Ontogeny, species identity, and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)

Abstract Background Kissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species. Methods To obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of five Triatoma species sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimised 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170 T. cruzi-negative individuals across all six instars. Results Triatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genus Dietzia dominates late-stage nymphs and adults of T. rubida, T. protracta, and T. lecticularia but is not present in the phylogenetically more distant T. gerstaeckeri and T. sanguisuga. Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genus Bartonella, acquired from the vertebrate hosts, are an abundant component of Triatoma microbiomes. Conclusion Our study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multiple Triatoma species. We hypothesise that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors.

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Ontogeny, species identity and environment dominate microbiome dynamics in wild populations of kissing bugs (Triatominae)

10.1101/2020.06.05.135871 ◽

2020 ◽

Author(s):

Joel J. Brown ◽

Sonia M. Rodríguez-Ruano ◽

Anbu Poosakkannu ◽

Giampiero Batani ◽

Justin O. Schmidt ◽

...

Keyword(s):

Bacterial Diversity ◽

Pathogenic Bacteria ◽

Life Stage ◽

Blood Feeding ◽

18S Rrna Gene ◽

Significant Loss ◽

Individual Variability ◽

Rrna Gene ◽

Species Identity ◽

Microbiome Composition

AbstractBackgroundKissing bugs (Triatominae) are blood-feeding insects best known as the vectors of Trypanosoma cruzi, the causative agent of Chagas’ disease. Considering the high epidemiological relevance of these vectors, their biology and bacterial symbiosis remains surprisingly understudied. While previous investigations revealed generally low individual complexity but high among-individual variability of the triatomine microbiomes, any consistent microbiome determinants have not yet been identified across multiple Triatominae species.MethodsTo obtain a more comprehensive view of triatomine microbiomes, we investigated the host-microbiome relationship of five Triatoma species sampled from white-throated woodrat (Neotoma albigula) nests in multiple locations across the USA. We applied optimized 16S rRNA gene metabarcoding with a novel 18S rRNA gene blocking primer to a set of 170 T. cruzi negative individuals across all six instars.ResultsTriatomine gut microbiome composition is strongly influenced by three principal factors: ontogeny, species identity, and the environment. The microbiomes are characterised by significant loss in bacterial diversity throughout ontogenetic development. First instars possess the highest bacterial diversity while adult microbiomes are routinely dominated by a single taxon. Primarily, the bacterial genus Dietzia dominates late-stage nymphs and adults of T. rubida, T. protracta, and T. lecticularia, but is not present in the phylogenetically more distant T. gerstaeckeri and T. sanguisuga. Species-specific microbiome composition, particularly pronounced in early instars, is further modulated by locality-specific effects. In addition, pathogenic bacteria of the genus Bartonella, acquired from the vertebrate hosts, are an abundant component of Triatoma microbiomes.ConclusionOur study is the first to demonstrate deterministic patterns in microbiome composition among all life stages and multiple Triatoma species. We hypothesize that triatomine microbiome assemblages are produced by species- and life stage-dependent uptake of environmental bacteria and multiple indirect transmission strategies that promote bacterial transfer between individuals. Altogether, our study highlights the complexity of Triatominae symbiosis with bacteria and warrant further investigation to understand microbiome function in these important vectors.

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Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales

Scientific Reports ◽

10.1038/s41598-020-72032-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Elizabeth R. Denison ◽

Ryan G. Rhodes ◽

William A. McLellan ◽

D. Ann Pabst ◽

Patrick M. Erwin

Keyword(s):

Gut Microbiome ◽

Life Stage ◽

Life History Stage ◽

Rrna Gene ◽

Sperm Whales ◽

Microbiome Composition ◽

Host Health ◽

Species Specific ◽

Kogia Sima ◽

Host Development

Abstract Gut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont ‘accumulation’ in K. sima and ‘winnowing’ in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.

