Skip to main content

Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru

Abstract

Background

Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The microbiome in ticks is an endosymbiotic, pathogenic and is yet to be fully understood.

Results

Adult male Amblyomma scalpturatum (A. scalpturatum) and Amblyomma ovale (A. ovale) ticks were collected from Tapirus terrestris (T. terrestris) captured in the rural area of San Lorenzo Village, and males Amblyomma sabanerae were collected from Chelonoidis denticulate (C. denticulate) of the Gamita Farm in the Amazon region of Madre de Dios, Peru. The Chao1 and Shannon–Weaver analyses indicated a greater bacterial richness and diversity in male A. sabanerae (Amblyomma sabanerae; 613.65–2.03) compared to male A. scalpturatum and A. ovale (A. scalpturatum and A. ovale; 102.17–0.40). Taxonomic analyses identified 478 operational taxonomic units representing 220 bacterial genera in A. sabanerae and 86 operational taxonomic units representing 28 bacterial genera in A. scalpturatum and A. ovale. Of the most prevalent genera was Francisella (73.2%) in A. sabanerae, and Acinetobacter (96.8%) in A. scalpturatum and A. ovale to be considered as the core microbiome of A. sabanerae and A. scalpturatum/A. ovale respectively.

Conclusions

We found a high bacterial diversity in male of A. sabanerae collected from C. denticulata showed prevalence of Francisella and prevalence of Acinetobacter in male A. scalpturatum and A. ovale collected from T. terrestris. The greatest bacterial diversity and richness was found in males A. sabanerae. This is the first bacterial metagenomic study performed in A. scalpturatum/A. ovale and A. sabanerae collected from T. terrestris and C. denticulata in the Peruvian jungle.

Peer Review reports

Background

Ticks are vectors of pathogens for different organisms and are one of the main vectors related to metaxene diseases [1]. Ticks transmit pathogenic protozoa and bacteria such as Babesia and Rickettsia respectively, can be identified by microbiological methods such as microscopy and culture in addition to molecular methods such as new generation sequencing techniques (NGS) [2, 3]. Metagenomics in ticks can identify commensal and symbiotic bacteria [4, 5] as well as pathogenic bacteria of veterinary and human interest [6]. The microbiome in ticks has yet to be explored in search of elucidating whether it has a neutral, harmful, or beneficial role for arthropods as well as for their potential hosts [6]. In this sense, previous studies on Ixodes pavlovskyi have described Rickettsia, Anaplasma, Erlichia and Borrelia burgdorferi and their implication in the vector and the hosts [6, 7]. Another study in Dermacentor occidentalis identified Rickettsia philipii, and two new bunyaviruses [8]. Additionally, in ticks of the genera Amblyomma sp., Ixodes sp., and Haemaphysalis sp., bacteria such as Anaplasma, Bartonella, Borrelia, Ehrlichia, Francisella and Rickettsia have been identified [9]. Amblyomma scalpturatum and Amblyomma ovale (Amblyomma scalpturatum/Amblyomma ovale) and Amblyomma sabanerae show a distribution in tropical forests and could be involved in the transmission of pathogens between forest animals and humans [10].

As shown, metagenomics is a very useful tool to identify potential infectious agents in ticks and to study the ecology of these agents within the framework of Public Health regarding the prevention of diseases caused by microorganisms transmitted by ticks.

Studies on microbial agents in ticks such as in western Brazil detected the presence of Rickettsia bellii in A. ovale and A. scalpturatum [11]. In the case of A. scalpturatum, it is a native tick from South America and usually parasitizes tapirs and suidae [12]. In A. sabanerae it has also been detected by molecular methods R. bellii in El Salvador [13]. Another study in Mexico, the bacterium Rickettsia parkeri was identified in A. ovale [14]. Additionally, in a multicenter study in Brazil, R. parkeri, R. bellii, R. asemboensis and R. felis were identified in A. ovale [15]. In Peru there is not much information on the study of ticks and their microorganisms, so our study is considered a pioneer in this type.

The objective of this study was to identify the bacterial microbiome through metagenomics in Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris (T. terrestris) and Amblyomma sabanerae collected from Chelonoidis denticulata (C. denticulata), Madre de Dios- Peru.

Material and methods

Ethical aspects

This study was approved by the Office of Public Health and Environment of the Regional Council of Madre de Dios (Oficina de Salud Pública y Medio Ambiente del Consejo Regional de Madre de Dios), Peru. Laboratory procedures for bacterial identification were conducted in accordance with the international guidelines for the use of animals in research and the standards of the Animal Care and Use Committee of the Health Research Area of the Madre de Dios Regional Council Board (Comité de Cuidado y Uso de Animales del Área de Investigación en Salud de la Junta del Consejo Regional de Madre de Dios). The study was carried out in compliance with the ARRIVE guidelines.

