Gastrointestinal helminths of terrestrial small mammals in West Africa

Latest version published by CBGP (UMR INRAE, Cirad, IRD, Institut Agro | Montpellier) on 09 February 2024 CBGP (UMR INRAE, Cirad, IRD, Institut Agro | Montpellier)
Publication date:
09 February 2024
CC-BY 4.0

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The dataset contains occurrences of gastrointestinal helminths (mainly Nematoda and Cestoda) from terrestrial small mammals (Rodentia and Soricomorpha) trapped in more than 280 sampling sites of several countries from sub-Saharan Africa. Numbers given in the following fields concern the original version of the dataset released in Dec. 2023 which gathers data from 287 sampling sites from seven countries.

Data have been collected through field trips organised in the frame of various research programs and cover different timeframes mostly in Senegal (2002-2019), Mali (2002-2010), Niger (2005-2011), and more occasionally in Benin (2004), Burkina Faso (2004-2006), Guinea (2005), and Mauritania (2006-2007). The sampling sites correspond to various environments (cities, villages, fields, orchards, savannas, or forests).

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 5,281 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.


The table below shows only published versions of the resource that are publicly accessible.


Researchers should respect the following rights statement:

The publisher and rights holder of this work is CBGP (UMR INRAE, Cirad, IRD, Institut Agro | Montpellier). This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: cb0e54b8-98c7-4df1-93ed-a58ecb75d930.  CBGP (UMR INRAE, Cirad, IRD, Institut Agro | Montpellier) publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF France.


Occurrence; Specimen


  • Originator
Chargée de recherche
CBGP, IRD, CIRAD, INRAE, Montpellier SupAgro, Univ Montpellier, Montpellier, France
Centre de Biologie pour la Gestion des Populations - CBGP
34980 Montferrier-sur-Lez
Christophe DIAGNE
  • Originator
Chargé de recherche
CBGP, IRD, CIRAD, INRAE, Montpellier SupAgro, Univ Montpellier, Montpellier, France
Centre de Biologie pour la Gestion des Populations - CBGP
Emmanuelle ARTIGE
  • Curator
  • Point Of Contact
Ingénieure d'études
CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
Centre de Biologie pour la Gestion des Populations - CBGP
34980 Montferrier-sur-Lez

Geographic Coverage

The data were collected in seven countries of Sahelo-Sudanian Africa: Benin (3 sampling sites), Burkina Faso (5 sampling sites), Guinea (2 sampling sites), Mali (37 sampling sites), Mauritania (10 sampling sites), Niger (25 sampling sites, of which 19 were different districts from Niamey), and Senegal (205 sampling sites)

Bounding Coordinates South West [8, -17.52], North East [20.33, 8.93]

Taxonomic Coverage

5270 samples (each of them being composed of 1 to several individuals of a given taxon) of gastrointestinal helminths were collected from 4116 small mammals* from at least 38 species belonging to 17 genera of rodents (mostly Muridae, but also some Dipodidae, Gliridae, Nesomyidae, and Sciuridae; many of them being identified at the species level (following Happold 2013) using morphological, molecular and/or chromosomal data), and to two species of shrews (Soricidae). Gastrointestinal helminths that were collected covered three taxonomic phyla (Nematoda, Platyhelminthes and Acanthocephala). Among the 2950 samples classified as Nematoda, 1606 were identified at the genus level and 236 were identified at the species level. Among the 2163 samples classified as Cestoda, 115 were identifed at the genus level and 149 at the species level. The 34 samples of Trematoda remain unidentified. Among the 32 samples classified as Acanthocephala, seven were identified at the species level. Five hundred thirty-three samples remain either unclassified due to the insufficient quality of materials to be unambiguously scrutinized, or to be identified as the recorded samples are progressively identified using morphological and/or molecular tools.

Phylum Acanthocephala, Nematoda, Platyhelminthes
Class Cestoda, Trematoda
Order Enoplida
Superfamily Oxyuroidea, Trichostrongyloidea
Family Oxyuridae, Spiruridae, Trichostrongylidae
Genus Anatrichosoma, Aspiculuris, Capillaria, Gongylonema, Heligmonina, Hymenolepis, Mastophorus, Mathevotaenia, Oxynema, Physaloptera, Protospirura, Pseudophysaloptera, Pterygodermatites, Raillietina, Skrjabinotaenia, Subulura, Syphacia, Syphatineria, Trichuris
Species Anatrichosoma gerbillis, Aspiculuris africana, Aspiculuris tetraptera, Hymenolepis diminuta, Hymenolepis stramina, Moniliformis moniliformis, Neoheligmonella granjoni, Oxynema xerusi, Protospirura muricola, Pterygodermatites niameyiensis, Pterygodermatites senegalensis, Raillietina (Raillietina) baeri, Raillietina (Raillietina) trapezoides, Syphacia obvelata, Trichuris duplantieri, Trichuris mastomysi

Temporal Coverage

Start Date / End Date 2002-12-11 / 2019-04-06

Project Data

Data were collected through field trips organised in the frame of various research programs led by or involving our labs (described in "Funding" part). Its gathering was part of the ObsMiCE (West African Observatory on small Mammals as indicators of Environmental Changes) activities.