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Maternal Influence and Murine Housing Confound Impact of NLRP1 Inflammasome on Microbiome Composition

Journal of Innate Immunity ◽

10.1159/000495850 ◽

2019 ◽

Vol 11 (5) ◽

pp. 416-431 ◽

Cited By ~ 2

Author(s):

Veronica M. Ringel-Scaia ◽

Yufeng Qin ◽

Cassidy A. Thomas ◽

Kathleen E. Huie ◽

Dylan K. McDaniel ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Maternal Influence ◽

Rrna Gene ◽

Wild Type ◽

Microbiome Composition ◽

Nlrp1 Inflammasome ◽

Microbiome Research ◽

Inflammatory Bowel ◽

The 16S Rrna Gene ◽

V3 Region

The NLRP1 inflammasome attenuates inflammatory bowel disease (IBD) progression and colitis-associated tumorigenesis. A possible mechanism postulates that the lack of the NLRP1 inflammasome creates permissive niches in the gut for pathogenic bacteria to flourish, causing dysbiosis and increased IBD susceptibility. To evaluate this hypothesis, we characterized the gut microbiome of wild-type, Nlrp1b–/–, and Asc–/– mice under naïve conditions by sequencing the V3 region of the 16s rRNA gene. For both genetically modified mouse lines, the microbiome composition reflected overrepresentation of bacteria associated with dysbiosis relative to wild-type animals. Measurement of short- and medium-chain fatty acids by mass spectrometry further revealed significant differences between genotypes. However, prior to concluding that the NLRP1 inflammasome plays a role in regulating the composition of the microbiome, we evaluated two additional strategies for cohousing wild-type and Nlrp1b–/– mice: breeding homozygous parents and cohousing at weaning, and breeding from heterozygous parents and cohousing littermates. We found that maternal influence was the greater predictor of microbiome composition rather than genotype. With the rise in microbiome research across disciplines, our study should be viewed as a cautionary example that illustrates the importance of careful breeding and housing strategies when evaluating host-microbiome interactions.

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Terminal Restriction Fragment Length Polymorphism for Identification of Cryptosporidium Species in Human Feces

Applied and Environmental Microbiology ◽

10.1128/aem.01341-08 ◽

2008 ◽

Vol 75 (1) ◽

pp. 108-112 ◽

Cited By ~ 25

Author(s):

L. S. Waldron ◽

B. C. Ferrari ◽

M. R. Gillings ◽

M. L. Power

Keyword(s):

Species Identification ◽

Restriction Fragment ◽

Rflp Analysis ◽

Cost Effective ◽

18S Rrna Gene ◽

Individual Species ◽

Rrna Gene ◽

Species Identity ◽

Cryptosporidium Hominis ◽

Detection And Identification

ABSTRACT Effective management of human cryptosporidiosis requires efficient methods for detection and identification of the species of Cryptosporidium isolates. Identification of isolates to the species level is not routine for diagnostic assessment of cryptosporidiosis, which leads to uncertainty about the epidemiology of the Cryptosporidium species that cause human disease. We developed a rapid and reliable method for species identification of Cryptosporidium oocysts from human fecal samples using terminal restriction fragment polymorphism (T-RFLP) analysis of the 18S rRNA gene. This method generated diagnostic fragments unique to the species of interest. A panel of previously identified isolates of species was blind tested to validate the method, which determined the correct species identity in every case. The T-RFLP profiles obtained for samples spiked with known amounts of Cryptosporidium hominis and Cryptosporidium parvum oocysts generated the two expected diagnostic peaks. The detection limit for an individual species was 1% of the total DNA. This is the first application of T-RFLP to protozoa, and the method which we developed is a rapid, repeatable, and cost-effective method for species identification.

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Morphological and Molecular Identification of Fusarium oxysporum Sch. Isolated From Guava Wilt in Bangladesh

Bangladesh Journal of Botany ◽

10.3329/bjb.v41i1.11082 ◽

2012 ◽

Vol 41 (1) ◽

pp. 49-54 ◽

Cited By ~ 6

Author(s):

M Zakir Hussain ◽

MA Rahman ◽

Mohammad Nurul Islam ◽

MA Latif ◽

MA Bashar

Keyword(s):

Fusarium Oxysporum ◽

Psidium Guajava ◽

18S Rrna Gene ◽

Rrna Gene ◽

Chain Reaction ◽

Species Identity ◽

Specific Primers ◽

Polymerase Chain ◽

Serious Disease ◽

Species Specific

Wilt of guava plants (Psidium guajava L.) is a serious disease in Bangladesh. Sixteen isolates of Fusarium oxysporum Sch. were collected from the root and stem fragments of guava plants growing in six districts of Bangladesh. Species identity was based on the colony character, nature of conidiogenous cell, morphology of microconidia, macroconidia and chlamydospores. Eleven isolates were confirmed as F. oxysporum through polymerase chain reaction (PCR) using species specific primers designed from the conserved regions of 18S rRNA gene. DOI: http://dx.doi.org/10.3329/bjb.v41i1.11082 Bangladesh J. Bot. 41(1): 49-54, 2012 (June)

