Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota

Abstract

The phylum Minisyncoccota (formerly known as “Candidatus Patescibacteria”/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.

Understanding the role played by microbial communities in diverse environments has long been constrained by reliance on the biological functions of a limited number of cultivable microorganisms. The experimental technique for directly cloning the 16S rRNA gene from environmental samples was established in the mid-1980s, laying the foundation for culture-independent molecular ecology (Pace et al., 1986). This approach revealed that natural environments harbor vast microbial diversity that cannot be explained by known cultivated bacteria. Numerous “candidate phyla” were reported, highlighting the existence of broad uncultivated lineages that were not captured by traditional cultivation-based phylogenies. In recent years, advances in single-cell genomics and metagenomics have provided genomic information from uncultivated lineages present in the environment, which has led to a more detailed understanding of microbial phylogenetic classifications (Rinke et al., 2013; Hug et al., 2016; Parks et al., 2018). Minisyncoccota is a prime representative of a major bacterial phylogenetic group that includes largely uncultivated lineages, for which a limited number of co-cultures and enrichment-based systems have been reported in recent years (He et al., 2015; Batinovic et al., 2021; Kuroda et al., 2022a, 2022b, 2024; Yakimov et al., 2022; Xie et al., 2022; Nakajima et al., 2025). Genomic anal­yses of these lineages are also progressing, and their ecological functions are becoming increasingly evident. It is important to note that‍ ‍Minisyncoccota, formerly known as “Candidatus Patescibacteria” and the candidate phyla radiation (CPR), has been published under the International Code of Nomenclature for Prokaryotes (ICNP) (Oren and Göker, 2025), while its SeqCode designation is Patescibacteriota (Dutkiewicz et al., 2025), as of October 2025. SeqCode is a new code of nomenclature for prokaryotes that uses genome sequences as nomenclatural types (Hedlund et al., 2022). Following the rejection by the International Committee on Systematics of Prokaryotes (ICSP) of proposals to incorporate DNA sequences as nomenclatural types within the ICNP, it was suggested as an independent framework to enable the naming of uncultivated microorganisms. Hereafter, unless specified otherwise, this review will use the taxonomic name Minisyncoccota. Several Minisyncoccota members have been reported in host-associated co-cultures or enrichment-based systems; however, none of these cultures were publicly available through culture collections. Although recent progress has enabled the deposition of the first two-strain co-culture of Minisyncoccus archaeiphilus strain PMX.108^T (=JCM 39522^T) with the host archaeon, Methanospirillum hungatei (Nakajima et al., 2025), the majority of this phylogenetic group remains uncultivated. Information on their physiology and ecology is fragmented and has yet to be systematically organized. In this review, we provide an overview of current knowledge of Minisyncoccota, with a focus on historical transitions in its phylogenetic classification, and summarize previous studies on PCR primer sets, fluorescence in situ hybridization (FISH) probes, metabolic characteristics, phylogenetic diversity, and parasitic interactions