Title Projects involved
Funding ANR projects ENEMI : ANR-11JSV7-0006; CHANCIRA : ANR-11-CEPL-010; Labex DRIIHM French programme ‘‘Investissements d’Avenir’’ : ANR-11-LABX-0010; FRB project CERISE : AAP-SCEN-20B III; GIP ECOFOR project : Programme ‘Ecosystèmes Tropicaux’, research convention 0000337 MEDD-IRD.

Sampling Methods

Gastrointestinal helminths were collected from the digestive tracts of small mammals that had been unrolled and stored in plasitic universal vials containing 95% ethanol. Each digestive tract was carefully scrutinised for helminths along its different sections (stomach, small intestine, large intestine and caecum) following Ribas et al. 2011. Gastrointestinal helminths were carefully removed, then classified by taxon (at the genus, family, order, class or phylum level) according to the knowledge of the person in charge of this work and to morphological characteristics observable at the binocular.

Study Extent Sampling sites of seven countries of sub-Saharan Africa (Benin, Burkina Faso, Guinea, Mali, Mauritania, Niger, and Senegal), corresponding to various environments (districts of cities, villages, field borders, orchards, savannas, or forests).
Quality Control Several samples were idenfied more thoroughly at the genus or species level combining morphological and molecular approaches as diagnostic tools. Morphological identification was carried out using conventional microscopy and generalist identification keys (Khalil et al., 1994; Anderson et al., 2009) or specific literature when available, with the involvement of specialist collaborators when possible (Alexis Ribas, Jerzy Behnke and Malick Diouf, Voitto Haukisalmi). For most identified taxa, at least one specimen* was identified per small mammal species was sequenced for cytochrome oxidase 1 (cox1) for nematodes and acanthocephalans, and nicotinamide adenine dinucleotide subunit 1 (NAD1) for cestodes (Diagne et al. 2016). This precise identification was done for seven Acanthocephala, 157 Cestoda, and 541 Nematoda. Additional data about the host individual (sex, body size, reproductive characteristics) are registered in the CBGP small mammal database (BPM, http://bpm-cbgp.science). All samples of the dataset are included in the CBGP reference collection of small mammals (https://doi.org/10.15454/WWNUPO).

Method step description:

  1. Ethical guidelines and standards have been followed at every single step of the data collection and transfer. Prior explicit agreement from relevant local authorities and individual owners was systematically obtained for each sampling campaign within private dwellings. Trapping sessions and transfer of biological samples were carried out in accordance with requirements of local and French legislations. We systematically received an explicit approval from the relevant institutional comitee (Centre de Biologie pour la Gestion des Populations (CBGP): Agrement pour l’utilisation d’animaux à des fins scientifiques D-34-169-1) for all protocols used to handle biological materials. We also ensured that any animal-related procedure was performed according to official ethical guidelines provided by the American Society of Mammalogists (Sikes and Gannon 2011). None of the rodent species investigated here has any protected status from the International Union for Conservation of Nature. The dataset is an extraction of the BPM database - internal Small Mammal database of the laboratory CBGP (Centre de Biologie pour la Gestion des Populations) to manage data and preserve specimen involved : field campain data, taxonomic data, sequenced data

Collection Data

Collection Name CBGP-SMaC : Small Mammal Collection
Collection Identifier doi:10.15454/WWNUPO
Specimen preservation methods Alcohol

Additional Metadata

Purpose This dataset aims to describe the biodiversity of gastrointestinal helminths parasiting small mammals in sahelo-sudanian Africa. It will enable to better understand the biotic and abiotic factors that structure parasite assemblages in small mammals in environments corresponding to various degrees of anthropisation. Together with the associated collections (https://doi.org/10.15454/WWNUPO), it should be a very helpful tool for studies that aim to improve taxonomy and systematics of gastro-intestinal helminths.
Maintenance Description The dataset will be regulary updated as new data are available.
Alternative Identifiers cb0e54b8-98c7-4df1-93ed-a58ecb75d930