Juan Manuel Peralta-Sánchez

Advancing Our Understanding of the Human Microbiome Using QIIME

High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.

Antimicrobial chemicals in hoopoe preen secretions are produced by symbiotic bacteria

Animals frequently use metabolites produced by symbiotic bacteria as agents against pathogens and parasites. Secretions from the preen gland of birds are used for this purpose, although its chemicals apparently are produced by the birds themselves. European hoopoes Upupa epops and green woodhoopoes Phoeniculus purpureus harbour symbiotic bacteria in the uropygial gland that might be partly responsible for the chemical composition of secretions. Here we investigate the antimicrobial activity of the volatile fraction of chemicals in hoopoe preen secretions, and, by means of experimental antibiotic injections, test whether symbiotic bacteria living within the uropygial gland are responsible for their production. Hoopoes produce two different kinds of secretions that differ drastically in their chemical composition. While the malodorous dark secretions produced by nestlings included a complex mix of volatiles, these chemicals did not appear in white secretions produced by non-nesting birds. All volatiles detected showed strong antibacterial activity, and a mixture of the chemicals at the concentrations measured in nestling glands inhibited the growth of all bacterial strains assayed. We found support for the hypothesized role of bacteria in the production of such antimicrobial chemicals because experimental clearance of bacteria from glands of nestlings with antibiotics resulted in secretions without most of the volatiles detected in control individuals. Thus, the presence of symbiotic bacteria in the uropygial gland provides hoopoes with potent antimicrobials for topical use.

Antibiotic-Producing Bacteria as a Possible Defence of Birds against Pathogenic Microorganisms

Theory strongly suggests that beneficial symbiotic bacteria could be common within birds. Our argument is based on the existence of within-host competition for resources between bacteria (i.e. bacterial interference), and on the differential effect that host fitness (i.e., reproductive success and probability of survival) has on fitness of different bacte- ria. If reproductive success of hosts is positively related to that of a first bacterium, and negatively related to that of a sec- ond bacterium, it would be of selective advantage for the former to develop chemicals that prevent host infection by the later pathogenic bacterium. Furthermore, we exemplify the possibility that hosts use antibiotic producing bacteria to pre- vent infections in different body parts (i.e., replacement therapy) or environment (i.e. nest sanitation). We review the up to now few available results suggesting associations of birds with antibiotic producing bacteria that result in fitness advan- tages to hosts. Evidence for such beneficial associations, however, has been very scarce so far, and an important research effort testing predictions of that relationship in different contexts is needed for a generalization of the hypothesis.

The evolution of size of the uropygial gland: mutualistic feather mites and uropygial secretion reduce bacterial loads of eggshells and hatching failures of European birds

Potentially, pathogenic bacteria are one of the main infective agents against which a battery of chemical and physical barriers has evolved in animals. Among these are the secretions by the exocrine uropygial gland in birds. The antimicrobial properties of uropygial secretions may prevent colonization and growth of microorganisms on feathers, skin and eggshells. However, uropygial gland secretions also favour the proliferation of feather mites that feed on secretions and microorganisms living on feathers that would otherwise reach eggshells during incubation if not consumed by feather mites. Therefore, at the interspecific level, uropygial gland size (as an index of volume of uropygial secretion) should be positively related to eggshell bacterial load (i.e. the risk of egg infection), whereas eggshell bacterial loads may be negatively related to abundance of feather mites eating bacteria. Here, we explore these previously untested predictions in a comparative framework using information on eggshell bacterial loads, uropygial gland size, diversity and abundance of feather mites and hatching success of 22 species of birds. The size of the uropygial gland was positively related to eggshell bacterial loads (mesophilic bacteria and Enterobacteriaceae), and bird species with higher diversity and abundance of feather mites harboured lower bacterial density on their eggshells (Enterococcus and Staphylococcus), in accordance with the hypothesis. Importantly, eggshell bacterial loads of mesophilic bacteria, Enterococcus and Enterobacteriaceae were negatively associated with hatching success, allowing us to interpret these interspecific relationships in a functional scenario, where both uropygial glands and mutualistic feather mites independently reduce the negative effects of pathogenic bacteria on avian fitness.

