Gut microbiota has a strong influence on the onset and development of systemic lupus erythematosus (SLE), and several studies have demonstrated the effectiveness of microbiota-derived butyrate to ameliorate SLE. However, the roles of butyrate on gut microbiota in SLE are not understood. Using MRL/lpr lupus-prone mice, we examined gut microbiota profiles after butyrate treatment by 16S rRNA sequencing. Alterations in intestinal microbiome in mice with lupus-like disease were mainly characterized by a reduction in microbial diversity, with an increased abundance of Bacteroidetes and a decrease of Firmicutes. Treatment of lupus-prone mice with butyrate resulted in increased abundance of Firmicutes (
P
= 0.003), Clostridia (
P
= 0.005), Clostridiales (
P
= 0.005),
Lachnospiraceae
(
P
= 0.009),
Ruminococcaceae
(
P
= 0.021),
Peptostreptococcaceae
(
P
= 0.021),
Ruminiclostridium
(
P
= 0.016),
Oscillibacter
(
P
= 0.048),
Romboutsia
(
P
= 0.025),
Lachnoclostridium
(
P
= 0.012),
Coprococcus
(
P
= 0.015),
Ruminococcus
(
P
= 0.011),
Clostridium leptum
(
P
< 0.05), and
Dorea_spp
. (
P
= 0.019), and a reduced proportion of Bacteroidetes (
P
= 0.004), Bacteroidia (
P
= 0.004), and Bacteroidales (
P
= 0.004). Further, butyrate supplementation could ameliorate kidney damage. Overall, this study suggests that gut microbiota alterations occur in MRL/lpr lupus-prone mice following treatment with butyrate. Butyrate supplementation ameliorated gut microbiota dysbiosis. These findings support the use of butyrate and butyrate-producing bacteria as potential treatments for SLE.