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Identification of a Putative Mexican Strain of Serratia entomophila Pathogenic against Root-Damaging Larvae of Scarabaeidae (Coleoptera)

Applied and Environmental Microbiology ◽

10.1128/aem.01074-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 802-810 ◽

Cited By ~ 24

Author(s):

M. Eugenia Nuñez-Valdez ◽

Marco A. Calderón ◽

Eduardo Aranda ◽

Luciano Hernández ◽

Rosa M. Ramírez-Gama ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Phylogenetic Analyses ◽

Significant Loss ◽

Management Program ◽

Extracellular Proteins ◽

Proteinase K ◽

Rrna Gene ◽

White Grubs ◽

Disease Symptoms ◽

Lepidopteran Insect

ABSTRACT The larvae of scarab beetles, known as “white grubs” and belonging to the genera Phyllophaga and Anomala (Coleoptera: Scarabaeidae), are regarded as soil-dwelling pests in Mexico. During a survey conducted to find pathogenic bacteria with the potential to control scarab larvae, a native Serratia sp. (strain Mor4.1) was isolated from a dead third-instar Phyllophaga blanchardi larva collected from a cornfield in Tres Marías, Morelos, Mexico. Oral bioassays using healthy P. blanchardi larvae fed with the Mor4.1 isolate showed that this strain was able to cause an antifeeding effect and a significant loss of weight. Mortality was observed for P. blanchardi, P. trichodes, and P. obsoleta in a multidose experiment. The Mor4.1 isolate also caused 100% mortality 24 h after intracoelomic inoculation of the larvae of P. blanchardi, P. ravida, Anomala donovani and the lepidopteran insect Manduca sexta. Oral and injection bioassays were performed with concentrated culture broths of the Mor4.1 isolate to search for disease symptoms and mortality caused by extracellular proteins. The results have shown that Mor4.1 broths produce significant antifeeding effects and mortality. Mor4.1 broths treated with proteinase K lost the ability to cause disease symptoms and mortality, in both the oral and the injection bioassays, suggesting the involvement of toxic proteins in the disease. The Mor4.1 isolate was identified as a putative Serratia entomophila Mor4.1 strain based on numerical taxonomy and phylogenetic analyses done with the 16S rRNA gene sequence. The potential of S. entomophila Mor4.1 and its toxins to be used in an integrated pest management program is discussed.

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First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes

Microorganisms ◽

10.3390/microorganisms9071454 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1454

Author(s):

Julia Moll ◽

Friederike Roy ◽

Claus Bässler ◽

Jacob Heilmann-Clausen ◽

Martin Hofrichter ◽

...

Keyword(s):

Tree Species ◽

Forest Ecosystems ◽

Amplicon Sequencing ◽

Wood Properties ◽

18S Rrna Gene ◽

Rrna Gene ◽

Species Identity ◽

Nematode Communities ◽

Terrestrial Environments ◽

Nematode Diversity

Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes’ distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.

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Cross-Genera PCR Amplification of DNA from Apicomplexan Parasites

Journal of Arthropod-Borne Diseases ◽

10.18502/jad.v12i3.83 ◽

2018 ◽

Author(s):

Philippe Gil de Mendonça

Keyword(s):