Taxonomic transitions and phylogenetic tree of the phylum Minisyncoccota

Minisyncoccota represents a recently recognized bacterial lineage, proposed as a novel phylum with a cultured representative Minisyncoccus archaeiphilus within the kingdom Bacillati of domain Bacteria (Nakajima et al., 2025). The taxonomic name of this group has undergone frequent revisions as new lineages have been discovered and reclassified. We herein chronologically summarized major taxonomic changes at the class level for Minisyncoccota reported between 1995 and the present date, tracing their historical taxonomic name in the literature and mainly aligning them with the Genome Taxonomy Database (GTDB) taxonomy Release 226 (Fig. 1) (Parks et al., 2018). In this section, taxonomic names follow those originally employed in the cited literature to ensure consistency with Fig. 1. Bond et al. (1995) first reported partial 16S rRNA gene sequences obtained from a laboratory-scale activated sludge reactor and assigned them as “unaffiliated groups”. Rheims et al. (1996) proposed the designation TM7 for this unclassified lineage discovered in 16S rRNA gene clone libraries. This provisional naming convention persisted until 2013, when Rinke et al. introduced the taxonomy of uncultured microorganisms based on single-cell amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) (Table 1). During this period, multiple novel lineages were described: OP11 from hot spring environments (Hugenholtz et al., 1998), WS6 from groundwater (Dojka et al., 1998), BD1-5 from deep-sea sediments (Li et al., 1999), OD1 and SR1 as subdivisions of OP11 (Harris et al., 2004), GN02 later recognized as being synonymous with BD1-5 (Ley et al., 2006), and WWE3 from wastewater treatment facilities (Guermazi et al., 2008). Miyoshi et al. (2005) phylogenetically characterized microorganisms captured from deep aquifers in Japan using filters with pore sizes of 0.2 and 0.1 μm. Their findings revealed that candidate divisions OD1 and OP11 were highly enriched in the filtered fraction, providing the first evidence that these lineages consist of ultra-small bacteria. Wrighton et al. (2012) applied metagenomics and proteomics to groundwater samples, reporting additional lineages including PER, ACD58, and ACD80. Rinke et al. (2013) conducted single-cell genomic anal­yses of diverse environmental samples and reconstructed a comprehensive phylogeny of Bacteria and Archaea. Their anal­yses indicated that OP11, OD1, and GN02 (BD1-5), previously regarded as distinct phyla, constitute a single higher-order lineage. At this stage, each group was still recognized as a phylum; however, the overarching clade was newly proposed as the “superphylum Patescibacteria”. Concurrently, OP11, OD1, and GN02 were renamed Microgenomates, Parcubacteria, and Gracilibacteria, respectively. During the‍ ‍same period, Albertsen et al. (2013) reconstructed a complete MAG from activated sludge that had previously been affiliated with TM7 and redefined it as the phylum Saccharibacteria. Wrighton et al. (2014) proposed Berkelbacteria for a lineage previously designated as ACD58. Brown et al. (2015) expanded on these findings, introducing the collective term “candidate phyla radiation (CPR)” to encompass OP11, OD1, and GN02 together with newly identified groups. This study proposed the superphyla Parcubacteria (OD1) and Microgenomates (OP11) and subdivided them into 14 and 11 phylum-level lineages, respectively. It also proposed three novel phyla (CPR1–3) and clarified the taxonomic name of PER as Peregrinibacteria. Additional lineages, such as Kazan and SM2F11, were also reported, but without prior documentation linking them to Patescibacteria.

Fig. 1. Transitions in the phylogenetic nomenclature of each class. Taxonomic names follow those originally employed in the cited literature: undefined (Bond et al., 1995); TM7 (Rheims et al., 1996); OP11 (Hugenholtz et al., 1998); WS6 (Dojka et al., 1998); BD1-5 (Li et al., 1999); OD1 and SR1 (Harris et al., 2004); GN02 (Ley et al., 2006); WWE3 (Guermazi et al., 2008); PER, ACD58, and ACD80 (Wrighton et al., 2012); Microgenomates, Parcubacteria, and Gracilibacteria (Rinke et al., 2013); Saccharibacteria (Albertsen et al., 2013); Berkelbacteria (Wrighton et al., 2014); Peregrinibacteria, Kazan, and SM2F11 (Brown et al., 2015); Absconditabacteria and Katanobacteria (Hug et al., 2016); Dojkabacteria (Wrighton et al., 2016); Abawacabacteria and Andersenbacteria (Anantharaman et al., 2016b); Saccharimonadia, Microgenomatia, Paceibacteria, and ABY1 (Parks et al., 2018); Minisyncoccia (Nakajima et al., 2025); Patescibacteriia (Dutkiewicz et al., 2025).

