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Background  The gut microbiota is known to play a role in a mosquito vector’s life history, a subject of increasing research. Laboratory experiments are essential for such studies and require laboratory colonies. In this study, the conservation of field-obtained midgut microbiota was evaluated in laboratory-reared  Anopheles gambiae  ( s.l. ) mosquitoes continuously hatched in water from field breeding habitats.    Methods  Pupae and late instars were obtained from the field and reared, and the emerged adults were blood-fed. The eggs obtained from them were hatched in either water from the field or in dechlorinated tap water. The mosquito colonies were maintained for 10 generations. Midguts of female adults from unfed F 0  (emerging from field-caught pupae and larvae), F 5  and F 10  were dissected out and genomic DNA was extracted for  16S  metagenomic sequencing. The sequences were compared to investigate the diversity and bacterial compositional differences using ANCOM and correlation clustering methods.    Results  Less than 10% of the bacterial families identified had differential relative abundances between generational groups and accounted for 46% of the variation observed. Although diversity reduced in F 10  mosquitoes during laboratory colonization (Shannon-Weaver;  P -value < 0.05), 50% of bacterial genera were conserved in those bred continuously in field-water compared to 38% in those bred in dechlorinated tap water.    Conclusions  To our knowledge, this study is the first report on the assessment of gut bacterial community of mosquitoes during laboratory colonization and recommends the use of water from the natural breeding habitats if they are intended for microbiota research.    Electronic supplementary material  The online version of this article (10.1186/s13071-019-3287-0) contains supplementary material, which is available to authorized users.

parasites and vectors

Generational conservation of composition and diversity of field-acquired midgut microbiota in Anopheles gambiae (sensu lato) during colonization in the laboratory