Migratory divides and their consequences for dispersal, population size and parasite–host interactions

Populations of migratory birds differ in their direction of migration with neighbouring populations often migrating in divergent directions separated by migratory divides. A total of 26% of 103 passerine bird species in Europe had migratory divides that were located disproportionately often along a longitudinal gradient in Central Europe, consistent with the assumption of a Quaternary glacial origin of such divides in the Iberian and Balkan peninsulas followed by recolonization. Given that studies have shown significant genetic differentiation and reduced gene flow across migratory divides, we hypothesized that an absence of migratory divides would result in elevated rates of gene flow and hence a reduced level of local adaptation. In a comparative study, species with migratory divides had larger population sizes and population densities and longer dispersal distances than species without migratory divides. Species with migratory divides tended to be habitat generalists. Bird species with migratory divides had higher richness of blood parasites and higher growth rates of Staphylococcus on their eggs during the incubation period. There was weaker cell‐mediated immunity in adults and stronger cell lysis in species with migratory divides. These findings may suggest that migratory divides constitute barriers to dispersal with consequences for ecology and evolution of distributions, population sizes, habitats and parasite–host interactions. They also suggest that migratory divides may play a role in local adaptation in host–parasite interactions.

Goshawk prey have more bacteria than non‐prey

1. Predators often prey on individuals that are sick or otherwise weakened. Although previous studies have shown higher abundance of parasites in prey, whether prey have elevated loads of micro-organisms remains to be determined. 2. We quantified the abundance of bacteria and fungi on feathers of woodpigeons Columba palumbus L., jays Garrulus glandarius L. and blackbirds Turdus merula L. that either fell prey to goshawks Accipiter gentilis L. or were not depredated. 3. We found an almost three-fold increase in bacterial load of prey compared with non-prey, while there was no significant difference between prey and non-prey in level of fungal infection of the plumage. 4. The results were not confounded by differences in size or mass of feathers, date of collection of feathers, or date of analysis of feathers for micro-organisms. 5. These findings suggest a previously unknown contribution of bacteria to risk of predation, with important implications for behaviour, population ecology and community ecology.

DNA sampling from eggshell swabbing is widely applicable in wild bird populations as demonstrated in 23 species

There is increasing interest in noninvasive DNA sampling techniques. In birds, there are several methods proposed for sampling DNA, and of these, the use of eggshell swabbing is potentially applicable to a wide range of species. We estimated the effectiveness of this method in the wild by sampling the eggs of 23 bird species. Sampling of eggs was performed twice per nest, soon after the clutch was laid and again at the end of egg incubation. We genotyped DNA samples using a set of five conserved microsatellite markers, which included a Z‐linked locus and a sex‐typing marker. We successfully collected avian DNA from the eggs of all species tested and from 88.48% of the samples. In most of the cases, the DNA concentration was low (ca. 10 ng/μL). The number of microsatellite loci amplified per sample (0–5) was used as a measure of the genotyping success of the sample. On average, we genotyped 3.01 ± 0.12 loci per sample (mean ± SE), and time of sampling did not seem to have an effect; however, genotyping success differed among species and was greater in those species that used feather material for lining their nest cups. We also checked for the occurrence of possible genotyping errors derived from using samples with very low DNA quantities (i.e. allelic dropout or false alleles) and for DNA contamination from individuals other than the mother, which appeared at a moderate rate (in 44% of the PCR replicates and in 17.36% of samples, respectively). Additionally, we investigated whether the DNA on eggshells corresponded to maternal DNA by comparing the genotypes obtained from the eggshells to those obtained from blood samples of all the nestlings for six nests of magpies. In five of the six magpie nests, we found evidence that the swab genotypes were a mixture of genotypes from both parents and this finding was independent of the time of incubation. Thus, our results broadly confirm that the swabbing of eggshells can be used as a noninvasive method for obtaining DNA and is applicable across a wide range of bird species. Nonetheless, genotyping errors should be properly estimated for each species by using a suite of highly polymorphic loci. These errors may be resolved by sampling only recently laid eggs (to avoid non‐maternal DNA contamination) or by performing several PCR replicates per sample (to avoid allelic dropout and false alleles) and/or by increasing the amount of DNA used in the PCR through increasing the volume of the PCR or increasing the concentration of template DNA.