Geographic location

The study was conducted in the outskirts of San Lorenzo, district of Tahuamanu ( 11° 27′ 13.73" S, 69° 20′ 2.54" W; World Geodetic System (WGS) 285 m. a. s. l), Tahuamanu province and Chacra Gamitana, district of Las Piedras (12° 30′ 36.76" S, 68° 58´ 49.3" W; WGS, 250 m. a. s. l), Tambopata province in Madre de Dios region, Peru (Fig. 1). The collection site corresponds to a forest area where hunting of wild animals is allowed. The average annual rainfall in the study area is 1,600 mm3, and the average annual temperature is 25 °C. The area is in the tropical wet forest zone. During sample collection, the weather was hot and humid.

Fig. 1
figure 1

San Lorenzo Village and Gamitana Farm where T. terrestris and C. denticulata were collected respectively. This map was created with the Geoservidor https://geoservidor.minam.gob.pe/ edited with ArcGis 10.3.1 version 2015

Sample collection

A wild T. terrestris was captured in San Lorenzo Village (11° 27′ 13,73" S, 69° 20′ 2,54" W; WGS, 285 m. a. s. l) in June 2012. 5 ticks were collected from its abdominal region 3 h after its sacrifice using forceps and were individually placed in 2 ml cryovials containing 96% ethyl alcohol. Cryovials were labeled with an identification code for the sampling site and the animal from which the sample was collected. Similarly, in the case of the Gamitana Farm, Las Piedras district, located on the left bank of the Bajo Madre de Dios River (12° 30′ 36.76" S, 68° 58´ 49.3" W; WGS, 250 m. a. s. l), manual collections of 10 “males” ticks, were taken from one C. denticulata. These collections were made during the daytime between 9:00 a. m. and 11 a. m.

On sterile plates ticks were washed for 15 min in a solution 0.9% isotonic sterile sodium chloride saline followed by 15 min in a solution of 96% ethanol to remove surface contaminants. Excess solution was absorbed and ticks were air-dried prior to manipulation under sterile conditions. Each tick was individually cut in half lengthwise using sterile scalpels number 15.

Taxonomic classification

The taxonomy of the ticks was through morphological identifications using the keys of Barros-Battesti [10] at the Entomology Laboratory of the National Institute of Health of Peru in Lima (Laboratorio de Entomología del Instituto Nacional de Salud del Perú en Lima).

DNA extraction

Total intestinal viscera DNA extraction from ticks was performed using Gentra Puregene Tissue kits (QIAGEN, Halden-Germany) according to the manufacturer’s instructions [16] from pools for each group of ticks from each animal collected (T. terrestris and C. denticulata).

Metagenomics

To study the bacterial diversity and richness in the microbiota from ticks, the presence and quality of the extracted DNA was verified by PCR amplification of the 16S rRNA gene using the universal primers 27F (5'- AGAGTTTAGTCMTGGCTCAG-3 ') and 1492R (5'-GGYTACCTTGTTACGACTT-3') that generate a product of about 1500 base pairs (bp) [17]. All reactions were performed in 25 μl (total volume) mixtures containing 2.5 μl 10X buffer, 2.5 μl 25 mM MgCl2, 0.6 μl 10 mM dNTPs, and 2 U of Taq DNA polymerase (THERMO SCIENTIFIC). The PCR conditions were as follows: initial denaturation at 95 °C for 5 min followed by 35 cycles of denaturation at 95 °C for 30 s, hybridization at 55 °C for 45 s, elongation at 72 °C for 1 min, and a final elongation at 72 °C for 10 min. The PCR products were visualized by electrophoresis on a 1.5% agarose gel.

Total DNA extractions were analyzed by spectrophotometry (NANODROP EPPENDORF), and the samples with sufficient quality and quantity were shipped to MR DNA (Shallowater, TX, USA) and sequenced on the PGM platform (Ion Personal Genome Machine System, THERMO FISHER SCIENTIFIC). Metagenomic analysis was performed on the PCR amplification products of the V4 hypervariable region of the 16S rRNA gene using the 515F/806R primers [18].

Analysis and processing of metagenomic data

The sequences generated by Ion Torrent were analyzed with QIIME v1.9.1 [19], where the initial sequences were processed based on filtering of barcodes ≤ 6 bp, Q25 quality scores, 150 bp sequence length, and chimera detection using usearch61 [19, 20]. High-quality sequences were assigned to operational taxonomic units (OTUs) with a 97% identity cutoff for bacteria. The final OTUs were classified taxonomically using the High-Quality Ribosomal RNA Databases “SILVA” v132 database (https://www.arb-silva.de/). Likewise, unrepresentative OTUs ≤ 0.005% were filtered during analysis [21].