Table 1.Phylogenetic Correspondences

Former name			Current names under ICNP			Current names under SeqCode			Current names in databases
Shorter	Longer		Name	Status		Name	Status		GTDB	SILVA 138.2	MiDAS 5.3
TM7	Saccharibacteria		“Ca. Saccharimonadia”	pro-validly		N/A	N/A		Saccharimonadia	Saccharimonadia	Saccharimonadia
OD1	Parcubacteria/Paceibacteria		Minisyncoccia	validly		Minisyncoccia	Valid (ICNP)		Minisyncoccia	Parcubacteria	Parcubacteria
			“Ca. Patescibacteriia”	not pro-validly		Patescibacteriia	Valid (SeqCode)		Patescibacteriia	ABY1	ABY1
OP11	Microgenomates		“Ca. Microgenomatia”	not pro-validly		“Microgenomatia”	Automated discovery		Microgenomatia	Microgenomatia	Microgenomatia
BD1-5/GN02	Gracilibacteria		“Ca. Gracilibacteria”	not pro-validly		“Gracilibacteria”	Draft		JAEDAM01	Gracilibacteria	Gracilibacteria
SR1 (ACD80)	Absconditabacteria		“Ca. Gracilibacteria”	not pro-validly		“Gracilibacteria”	Draft		JAEDAM01	Gracilibacteria	Gracilibacteria
PER	Peregrinibacteria		“Ca. Gracilibacteria”	not pro-validly		“Gracilibacteria”	Draft		Gracilibacteria	Gracilibacteria	Gracilibacteria
WS6	Dojkabacteria		“Ca. Dojkaibacteriota”	pro-validly		“Dojkabacteria”	Automated discovery		Dojkabacteria	Dojkabacteria	Dojkabacteria
WWE3	Katanobacteria		“Ca. Katanibacteriota”	pro-validly		N/A	N/A		WWE3	WWE3	WWE3
ACD58	Berkelbacteria		“Ca. Berkeliibacteriota”	pro-validly		N/A	N/A		UBA1384	Berkelbacteria	Berkelbacteria
SM2F11	Doudnabacteria		“Ca. Doudnaibacteriota”	pro-validly		“Doudnabacteria”	Automated discovery		Doudnabacteria	Parcubacteria	Parcubacteria
N/A	Andersenbacteria		“Ca. Anderseniibacteriota”	pro-validly		“Andersenbacteria”	Automated discovery		Andersenbacteria	N/A	N/A
N/A	Kazan		N/A	not available		N/A	N/A		Kazan-3B-28	Kazania	Kazania

N/A: Not Available.

Validly: the nomenclatural status is validly published under the ICNP. Pro-validly: the nomenclatural pro-status is pro-validly published under the ICNP. Not pro-validly: the nomenclatural pro-status is not pro-validly published.

Valid (ICSP): this name has been validly published under the rules of the ICNP and has priority in the scientific record. Valid (SeqCode): this name has been validly published under the rules of SeqCode and has priority in the scientific record. Draft/Automated discovery: this name was automatically created by the system and has not undergone expert review.

Hug et al. (2016) reconstructed a large-scale phylogenetic tree encompassing all three domains of life based on 1,011 newly obtained MAGs. This study allowed us to visualize Patescibacteria as a broad phylogenetic group, together with the renaming of SR1 to Absconditabacteria and WWE3 to Katanobacteria. Anantharaman et al. (2016b) proposed 27 additional phylum-level lineages within CPR from a groundwater metagenomic anal­ysis, and Wrighton et al. (2016) reclassified WS6 as Dojkabacteria. Parks et al. (2018) proposed GTDB, introducing a genome-based standardized taxonomy that has since become the dominant framework for bacterial and archaeal systematics. Under GTDB, Patescibacteria/CPR were consolidated as a single phylum, with phylum-level groups being reassigned to the class rank. Names were further refined, with Parcubacteria being renamed as Paceibacteria and Microgenomates as Microgenomatia, and many previously proposed phyla were reorganized into orders or lower ranks. Several groups were further subdivided, e.g., Parcubacteria was split into Paceibacteria and ABY1. Moreover, some names were replaced with provisional UBA codes (e.g., Berkelbacteria to UBA1384). GTDB has since undergone frequent updates, further subdividing and reorganizing CPR lineages. Gracilibacteria has been split into Gracilibacteria and JAEDAM01, with the lineage originally being designated as‍ ‍Gracilibacteria by Rinke et al. (2013) and Absconditabacteria by Hug et al. (2016) assigned to JAEDAM01, whereas the lineages previously referred to as Peregrinibacteria by Wrighton et al. and Abawacabacteria by Anantharaman et al. (2016b) were reassigned to Gracilibacteria.