Antimicrobial activity and genetic profile of Enteroccoci isolated from hoopoes uropygial gland.

Symbiotic microorganisms may be directly transferred from parents to offspring or acquired from a particular environment that animals may be able to select. If benefits for hosts vary among microbial strains, natural selection may favour hosts holding the most beneficial one. Enterococci symbionts living in the hoopoe (Upupa epops) uropygial gland are able to synthesise bacteriocins (antimicrobial peptides that inhibit the growth of competitor bacteria). We explored variability in genetic profile (through RAPD-PCR analyses) and antimicrobial properties (by performing antagonistic tests against ten bacterial indicator strains) of the different isolates obtained from the uropygial glands of hoopoe females and nestlings. We found that the genetic profile of bacterial isolates was related to antimicrobial activity, as well as to individual host identity and the nest from which samples were obtained. This association suggest that variation in the inhibitory capacity of Enterococci symbionts should be under selection.

Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow Nests

The use of feathers to line bird’s nests has traditionally been interpreted as having a thermoregulatory function. Feather-degrading bacteria growing on feathers lining nests may have antimicrobial properties, which may provide an additional benefit to lining nests with feathers. We test the hypothesis that the production of antimicrobial substances by feather bacteria affects the microbiological environment of the nest, and therefore the bacterial density on eggshells and, indirectly, hatching success. These effects would be expected to differ between nests lined with pigmented and white feathers, because bacteria grow differently on feathers of different colors. We experimentally manipulated the composition of pigmented and unpigmented feathers in nests of the barn swallow (Hirundo rustica) and studied the antimicrobial properties against the keratin-degrading bacterium Bacillus licheniformis of bacteria isolated from feathers of each color. Analyzed feathers were collected at the end of the incubation period, and antimicrobial activity was defined as the proportion of bacteria from the feathers that produce antibacterial substances effective against B. licheniformis. Our experimental manipulation affected antimicrobial activity, which was higher in nests with only white feathers at the beginning of incubation. Moreover, white feathers showed higher antimicrobial activity than black ones. Interestingly, antimicrobial activity in feathers of one of the colors correlated negatively with bacterial density on feather of the opposite color. Finally, antimicrobial activity of white feathers was negatively related to eggshell bacterial load. These results suggest that antimicrobial properties of feathers in general and of white feathers in particular affect the bacterial environment in nests. This environment in turn affects the bacterial load on eggshells, which may affect hatching success.

Environmental Factors Shape the Community of Symbionts in the Hoopoe Uropygial Gland More than Genetic Factors

ABSTRACT Exploring processes of coevolution of microorganisms and their hosts is a new imperative for life sciences. If bacteria protect hosts against pathogens, mechanisms facilitating the intergenerational transmission of such bacteria will be strongly selected by evolution. By disentangling the diversity of bacterial strains from the uropygium of hoopoes (Upupa epops) due to genetic relatedness or to a common environment, we explored the importance of horizontal (from the environment) and vertical (from parents) acquisition of antimicrobial-producing symbionts in this species. For this purpose, we compared bacterial communities among individuals in nonmanipulated nests; we also performed a cross-fostering experiment using recently hatched nestlings before uropygial gland development and some nestlings that were reared outside hoopoe nests. The capacity of individuals to acquire microbial symbionts horizontally during their development was supported by our results, since cross-fostered nestlings share bacterial strains with foster siblings and nestlings that were not in contact with hoopoe adults or nests also developed the symbiosis. Moreover, nestlings could change some bacterial strains over the course of their stay in the nest, and adult females changed their bacterial community in different years. However, a low rate of vertical transmission was inferred, since genetic siblings reared in different nests shared more bacterial strains than they shared with unrelated nestlings raised in different nests. In conclusion, hoopoes are able to incorporate new symbionts from the environment during the development of the uropygium, which could be a selective advantage if strains with higher antimicrobial capacity are incorporated into the gland and could aid hosts in fighting against pathogenic and disease-causing microbes.