Lastly, the final OTUs were processed to analyze the Shannon–Weaver (SW) alpha diversity index, Chao1 richness index, beta diversity (venn and heatmap), and taxonomic abundance (barplot) of the microbial communities using the phyloseq and ampvis packages with the statistical program RStudio version 3.2.3. [19, 22, 23]. Sequences shorter than 250 bp were removed. The obtained OTUs were then taxonomically classified using BLASTn and compared with a curated database derived from Greengenes, RPDII, and NCBI (www.ncbi.nlm.nih.gov [24], http://rdp.cme.msu.edu [18]. The sequences were registered in Metagenomics Analysis Server “MG-RAST” ID: mgp98880; available at, https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp98880

Results

Ticks collected from Tapirus terrestris and Chelonoidis denticulata

Morphological identification indicated that ticks from T. terrestris belong to Amblyomma scalpturatum (4 males) and Amblyomma ovale (1 male) and ticks from C. denticulata belong to Amblyomma sabanerae (10 males) in Madre de Dios [10]. The ticks were collected in San Lorenzo Village and Gamitana Farm respectively (Fig. 1).

Statistical values and diversity in Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae

Microbiome analysis using the 16 s-515F/16 s-806R primers and amplicon sequencing on Ion Torrent PGM (Ion Personal Genome Machine System, THERMO FISHER SCIENTIFIC) generated a total of 173,945 raw reads (86,972.5 average) from the two analyzed samples [16,17,18] (Table 1). After rigorous data curation, 96,696 high-quality sequences were retained with an average of 48,348 sequences per sample and an average length of 150 bp and quality > 25 [19, 20]. The maximum number of filtered sequences number of assigned sequences OTUs 66,792 was obtained in the mix from Amblyomma scalpturatum and Amblyomma ovale, which exceeded those found in Amblyomma sabanerae by 223.4% [21]. These sequences were assigned to 564 total unique sequences corresponding to 282 abundant (< 0.005%) OTUs based on a > 97% identity cutoff for bacterial 16S rRNA genes [21]. At the individual sample level, the microbiome from Amblyomma sabanerae surpassed that from the mix from Amblyomma scalpturatum and Amblyomma ovale (478 and 86 OTUs, respectively). At the taxonomic level, a total of 28 genera distributed in 25 families, 17 orders, 10 classes, and 7 phyla were detected in the mix from Amblyomma scalpturatum/ Amblyomma ovale and 220 genera distributed in 134 families, 68 orders, 35 classes, and 20 phyla were detected in Amblyomma sabanerae respectively.

Table 1 Statistical summary of the microbiome of Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae

The SW index reflects the specific diversity of each sample, whose value increases as the number of different OTUs increases. In this study, the microbiome obtained from Amblyomma sabanerae ticks samples showed a higher SW index than the in the mix from Amblyomma scalpturatum /Amblyomma ovale microbiomes. On the other hand, Chao1, the index that evaluates specific richness, showed that the number of expected OTUs decreased from 613.65 in Amblyomma sabanerae to 102.17 in the mix from Amblyomma scalpturatum/Amblyomma ovale after the standardization of the sample size to 12,364 sequences. Statistical analyses of variance of the SW and Chao1 indexes in the Amblyomma sabanerae and in the mix from Amblyomma scalpturatum and Amblyomma ovale samples showed significant differences (P < 0.05) [22,23,24].

Composition of the core and shared and individual microbiome from Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae

The comparative analysis of the composition of the microbiota from Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae revealed that 8.8% out of the 228-genus found in mix from Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae were common in the two groups. This shared community is considered as the core microbiome of Amblyomma ticks. The percentages showed a decreasing proportionality in Amblyomma sabanerae and Amblyomma scalpturatum/Amblyomma ovale in relation to the non-shared bacterial genus.

Microbiota between twenty-three most prevalent bacterial genera in Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae

Regarding the abundance of bacterial genera in Amblyomma scalpturatum/Amblyomma ovale, Acinetobacter was the most abundant genus (96.8%), while Francisella was the most abundant genus in Amblyomma sabanerae (73.2%) (Fig. 2).

Fig. 2
figure 2

Microbiome abundance according to Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae. (Rstudio version 3.2.3. https://cran.rstudio.com/bin/windows/base/old/3.2.3/)

Microbiome richness estimation in Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae

The analysis of the rarefaction curves illustrates the differences obtained between the high OTUs number with a high richness and biodiversity of 613.65 and 2.03 respectively at a lower sequencing depth (29,904 assigned reads) of Amblyomma sabanerae compared with a lower richness at a higher sequencing depth (66,792 assigned reads) of Amblyomma scalpturatum/Amblyomma ovale (Fig. 3). Nevertheless, rarefactions curves also show a plateau phase profile that indicates that most of the OTUs present in the samples have been identified.

