of Molecular survey of Enterocytozoon bieneusi in sheep and goats in China

FIG 1 Phylogenetic relationships of the E. bieneusi genotypes identified in this study and other reported genotypes, as inferred by neighbor-joining analysis of ITS gene sequences based on the distances calculated using the Kimura 2-parameter model. Bootstrap values >50 % from 1000 replicates are shown on the nodes. The tree was rooted with GenBank sequence AF059610 from a dog. Known genotypes observed in goats and sheep are marked with open squares and triangles, and the new genotypes in goats and sheep from this study are indicated by filled squares and triangles. (TIF 2078 kb

Additional file 1: Table S1. of Molecular characterization of hemotropic mycoplasmas (Mycoplasma ovis and ‘Candidatus Mycoplasma haemovis’) in sheep and goats in China

Prevalence of hemoplasmas (Mycoplasma ovis and ‘Candidatus Mycoplasma haemovis’) of sheep and goats in different farms. Table S2. The origins of the 103 selected positive specimens. Figure S1. Collection sites (indicated by black circles) in Henan province. Figure S2. The binding sites of nested PCR primers. (DOCX 97 kb

Additional file 2: of Molecular survey of Enterocytozoon bieneusi in sheep and goats in China

Nucleotide substitutions among some new genotypes of E. bieneusi from this study versus the reported genotype BEB6 (EU 153584). (DOC 132 kb

Additional file 2: Table S2. of High prevalence of Enterocytozoon bieneusi zoonotic genotype D in captive golden snub-nosed monkey (Rhinopithecus roxellanae) in zoos in China

Nucleotide substitutions among all sequences found in this study versus the reported genotype J (KU557671). (XLS 49 kb

Multilocus Sequence Subtyping and Genetic Structure of <em>Cryptosporidium muris</em> and <em>Cryptosporidium andersoni</em>

<div><p>In this study, nine <em>C. muris</em> and 43 <em>C. andersoni</em> isolates from various animals in China were subtyped by a multilocus sequence typing (MLST) tool. DNA sequence analyses showed the presence of 1–2 subtypes of <em>C. muris</em> and 2–6 subtypes of <em>C. andersoni</em> at each of the four loci (MS1, MS2, MS3, and MS16), nine of which represented new subtypes. Altogether, two <em>C. muris</em> and 10 <em>C. andersoni</em> MLST subtypes were detected. Linkage disequilibrium analysis indicated although the overall population structure of the two parasites was clonal, the Chinese <em>C. andersoni</em> in cattle has an epidemic structure. Three and two clusters were produced in the <em>C. muris</em> and <em>C. andersoni</em> populations by Structure 2.3.3 analysis, with Chinese <em>C. muris</em> and <em>C. andersoni</em> substructures differing from other countries. Thus, this study suggested the prevalence of <em>C. andersoni</em> in China is not attributed to the introduction of dairy cattle. More studies involving more genetic loci and systematic sampling are needed to better elucidate the population genetic structure of <em>C. muris</em> and <em>C. andersoni</em> in the world and the genetic basis for the difference in host specificity among the two most common gastric parasites.</p> </div

Analysis of linkage disequilibrium in <i>C. andersoni</i> and <i>C. muris</i> populations.

<p><b>Note</b>: <i>V</i>_D = the pairwise variance, <i>L = </i>95% critical value; ^awith the same MLST type as one individual; the data of the non-Chinese isolates came from a recently published paper <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043782#pone.0043782-Feng1" target="_blank">[³¹]</a>.</p

The nature of minisatellite repeats at four genetic loci.

<p>The nature of minisatellite repeats at four genetic loci.</p

Population structure inferred by Bayesian clustering using multilocus subtype information.

<p>A, <i>Cryptosporidium muris</i>; B, <i>Cryptosporidium andersoni</i>. Each individual is shown as a thin vertical line, which is partitioned into <i>K</i> colored components representing estimated membership fractions in <i>K</i> genetic clusters, and the geographic locations are at the bottom. The pie charts show the distribution of genetic clusters in different countries and various animals. JP = Japan; PE = Peru; Ken = Kenya; EG = Egypt; CS = Czech Republic; CN = China; B = beef cattle; C = bactrian camel; D = dairy cattle; H = hamster; S = sheep.</p

Specific locations at which specimens were collected in this study.

<p>★locations of zoos.</p

Isolates used in this study and their subtype identity at the four minisatellite loci.

<p>Isolates used in this study and their subtype identity at the four minisatellite loci.</p