TABLE 6.

Infant gut microbiome biomarkers measured across the retained studies (N = 13)

	Study
Infant gut microbiome biomarker	Rozé et al. (2020)	Aatsinki et al. (2022)	Aatsinki et al. (2019)	Kelsey et al. (2021)	Laue et al. (2020)	Loughman et al. (2020)	Loughman et al. (2021)	Christian et al. (2015)	Rothenburg et al. (2021)	Carlson et al. (2018)	Gao et al. (2019)	Sordillo et al. (2019) a	Van den Berg et al. (2016)
Final N	577	131	301	63	140	201	118	77	46	89	39	309	79
Alpha diversity
Shannon–Wiener	S–	T–	T↑	T↓	E↓	E↓	E↓	T↕	M–C–	C↓	C–	C↓L↓M↓E↓
Simpson					E↓	E↓
Chao1		T–	T–	T↑		E↓	E↓			C↓	C–
Phylogenetic								T↑	M–C–	C↓	C–
Other(s)							E↓		M–C–				C–M–
Gene ontology
Virulence factors				T↑
Resistome genes				T–
Observed taxa	S–	T–	T–	T–	E↑	E↓	E↓		M–C–	C↓	C–
Taxa count					E↑								C–M–
Beta diversity
Unifrac (Weighted/Unweighted)					E↑	E↓	E↓	T↑	M–C–
Aquificae
Thermovibrio guaymasensis				T–
Firmicutes	S↓
Anaerococcus
Anaerostipes									M–C–
Blautia									M–C–
Blautia producta					E↓
Butyricicoccus pullicaecorum
Catenibacterium
Cellulosibacter									M–C–
Clostridiales												C–L↓M–E–
Clostridium			T–	T–			E↓		M–C–			C–L–M–E–
Clostridium perfringens				T–
Clostridium disporicum				T–
Clostridium sensu stricto	S–
Coprobacillus
Coprococcus					E↓				M–C–
Dialister								T↑
Enterococcus
Enterococcus faecalis	S–			T–
Eubacterium
Eubacterium hallii
Eubacterium dolichum
Faecalibacterium									M–C–	C–
Flavonifractor									M–C–
Flavonifractor plautii					E↓
Fusicatenibacter									M–C–
Gemmiger									M–C–
Holdemania
Lactobacillus							E↓
Lachnospiraceae				T–	E↓	E↓			M–C–			C–L–M–E–
Lactococcus
Megasphaera
Megamonas									M–C–
Oscillibacter									M–C–
Phascolarctobacterium									M–C–
Peptoniphilus
Roseburia
Roseburia peoriensis				T–
Ruminococcaceae								T↑		C–
Ruminococcus									M–C–
Ruminococcus gnavus					E↓		E↓
Ruminococcus torques					E↓
Bacterium_6_1_63FAA					E↓
Sarcina
Sporacetigenium
Streptococcus			T↑						M–C–
Streptococcus salivarius				T–
Streptococcus vestibularis				T–
Staphylococcus	S–						E↓
Weissella
Veillonella												C–L–M–E–
Bacteroidetes
Alistipes									M–C–
Alloprevotella
Bacteroides			T↓						M–C–	C–		C–L–M–E–
Bacteroides fragilis			T–
Bacteroides caccae				T–
Porphyromonas
Parabacteroides								T↑	M–C–
Prevotella						E↓
Rikenellaceae								T↑
Actinobacteria
Actinomyces							E↑
Adlercreutzia equolifaciens					E↓
Bifidobacterium			T↑		E↓		E↕		M–C–			C–L–M–E–	C↑M–
Bifidobacterium catenulatum				T–
Bifidobacterium dentium				T–
Bifidobacterium pseudocatenulatum				T–
Collinsella									M–C–
Rothia							E↓
Proteobacteria	S↑
Campylobacter
Enterobacteriaceae			T↑									C–L–M–E–
Enterobacter aerogenes	S–
Erwinia			T↓
Escherichia	S–											C–L–M–E–
Escherichia coli	S–			T–
Escherichia shigella									M–C–
Klebsiella							E↓
Shigella	S–
Succinivibrio
Sutterella
Campylobacter
Verrucomicrobia
Akkermansia	S–
Coriobacteriaceae
Atopobium	S–		T↓

Note: Associations depicted in red denote at least one statistically significant association between biomarker and neurodevelopmental outcome reported by study authors. Biomarker names are derived from the naming conventions used in each of the included studies. However, it is important to recognize that certain phyla were renamed as part of the NCBI Taxonomy to include phylum rank in taxonomic names. C, cognitive development; L, language/communication development; M, motor development; A, adaptive behavior; E, social–emotional development; S, neurodevelopmental outcome composed of several domains; T, Temperament. ↓ = associated with poorer neurodevelopmental outcome. ↑ = associated with better neurodevelopmental outcome. ↕ = mixed (positive and negative) association with better outcome across specific domains of subtypes neurodevelopmental outcome (e.g., vocabulary produced, or vocabulary understood as subtypes of language/communication development), timing of the biosample (e.g., sampled at multiple points in time), or source of biosample (e.g., blood and cerebrospinal fluid). – = direction and/or significance of association with neurodevelopmental outcome not reported.

^a Study identified clustered or grouped specific phylum.