Fig. 3
figure 3

Rarefaction curves representing microbiome richness presents in Amblyomma scalpturatum/Amblyomma ovale and Amblyomma sabanerae, collected from T. terrestris and C. denticulata. (Rstudio version 3.2.3. https://cran.rstudio.com/bin/windows/base/old/3.2.3/)

Discussion

The richness and diversity indexes revealed that the microbiota present in Amblyomma sabanerae exhibit greater bacterial genera diversity and richness than the microbiota in Amblyomma scalpturatum/Amblyomma ovale. Previous studies in ticks of Ixodes ovatus, I. persulcatus, and Amblyomma variegatum have shown differentiated microbiome profiles both at the taxonomic and functional levels between sexes of the same tick species [25], however in our study all ticks (4 A. scalpturatum), (1 Amblyomma ovale) collected from T. terrestris and (10 A. sabanerae) collected from C. denticulata were males. Therefore, the difference in the microbiome by sex was not determined.

In addition, geographical location, temperature, humidity, species, sex, anatomical location, and type of diet have been shown to affect the microbiome of ticks [26,27,28,29,30,31]. In our study, although ticks were of the same genus, statistically (p < 0.05) significant differences were found in bacterial diversity and richness related to the animal collected, in the case of A. sabanerae collected from the C. denticulata reported higher richness and diversity (613.65–2.03) compared to A. scalpturatum/A. ovale (102.17–0.46) collected from the T. terrestris respectively.

Among the 228 different genera identified, the core microbiome that included the majority of the most prevalent genera stood out. Several of the identified genera within the core microbiome are known to be human pathogens (Streptococcus, Francisella, Pseudomonas, Staphylococcus, Acinetobacter). Staphylococcus, is mainly related to infections in soft tissues and has been previously reported in the gut of R. microplus and with a high prevalence in female Amblyomma variegatum [9, 25], Pseudomonas has been suggested to be involved in the infection of soft tissues, including the tissues of the respiratory system [32, 33]. Streptococcus is bacteria can cause many diseases ranging from mild skin infections to respiratory infections [34].

In addition, a moderate bacterial microbiome was shared between A. sabanerae and A. scalpturatum/A. ovale ticks [20 (8.8%)] compared to the specific bacteria genus in A.scalpturatum/A. ovale [8 (3.5%)] and A. sabanerae ticks [200 (87.3%)]. We suggest that these differences have a behavioral origin related to the host (T. terrestris and C. denticulata) [11,12,13]. Thus, female and nymph ticks are more prone to remain on the same host, whose microbiota impact on the tick gut microbiome, while male ticks frequently change hosts as our case where all ticks were male [25]. This hypothesis is supported by studies on other genera that reported higher relative abundance and alpha diversity in female ticks than in male ticks, however in our case we cannot compared genders because all ticks were males so the richness and diversity will be because the males A. sabanerae collected from C. denticulata change host that are linked to different genus of reptiles compared male A. scalpturatum collected from T. terrestris which are more specific for its host [13,14,15, 35, 36]. Additionally, it is necessary to consider that the role of nuclei bacterial genera and the species included in these may present different roles as pathogens or symbionts depending on whether they are found in the arthropod or in the vertebrate that hosts the arthropod.

The most prevalent bacterial genus among of A. scalpturatum/A. ovale was identified as Acinetobacter (96.8%), whose members cause infections at the level of the respiratory, urinary system and wound, in addition this bacterium tends to acquire resistance to various antibiotics and is of importance in Public Health, especially at the hospital level, Acinetobacter has been reported in a metagenomic study in I. persulcatus, I. pavlovskyi, and Dermacentor reticulatus [37]. Rhodococcus (2.5%) the second most abundant genus in A. scalpturatum/A. ovale has the ability to metabolize a large number of substrates and cause pulmonary infections, especially in immunocompromised people [38].

In A. sabanerae, Francisella (73.2%) was the most prevalent bacterial genus. Regarding the role of bacteria in ticks, note that nonpathogenic microorganisms present in ticks could cause infections in humans and other animals. For example, ecological studies have shown that Rickettsia, Francisella, and Coxiella, which are considered vertebrate pathogens, can change their pathogenic role and have a mutualistic and symbiotic relationship with ticks [1]. In the case of Francisella it is considered as a representative genus of endosymbionts related to pathways for biotin, folic acid, and riboflavin biosynthesis and it is found on rare occasions in some ticks and in the case of F. tularensis as a causal agent of tularemia, a very contagious and life-threatening disease [1, 39, 40]. Therefore, studying the interaction between the bacterial microbiota and ticks is of utmost importance for the control of pathogens [1]. Symbiotic bacteria as Coxiella sp. and Francisella sp. are linked to the synthesis of vitamins necessary for the survival of Amblyomma and Rhipicephalus [41,42,43,44,45]. Likewise, other symbiotic bacteria, such as Rickettsia, and Rickettsiella, have been reported in ticks [39]. However, in our study not Coxiella neither Rickettsia was found.