Pathogenic Bacteria ◽

Hypervariable Region ◽

Pcr Amplification ◽

18S Rrna Gene ◽

Rrna Gene ◽

Apicomplexan Parasites ◽

Diagnostic Samples ◽

Successful Amplification ◽

Babesia Spp ◽

Theileria Spp

Background: The discovery of an unexpected genetic sequence raised doubts about the specificity of a primer pair targeting Babesia spp. and Theileria spp. This study aimed to check the specificity of this primer pair. Methods: Conventional end-point PCR and real-time PCR protocols using primers targeting the 18S rRNA gene V4 hypervariable region of Babesia spp. and Theileria spp. were tested for potential cross-genera amplification using DNA from a palette of parasitic protists and pathogenic bacteria as a template. These investigations took place at the Ludwig Maximilian University of Munich (Germany) in 2010 as part of the EDEN project. Results: Successful amplification was obtained with DNA from five apicomplexan genera: Babesia, Theileria, Hepatozoon, Toxoplasma, and Hammondia. No amplicons were obtained when DNA from Leishmania infantum or bacteria within the genera Borrelia, Leptospira or Anaplasma was used as a template. Conclusion: This cross-genera amplification ability is useful for the quick exclusion of many parasite species from PCR negative diagnostic samples. Accurate species identification from PCR positive samples requires genetic sequencing of the amplicon.

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Evaluating the contingency treatment performance of advanced electro-catalysis oxidation processes for marine bacteria in ballast water

Water Science & Technology ◽

10.2166/wst.2021.365 ◽

2021 ◽

Author(s):

Yulin Xu ◽

Qiong Wang ◽

Huixian Wu

Keyword(s):

Bacterial Diversity ◽

Marine Bacteria ◽

Ballast Water ◽

Pathogenic Bacteria ◽

Viable Count ◽

Rrna Gene ◽

E Coli ◽

Oxidation Processes ◽

Treatment Performance ◽

Electro Catalysis

Abstract Effects of ballast water (BW) treatment by Advanced Electro-Catalysis Oxidation Processes (AEOP) on abundance, activity, and diversity of marine bacteria were examined in a full-scale ballast water management system (BWMS) at Yangshan Port, Shanghai, China. Water samples were collected immediately after treatment and at discharge to evaluate the contingency treatment performance of the BWMS for bacteria. After treatment, the total viable count reduced to 0.7 × 104 CFU·mL−1, and both E. coli and enterococci decreased to 10 CFU·100 mL−1, satisfied the D-2 Standard of the International Maritime Organization (IMO). AEOP can be as an effective contingency reception facility. Sequencing of 16S rRNA gene amplicons demonstrated the declining trend in bacterial diversity, while the treatment did not completely eliminate the risk of bacterial dispersal, including potentially pathogenic bacteria, survived in treated and discharged samples. Bacterial diversity is of greater concern when evaluating effects of ballast water treatment on microorganisms, because the bacteria which can develop adaptive mechanisms to environmental change will have a greater potential for invasion in the new environment.

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Diversity and Distribution of Marine Microbial Eukaryotes in the Arctic Ocean and Adjacent Seas

Applied and Environmental Microbiology ◽

10.1128/aem.72.5.3085-3095.2006 ◽

2006 ◽

Vol 72 (5) ◽

pp. 3085-3095 ◽

Cited By ~ 186

Author(s):

C. Lovejoy ◽

R. Massana ◽

C. Pedrï¿½s-Aliï¿½

Keyword(s):

Arctic Ocean ◽

18S Rrna Gene ◽

Ocean Basin ◽

Significant Loss ◽

Canada Basin ◽

The Arctic ◽

Rrna Gene ◽

The North ◽

The Arctic Ocean ◽

Upper Mixed Layer

ABSTRACT We analyzed microbial eukaryote diversity in perennially cold arctic marine waters by using 18S rRNA gene clone libraries. Samples were collected during concurrent oceanographic missions to opposite sides of the Arctic Ocean Basin and encompassed five distinct water masses. Two deep water Arctic Ocean sites and the convergence of the Greenland, Norwegian, and Barents Seas were sampled from 28 August to 2 September 2002. An additional sample was obtained from the Beaufort Sea (Canada) in early October 2002. The ribotypes were diverse, with different communities among sites and between the upper mixed layer and just below the halocline. Eukaryotes from the remote Canada Basin contained new phylotypes belonging to the radiolarian orders Acantharea, Polycystinea, and Taxopodida. A novel group within the photosynthetic stramenopiles was also identified. One sample closest to the interior of the Canada Basin yielded only four major taxa, and all but two of the sequences recovered belonged to the polar diatom Fragilariopsis and a radiolarian. Overall, 42% of the sequences were <98% similar to any sequences in GenBank. Moreover, 15% of these were <95% similar to previously recovered sequences, which is indicative of endemic or undersampled taxa in the North Polar environment. The cold, stable Arctic Ocean is a threatened environment, and climate change could result in significant loss of global microbial biodiversity.

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