As of 2025, two competing phylum names have been proposed for CPR. Nakajima et al. (2025), based on a cultivated representative, introduced Minisyncoccota as a novel phylum under ICNP, whereas Dutkiewicz et al. (2025), based on MAGs registered in SeqCode, re-proposed Patescibacteriota as the phylum name under SeqCode. In the List of Prokaryotic names with Standing in Nomenclature (LPSN), Minisyncoccota is recognized as the valid ICNP name, while Patescibacteriota is listed only as a Candidatus phylum and, thus, does not have standing under the ICNP (Freese et al., 2026). GTDB currently adopts Patescibacteriota (Parks et al., 2026) based on SeqCode. Additionally, Paceibacteria was renamed Minisyncoccia under ICNP, while ABY1 was renamed Patescibacteriia under SeqCode. Current phylogenetic correspondences are listed in Table 1. In summary, the taxonomic identity of the phylum Minisyncoccota has undergone substantial revisions since the mid-1990s. Notably, the establishment of GTDB in 2018 provided a genome-based standardized taxonomy, serving as a turning point for the systematic reclassification of Minisyncoccota and related lineages. Nakajima et al. (2025) demonstrated that Minisyncoccota constituted a monophyletic phylum that formed a sister relationship with Chloroflexota, even when different marker gene sets were used. This phylogenetic placement is also consistent with recent studies on bacterial evolution (Coleman et al., 2021; Beaud et al., 2025). Comparative phylogenetic anal­yses in this review, including trees reconstructed using concatenated 120 single-copy marker genes based on GTDB and a subset only including replication/transcription/translation-related genes (Nishihara et al., 2024; Nakajima et al., 2025) (Fig. 2), supported the monophyly of Minisyncoccota and its sister relationship with Chloroflexota. Furthermore, positional inconsistencies among certain lineages were revealed. These discrepancies, which were also observed by Nakajima et al. (2025) highlight the impact of marker gene selection and methodological differences on phylogenetic inference, and underscore the importance of continued refinement to resolve the precise taxonomic placement of Minisyncoccota.

Fig. 2. Phylogenetic tree of the phylum Minisyncoccota. Comparative phylogenetic anal­yses in this review, including trees reconstructed using marker proteins proposed by (A) Nakajima et al. (2025) and (B) the 120-marker gene set of the Genome Taxonomy DataBase (GTDB). (A) follows nomenclature consistent with the International Code of Nomenclature of Prokaryotes (ICNP), whereas (B) follows the GTDB taxonomy. Scale bars=0.1. The data used for these anal­yses are provided in Table S4.

Detection of the phylum Minisyncoccota

PCR primer sets and FISH probes targeting the phylum Minisyncoccota have been developed for the 16S rRNA gene and, in some lineages, also for the 23S rRNA gene, enabling the specific detection of this phylum. The primers developed to date are summarized in Table S1 and S2. Amplicon sequencing using the commonly employed V4 and V3–V4 primer sets also detect Minisyncoccota (Hu et al., 2024). However, intron insertions are frequently found in the 16S rRNA genes of Minisyncoccota (Brown et al., 2015; Tsurumaki et al., 2024), which may hinder detection in certain lineages. Hu et al. (2024) modified conventional V4 primers to enhance the detection rate of Minisyncoccota without compromising the overall diversity of the bacteria detected. Among the lineages detected, “Ca. Saccharimonadia” has attracted attention, and numerous PCR primers have been designed, partly due to the establishment of methods for obtaining stable co-cultures. In contrast, although “Ca. Patescibacteriia” and “Ca. Microgenomatia” are frequently identified in environmental samples, information on specific primer sets remains limited. FISH probes are fewer in number and are generally more specific than PCR primer sets, with only TM7905 (Hugenholtz et al., 2001) and Pac683 (Singleton et al., 2021) being designed to cover broader phylogenetic ranges. Since the PCR primers and FISH probes developed during the early stages of research on Minisyncoccota were based on limited reference data, their specificity needs to be confirmed when applying them to current research.