Paracoccus, the second most abundant genus (5.4%) in A. sabanerae, is a coccobacillary bacterium that is typically present in a wide range of ecosystems and this bacterium is considered by its diversity of metabolic production in different ecological environments and with biotechnological interest [46].

In our case, A. scalpturatum that is found only in South America is a tick that mainly parasitizes T. terrestris. This tick exhibits host specificity so this is the reason for the specificity microbiome, sometimes A. scalpturatum can bite human and is related to transmit Rickettsia [11, 12]. A. scalpturatum was found in T. terrestris.

T. terrestris was likely infected by ticks in the jungle and them could infect human due to the proximity of San Lorenzo Village, where livestock farming and hunting are practiced. Previous studies highlight that A. scalpturatum can infect T. terrestris, Pecari tajacu, and humans [11, 12], with the potential risks of pathogen transmission that this implies. In the case of A. ovale collected from T. terrestris can parasite many mammals as P. tajacu and can transmit Rickettsia and is found predominantly in sylvatic areas [14, 15]. In our study it was found parasitizing T. terrestris.

A. sabanerae was collected from C. denticulata. A. sabanerae can parasite different types of reptile as turtle, a previous study showed Rickettsia in A. sabanerae collected from a turtle (Kinosternon sp). In our study A. sabanerae was found in a turtle (C. denticulata) in the Chacra Gamitana Village where the farming is practicing, so the farmer could be parasite by the ticks and infected with some pathogenic bacteria as Rickettsia and Francisella [13, 35, 36].

According to previous studies, the endosymbiont bacteria of a species of tick vary depending on the ecology and the number of ticks studied [46]. Therefore, the importance of our study is the finding of the new microbiome of A. scalpturatum/A. ovale collected from T. terrestris and A. sabanerae collected from C. denticulata.

The small number of ticks was justified by the fact that Amblyomma ticks are not very common studied on the wild host T. terrestris and C. denticulata in the jungle of Madre de Dios-Perú; therefore, we could not collect a larger sample of ticks. Our interest was to study the microbiota of ticks as A. scalpturatum/A. ovale and A. sabanerae that parasitizes T. terrestris and C. denticulata respectively and who live in the Peruvian Amazon.

Among the limitations of our study is the bacterial microbiome found in 5 males of ticks collected from T. terrestris and 10 males’ ticks collected from C. denticulata, which implies a bacterial microbiome representative of a specific circumstance and ecology. Therefore, studies with a greater number of samples could show a greater diversity of species and different percentages of bacterial abundance.

Conclusion

In this study, we found a high bacterial diversity in male of A. sabanerae collected from C. denticulata showed prevalence of Francisella and prevalence of Acinetobacter in male A. scalpturatum/A. ovale collected from T. terrestris. The greatest bacterial diversity and richness was found in males A. sabanerae. This is the first bacterial metagenomic study performed in A. scalpturatum/A. ovale and A. sabanerae collected from T. terrestris and C. denticulata in the Peruvian jungle. This study lays the foundations for future studies on the importance of the role of the identified bacteria on arthropods and animal and human health.

Availability of data and materials

All data generated or analyzed during this study are included in this published article. Raw data are available. The preprocessing, statistics, OTUS, abundancy, taxonomy, diagram of Venn are included in the Supplementary Text. The authors confirmed that all supporting data have been provided within the article or through supplementary materials.

Abbreviations

GART:

Ticks collected from C. denticulata

GARS:

Ticks collected from T. terrestris

m. a. s. l.:

Meters above sea level

PCR:

Polymerase chain reaction

SW:

Shannon–Weaver

OTU:

Operational taxonomic units

PGM:

Ion Personal Genome Machine System

NGS:

Next-generation sequencing

rRNA:

Ribosomal RNA

WGS:

World Geodetic System

SW:

Shannon–Weaver

NCBI:

National Center for Biotechnology Information

pb:

Base pairs

References

  1. Bonnet SI, Binetruy F, Hernández-Jarguín AM, Duron O. The Tick Microbiome: Why Non-pathogenic Microorganisms Matter in Tick Biology and Pathogen Transmission. Front Cell Infect Microbiol. 2017;7:236. https://doi.org/10.3389/fcimb.2017.00236.

