diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile
index b1432f4efde9..f0931e261767 100644
--- a/biology/py-biom-format/Makefile
+++ b/biology/py-biom-format/Makefile
@@ -1,34 +1,31 @@
 PORTNAME=	biom-format
-PORTVERSION=	2.1.10
-PORTREVISION=	1
+PORTVERSION=	2.1.16
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Biological Observation Matrix (BIOM) Format Project
 WWW=		https://biom-format.org/
 
 LICENSE=	BSD3CLAUSE
 
 BUILD_DEPENDS=	${PYNUMPY}
 RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
 		${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}future>=0.16.0:devel/py-future@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>=1:science/py-scipy@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=1.3.1:science/py-scipy@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pandas>=0.20.0:math/py-pandas@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}six>=1.10.0:devel/py-six@${PY_FLAVOR}
+		${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR}
 
 USES=		python
-USE_PYTHON=	autoplist concurrent cython distutils
+USE_PYTHON=	autoplist concurrent cython distutils pytest
 
 .include <bsd.port.pre.mk>
 
 post-extract:
 	${RM} -r ${WRKSRC}/tests
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biom/*.so
 
 .include <bsd.port.post.mk>
diff --git a/biology/py-biom-format/distinfo b/biology/py-biom-format/distinfo
index 8c8f7063441d..aeb31a00d278 100644
--- a/biology/py-biom-format/distinfo
+++ b/biology/py-biom-format/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1610333968
-SHA256 (biom-format-2.1.10.tar.gz) = f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488
-SIZE (biom-format-2.1.10.tar.gz) = 11671341
+TIMESTAMP = 1718787972
+SHA256 (biom-format-2.1.16.tar.gz) = 47f88d57a94ecaa4d06f3578ca394e78db6d12e46ab0886634743181e67dcfc9
+SIZE (biom-format-2.1.16.tar.gz) = 11720476