Microorganisms forming parasitic or predatory relationships with the phylum Minisyncoccota

The phylum Minisyncoccota is characterized by highly reduced MAG sizes and limited metabolic capabilities, suggesting that members of this lineage are generally unable to persist independently in the environment. Therefore, it is being increasingly reported that these microorganisms adopt symbiotic, parasitic, or predatory lifestyles that are dependent on other microbes (Fig. 3, Table S3). The oral environment has served as a representative model system in which “Ca. Nanosynbacter” species have been extensively investigated. “Ca. Nanosynbacter lyticus” strain TM7x was shown to associate with Schaaria odontolytica and Schaaria meyeri as host organisms, with cultivation experiments demonstrating its epibiotic lifestyle (He et al., 2015; Bor et al., 2016, 2018; Utter et al., 2020). Furthermore, co-cultures with Arachnia propionica yielded multiple isolates of “Ca. Nanosynbacter” and “Ca. Saccharimonas”, in which attachment and proliferation on the host cell surface were observed (Bor et al., 2020; Mukurgkar et al., 2020). These findings indicate that members of “Ca. Saccharimonadia” preferentially use bacteria within the phylum Actinomycetota as primary hosts. “Ca. Mycolatisynbacter gordoniilyticus” (synonym “Ca. Mycosynbacter amalyticus”), another member of “Ca. Saccharimonadia”, has been shown to engage in symbiosis with Gordonia amarae in activated sludge (Batinovic et al., 2021).

Fig. 3. Relationships between Minisyncoccota strains and their host microorganisms. Species and strain names are provided. Detail information is described in Table S3.

Members of “Ca. Gracilibacteria” (JAEDAM01 lineage in GTDB), such as “Ca. Vampirococcus lugosii”, “Ca. Absconditicoccus praedator”, and JAGOMW01-related organisms (in GTDB), have been identified as potential predators or symbionts of the class Gammaproteobacteria, including photosynthetic bacteria and Zoogloea (Moreira et al., 2021; Yakimov et al., 2022; Fujii et al., 2024), suggesting that this lineage preferentially establishes relationships with members of this class. Several novel lineages within Minisyncoccia have recently been reported to parasitize archaea. “Ca. Yanofskyibacterium parasiticum” and “Ca. Nealsoniibacteriota” (synonym “Ca. Nealsonbacteria”) were found to proliferate in association with Methanothrix spp. (Kuroda et al., 2022b, 2024; Chen et al., 2023), while Minisyncoccus archaeiphilus and “Ca. Microsyncoccus archaeolyticus” were associated with members of the genus Methanospirillum (Kuroda et al., 2022a, 2022b, 2024; Nakajima et al., 2025). Additionally, cases of Minisyncoccia inhabiting eukaryotic hosts have been documented (Gong et al., 2014) (Table S3). Collectively, these findings show that Minisyncoccota members establish parasitic or symbiotic relationships not only with bacteria, but also with archaea and eukaryotes, spanning across all three domains of life.

Morphological characteristics

Members of the phylum Minisyncoccota are generally characterized by coccoid or ovoid cell morphologies, although larger cells have also been reported, suggesting morphological diversity. Cell sizes typically range from approximately 200 to 800 nm in diameter, highlighting their small dimensions (Table 2). Therefore, fractionation by filtration may be an effective approach for recovering Minisyncoccota cells (Bor et al., 2018; Kagemasa et al., 2022, 2025). The presence of an S-layer has been reported in some species (Yakimov et al., 2022; Chen et al., 2023). Fig. 4 shows microscopic images of Minisyncoccota in a wastewater treatment system. Minisyncoccus archaeiphilus and “Ca. Yanofskyibacterium parasiticum” were detected in close proximity to methanogens, playing a crucial role as an anchor for organic matter decomposition in methanogenic environments (Fig. 4A and B) (Kuroda et al., 2022a, 2022b, 2023a, 2024; Nakajima et al., 2025). The cells belonging to‍ ‍an uncultured lineage within “Ca. Gracilibacteria”/JAEDAM01 lineage often coexisted with members of the genus Zoogloea, known for its extracellular polymeric substance (EPS)-producing, floc-forming bacteria (Fig. 4C) (Fujii et al., 2024). This close spatial association with host cells may represent one of the characteristic morphological features of Minisyncoccota. Previous studies demonstrated that “Ca. Mycolatisynbacter gordoniilyticus” attached to the cell surface of Gordonia amarae, a causative agent of sludge bulking, and existed in a parasitic relationship in wastewater treatment reactors (Batinovic et al., 2021). In addition, oral “Ca. Nanosynbacter” species have been shown to parasitize host bacteria through a close physical association, thereby attenuating host pathogenicity (Chipashvili et al., 2021). Taken together, these host-associated lifestyles involving direct attachment are consistent with the shared morphological traits of Minisyncoccota and provide important insights into their ecological strategies across different environments, as well as their potential for future applications.