    Article  Google Scholar 

  2. Burgdorfer W, Hayes S, Mavros A. Non-pathogenic rickettsiae in Dermacentor andersoni: a limiting factor for the distribution of Rickettsia rickettsii. In: Burgdorfer AA, Anacker RL, editors. Rickettsia and Rickettsial Disease. New York: Academic; 1981. p. 585–94.

    Google Scholar 

  3. Chauvin A, Moreau E, Bonnet S, Plantard O, Malandrin L. Babesia and its hosts: adaptation to long-lasting interactions as a way to achieve efficient transmission. Vet Res. 2009;40:37. https://doi.org/10.1051/vetres/2009020.

    Article  CAS  Google Scholar 

  4. Ravi A, Ereqat S, Al-Jawabreh A, Abdeen Z, Shamma O, Hall H, Pallen M, Nasereddin A. Metagenomic profiling of ticks: Identification of novel rickettsial genomes and detection of tick-borne canine parvovirus. PLoS Negl Trop Dis. 2019;13(1):1–19.

    Article  CAS  Google Scholar 

  5. Greay TL, Gofton AW, Paparini A, Ryan UM, Oskam CL, Irwin PJ. Recent insights into the tick microbiome gained through next-generation sequencing. Parasit Vectors. 2018;11(1):1–14.

    Article  Google Scholar 

  6. Rar V, Livanova N, Tkachev S, Kaverina G, Tikunov A, Sabitova Y, Igolkina Y, Panov V, Livanov S, Fomenko N, Babkin I, Tikunova N. Detection and genetic characterization of a wide range of infectious agents in Ixodes pavlovskyi ticks in Western Siberia. Russia Parasites and Vectors. 2017;10(1):1–24.

    Google Scholar 

  7. Filippova NA. Ixodid ticks of the subfamily Ixodinae. Fauna of the USSR. Arachnida. Leningrad: Publishing House Nauka; 1977.

    Google Scholar 

  8. Bouquet J, Melgar M, Swei A, Delwart E, Lane RS, Chiu CY. Metagenomic-based Surveillance of Pacific Coast tick Dermacentor occidentalis Identifies Two Novel Bunyaviruses and an Emerging Human Ricksettsial Pathogen. Sci Rep. 2017;7(1):1–10. https://doi.org/10.1038/s41598-017-12047-6.

    Article  CAS  Google Scholar 

  9. Nakao R, Abe T, Nijhof A, Yamamoto S, Jongejan F, Ikemura T, Sugimoto C. A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks. ISME J. 2013;7(5):1003–15. https://doi.org/10.1038/ismej.2012.171.

    Article  CAS  Google Scholar 

  10. Barros-Battesti, D., Arzua, M., Bechara, H. Carrapato de Importância Medico-Veterinaria da Região Neotropical: Um Guia Ilustrado para Identificação de Espécies [Ticks of Medical-Veterinary Importance in the Neotropical Region: An Illustrated Guide for Species Identification]. 10ma edição. Sao Paulo: Butantan Publicação. p. 223. 2006.

  11. Labruna MB, Whitworth T, Bouyer DH, McBride JW, Camargo LMA, Camargo EP, et al. Rickettsia bellii and Rickettsi amblyommii in Amblyomma ticks from the state of Rondônia, Western Amazon. Brazil J Med Entomol. 2004;41:1073–81.

    Article  Google Scholar 

  12. Aguirre A. Rodrigues V, Nunes da Costa I, Garcia M, Guimaraes B, Andreotti R, Fernandes J. Amblyomma scalpturatum Neumann, 1906 (Acari: Ixodidae): confirmation in Acre State, Brazil, and description of parasitism in a human. Braz. J. Vet. Parasitol. 2019: 1(1):1–6

  13. Barbieri A, Romero L, Labruna M. Rickettsia bellii infecting Amblyomma sabanerae ticks in El Salvador. Pathogens and Global Health. 2012;106(3):188–9.

    Article  Google Scholar 

  14. -Sánchez-Montes S, Ballados-Gónzales G, Hernández-Velasco A, Zazueta-Islas H, Solis-Cortés M, et. Al. Molecular Confirmation of Rickettsia parkeri in Amblyomma ovale Ticks, Veracruz, Mexico. Emerging Infectious Diseases • 25, (12),2019:2315–23–17

  15. Bitencourth K, Amorim M, de Oliveira SV, Voloch CM, Gazêta GS. Genetic diversity, population structure and rickettsias in Amblyomma ovale in areas of epidemiological interest for spotted fever in Brazil. Med Vet Entomol. 2019;33:256–68. https://doi.org/10.1111/mve.12363.

    Article  CAS  Google Scholar 

  16. QIAGEN. Gentra, Puregene (QIAGEN GROUP), 2007–2010. https://www.qiagen.com/us/shop/sample-technologies/dna/genomic-dna/gentra-puregene-tissue-kit/#orderinginformation. Accessed 9 Jun 2017.

  17. Sperling JL, et al. Comparison of bacterial 16S rRNA variable regions for microbiome surveys of ticks. Ticks Tick Borne Dis. 2017;8:453–61.

    Article  Google Scholar 

  18. Caporaso J, Lauber C, Walters W, Berg-Lyons D, Lozupone C, Turnbaugh P, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci. 2011;108(Supplement 1):4516–22.

    Article  CAS  Google Scholar 

  19. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–200.

    Article  CAS  Google Scholar 

  20. Glassing A, Dowd SE, Galandiuk S, Davis B, Jorden JR, Chiodini RJ. Changes in 16S RNA gene microbial community profiling by concentration of prokaryotic DNA. J Microbiol Methods. 2015;119: 239242.

    Article  Google Scholar 

  21. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Caporaso JG. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 2013;10(1):57–9.

    Article  CAS  Google Scholar 

  22. Andersen, K.S., Kirkegaard, R.H., Karst, S.M., Albertsen, M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. BioRxiv. 2018; ;299537. doi: https://doi.org/10.1101/299537.

  23. McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8(4):1–11.

    Article  Google Scholar 

  24. DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K, Huber T, Dalevi D, Hu P, Andersen G. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;7:5069–72.

    Article  Google Scholar 

  25. Obregón D, Bard E, Abrial D, Estrada-Peña A, Cabezas-Cruz A. Sex-Specific Linkages Between Taxonomic and Functional Profiles of Tick Gut Microbiomes. Front Cell Infect Microbiol. 2019;9:298. https://doi.org/10.3389/fcimb.2019.00298.

    Article  CAS  Google Scholar 

  26. Qiu Y, Nakao R, Ohnuma A, Kawamori F, Sugimoto C. Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens. PLoS One. 2014;9(8):e103961.

    Article  Google Scholar 

  27. Van Treuren W, Ponnusamy L, Brinkerhoff RJ, Gonzalez A, Parobek CM, Juliano JJ, Andreadis TG, Falco RC, Ziegler LB, Hathaway N, Keeler C, Emch M, Bailey JA, Roe RM, Apperson CS, Knight R, Meshnick SR. Variation in the microbiota of Ixodes ticks with regard to geography, species, and sex. Appl Environ Microbiol. 2015;81:6200–9. https://doi.org/10.1128/AEM.01562-15.

    Article  CAS  Google Scholar 

  28. G, Cagnacci F, Wittekindt NE, Zhao F, Qi J, Tomsho LP, Drautz D, Rizzoli A, Schuster S. Metagenomic Profile of the Bacterial Communities Associated with Ixodes Ricinus Ticks. PLoS ONE. 2011; 6(10): e25604. https://doi.org/10.1371/journal.pone.0025604

  29. Zhang X-C, Yang Z-N, Lu B, Ma X-F, Zhang C-X. The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal. Ticks Tick Borne Dis. 2014;5:864–70.

    Article  Google Scholar 

  30. Menchaca AC, Visi DK, Strey OF, Teel PD, Kalinowski K, Allen MS, Williamson P. Preliminary Assessment of Microbiome Changes Following Blood-Feeding and Survivorship in the Amblyomma americanum Nymph-to-Adult Transition using Semiconductor Sequencing. PLoS ONE. 2013;8(6): e67129. https://doi.org/10.1371/journal.pone.0067129.

    Article  CAS  Google Scholar 

  31. Clayton KA, Gall CA, Mason KL, Scoles GA, Brayton KA. The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick. Dermacentor andersoni Parasit Vectors. 2018;8:1–5.

    CAS  Google Scholar 

  32. Patro LPP, Rathinavelan T. Targeting the Sugary Armo-ñr of Klebsiella Species. Front Cell Infect Microbiol. 2019;9:1–23. https://doi.org/10.3389/fcimb.2019.00367.

    Article  CAS  Google Scholar 

  33. Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O, Hoiby N, Molin S. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Microbiol. 2019;2019(10):841–51. https://doi.org/10.1038/nrmicro2907.

    Article  CAS  Google Scholar 

  34. Graham MR, Smoot LM, Migliaccio CAL, Virtaneva K, Sturdevant DE, Porcella SF, et al. Virulence control in group a streptococcus by a two-component gene regulatory system: global expression profiling and in vivo infection modeling. Proc Natl Acad Sci U S A. 2002;99(21):13855–60 Available from: http://www.pnas.org/cgi/content/long/99/21/13855.

  35. Fairchild GB, Kohls GM, Tipton VJ. The ticks of Panama (Acarina: Ixodoidea). In: Wenzel WR, Tipton VJ, editors. Ectoparasites of Panama. Chicago (IL): Field Museum of Natural History; 1966. p. 167–219.