Table 2.Morphological characteristics and cell dimensions of members of the phylum Minisyncoccota

Species	Shape	Length (nm)*1	Width (nm)*1	Reference
“Ca. Sonnebornia yantaiensis”	rod	1,600–1,900	500–600	Gong et al., 2014
“Ca. Nanosynbacter lyticus”	coccoid	200–500	200–500	He et al., 2015; Bor et al., 2016, 2018; Utter et al., 2020
“Ca. Nanosynbacter” sp.	coccoid/ovoid	100–300	100–300	Ibrahim et al., 2021
“Ca. Mycolatisynbacter gordoniilyticus”	ovoid	424–478	224–264	Batinovic et al., 2021
“Ca. Vampirococcus lugosii”	flat	200–240	500–600	Moreira et al., 2021
“Ca. Absconditicoccus praedator”	coccoid	419–572	419–572	Yakimov et al., 2022
“Ca. Yanofskyibacterium parasiticum”	coccoid	330–590	290–430	Kuroda et al., 2022b, 2024
Minisyncoccus archaeiphilus	coccoid	630–830	400–520	Kuroda et al., 2022a, 2024; Nakajima et al., 2025
“Ca. Microsyncoccus archaeolyticus”	coccoid	330–510	240–320	Kuroda et al., 2022a, 2024
“Ca. Microsaccharimonas” sp.	coccoid	219–567	136–apx.300*2	Xie et al., 2022
“Ca. Nealsonbacteria” sp.	coccoid	200–800	200–800	Chen et al., 2023

*1 When “diameter” was reported in the original publication, the same value was used for both length and width for consistency.

*2 Estimated from figures in the original publication

Fig. 4. Transmission electron micrographs of (A) “Ca. Yanofskyibacterium parasiticum” parasitizing a Methanothrix cell, and (B) Minisyncoccus archaeiphilus parasitizing a Methanospirillum cell; arrows indicate Minisyncoccota cells (Reprinted with permission from the publisher from Kuroda et al., 2023a), and (C) fluorescence in situ hybridization (FISH) of uncultured clade “Ca. Gracilibacteria”/JAEDAM01 (red) and Zoogloea (green). The methods used to obtain the figures are described in Kuroda et al. (2023a) and Fujii et al. (2024).

Metabolic characteristics

To provide an integrated overview of the metabolic characteristics of the phylum Minisyncoccota, we summarized genomic features inferred from MAGs derived from both environmental samples and cultivated strains in a heatmap based on previously published datasets (Fig. 5). Genome sizes averaged 0.92‍ ‍Mbp (ranging from 0.42 to 2.13‍ ‍Mbp), which is in accordance with previously reported values for members of this phylum. Overall, the predicted metabolic characteristics were consistent with those described in MAG-based studies and reviews (Castelle et al., 2018; Bokhari et al., 2020; Lemos et al., 2020; Ji et al., 2022; Maatouk et al., 2023).

Fig. 5. Multi-symbol annotation map of metabolic features based on the findings of Prokka v1.13.0 (Seemann, 2014), DRAM v1.5 (Shaffer et al., 2020), and the MacsyFinder TFFScan or TXXScan model (Abby et al., 2016). Stars represent cultured and enriched strains. The data used for these analyses are provided in Table S5–S12.

Central metabolic pathways and the electron transport chain

Many MAGs partially retained genes associated with glycolysis, while complete pathways were rarely observed, suggesting a limited potential for full glucose catabolism and a dependence on external supplementation or the uptake of metabolic intermediates (Castelle et al., 2018; Bokhari et al., 2020; Lemos et al., 2020; Ji et al., 2022; Maatouk et al., 2023). “Ca. Gracilibacteria”/JAEDAM01 lacked most of the pathway, a feature frequently reported in this lineage (Sieber et al., 2019; Moreira et al., 2021; Yakimov et al., 2022; Kuroda et al., 2023b; Fujii et al., 2024). The pentose phosphate pathway was poorly represented, with most lineages possessing only a subset of enzymes. Similarly, the tricarboxylic acid (TCA) cycle and the reductive TCA cycle were largely absent, and when partially retained, their functions were limited to auxiliary roles for biosynthesis, such as cofactor generation (Wrighton et al., 2012; Anantharaman et al., 2016a; Danczak et al., 2017; Lemos et al., 2019; Fujii et al., 2022). Genes associated with the reductive pentose phosphate cycle (Calvin cycle) were also incomplete.