    Google Scholar 

  36. Jones EK, Clifford CM, Keirans JE, Kohls GM. The ticks of Venezuela (Acarina: Ixodoidea) with a key to the species of Amblyomma in the Western Hemisphere. Brigham Young Univ Sci Bull, Biol Ser. 1972;17:1–40.

    Google Scholar 

  37. Kurilshikov A, Livanova NN, Fomenko NV, Tupikin AE, Rar VA, Kabilov MR, Livanov S, Tikunova N. Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks. PLoS ONE. 2015;10(7): e0131413. https://doi.org/10.1371/journal.pone.0131413.

    Article  CAS  Google Scholar 

  38. Bazquéz-Boland J, Meijer W. The pathogenic actinobacterium Rhodococcus equi: what’s in a name? Mol Microbiol. 2019;112(1):1–15.

    Article  Google Scholar 

  39. Gerhart JG, Moses AS, Raghavan R. A Francisella-like endosymbiont in the Gulf Coast tick evolved from a mammalian pathogen. Sci Rep. 2016;6:33670. https://doi.org/10.1038/srep33670.

    Article  CAS  Google Scholar 

  40. Sjodin A, Svensson K, Ohrman C, Ahlinder J, Lindgren P, Duodu S, et al. Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. BMC Genomics. 2012;13:268. https://doi.org/10.1186/1471-2164-13-268.

    Article  Google Scholar 

  41. Duron O, Binetruy F, Noel V, Cremaschi J, McCoy K, Arnathau C, Plantard O, et al. Evolutionary changes in symbiont community structure in ticks. Mol Ecol. 2017;26:2905–21. https://doi.org/10.1111/mec.14094.

    Article  CAS  Google Scholar 

  42. Zhong J, Jasinskas A, Barbour AG. Antibiotic treatment of the tick vector Amblyomma americanum reduced reproductive fitness. PLoS ONE. 2017;2:1–7. https://doi.org/10.1371/journal.pone.0000405.

    Article  CAS  Google Scholar 

  43. Gottlieb Y, Lalzar I, Klasson L. Distinctive genome reduction rates revealed by genomic analyses of two Coxiella-like endosymbionts in ticks. Genome Biol Evol. 2015;7:1779–96. https://doi.org/10.1093/gbe/evv108.

    Article  CAS  Google Scholar 

  44. Gerhart, J.G., Moses, A.S., Raghavan, R. A. Francisella-like endosymbiont in the Gulf Coast tick evolved from a mammalian pathogen. Sci. Rep. 2016; 6.1–6. doi:https://doi.org/10.1038/srep3367.

  45. Sjodin A, Svensson K, Ohrman C, Ahlinder J, Lindgren P, Duodu S, et al. Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. BMC Genomics. 2012;13:1–13. https://doi.org/10.1186/1471-2164-13-268.

    Article  Google Scholar 

  46. Maj A, Dziewit L, Czarnecki J, Wlodarczyk M, Baj J, et al. Plasmids of Carotenoid-Producing Paracoccus spp. (Alphaproteobacteria) - Structure, Diversity and Evolution. PLoS ONE. 2013; 8(11): e80258. doi:https://doi.org/10.1371/journal.pone.0080258

Download references

Acknowledgements

Dr. Eric MiaIhe for funding the molecular studies; Cesar Chanta for his support in the laboratory procedures in Incabiotec SAC.

Funding

Not applicable.

Author information

Authors and Affiliations

Authors

Contributions

JRJ designed, performed the field work, and wrote and approved the final version of the article. GCN performed the field work and wrote and approved the final version of the article. DLS performed the analysis and bioinformatics study and approved the final version of the article. BD designed the molecular study and wrote and approved the final version of the article.

Corresponding author

Correspondence to Jesús Rojas-Jaimes.

Ethics declarations

Ethics approval and consent to participate

This study was approved by the Office of Public Health and Environment of the Regional Council Madre de Dios, Peru. Laboratory procedures for bacterial identification were conducted in accordance with the international guidelines for the use of animals in research and the standards of the Animal Care and Use Committee of the Health Research Area of the Madre de Dios Regional Council Board. Consent was not required. The study was carried out in compliance with the ARRIVE guideline.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

12866_2022_2717_MOESM1_ESM.xls

Additional file 1.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rojas-Jaimes, J., Lindo-Seminario, D., Correa-Núñez, G. et al. Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru. BMC Microbiol 22, 305 (2022). https://doi.org/10.1186/s12866-022-02717-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12866-022-02717-5

Keywords

  • Microbiome
  • Amblyomma scalpturatum
  • Amblyomma sabanerae
  • Tapirus terrestris
  • Chelonoidis denticulata
  • Peru