Complexes I–IV were largely absent, indicating that oxidative phosphorylation was generally not functional. However, some members of “Ca. Saccharimonadia”, “Ca. Doudnaibacteriota” (synonym “Ca. Doudnabacteria”), and other Minisyncoccota lineages retained partial complexes III–IV. “Ca. Saccharimonadia” has been reported to encode complex III, which may be involved in oxygen scavenging (Kantor et al., 2013; Starr et al., 2018; Lemos et al., 2019; Kagemasa et al., 2025). Lemos et al. (2019) further suggested that “Ca. Saccharimonadia”, although primarily reliant on fermentative metabolism, occasionally performs aerobic respiration. In this process, NAD⁺ is regenerated via a membrane-bound NADH dehydrogenase, which transfers electrons to ubiquinone. Ubiquinone then delivers electrons to cytochrome o ubiquinol oxidase, where oxygen is reduced to water, concurrently generating a proton motive force across the cytoplasmic membrane that drives ATP synthesis by ATP synthase (Lemos et al., 2019). In contrast, complex V (ATPase), either the F or V/A type, was frequently retained, suggesting that ATP synthesis via proton motive force—or, conversely, ion transport coupled to ATP hydrolysis—remains possible.

Fermentation, short-chain fatty acid metabolism, and other metabolic pathways

Genes encoding enzymes related to acetate production (acetate kinase and acetate-CoA ligase) were occasionally present, indicating that partial fermentative pathways operate in some lineages. In contrast, genes required for butyrate and propionate fermentation (butyrate kinase, propionate kinase, and propionate CoA-transferase) were largely absent, suggesting that typical butyrate- and propionate-producing fermentation is unlikely (Castelle et al., 2018; Lemos et al., 2020; Ji et al., 2022; Maatouk et al., 2023). However, “Ca. Parcunitrobacter nitroensis” has been reported to harbor genes associated with propionate fermentation (Castelle et al., 2017). Genes for lactate fermentation (l- and d-lactate dehydrogenase) were frequently detected, indicating that lactate fermentation constitutes one of the major energy metabolism pathways (Danczak et al., 2017; Hosokawa et al., 2021; Chiriac et al., 2022; Kuroda et al., 2023b; Kagemasa et al., 2025). Additional enzymes, such as formate C-acetyltransferase, were also partially retained, potentially enabling glycolysis-linked fermentation.

Genes required for the synthesis of amino acids, phospholipids, and nucleic acids were generally incomplete, suggesting that these compounds cannot be synthesized de novo. In contrast, genes for peptidoglycan biosynthesis were frequently observed, and in some bacteria, the complete pathway was identified (Castelle et al., 2018). Therefore, the autonomous biosynthetic capacity appears to be extremely limited, implying strong dependence on host- or symbiont-derived metabolites.

Although metagenomic studies on subsurface and sedimentary communities indicated that Minisyncoccota contribute to nitrogen and sulfur cycling (Anantharaman et al., 2016b; Danczak et al., 2017; He et al., 2021), detailed findings are not shown in this review. However, complete pathways are absent, with only one or two genes typically being present. Therefore, they are unlikely to perform multi-step redox transformations independently, instead occupying auxiliary roles within division-of-labor metabolic networks (Anantharaman et al., 2016b; He et al., 2021).

Additional features common to Minisyncoccota

Genes encoding ComEC, a protein involved in DNA uptake, were found in most MAGs, while ComEA was present in some. These findings suggest the potential for natural transformation and the acquisition of exogenous DNA. Nearly all members harbored the core gene set for type IV pili (T4P), which appears to be a hallmark of Minisyncoccota (Castelle et al., 2018; Lemos et al., 2020; Ji et al., 2022; Maatouk et al., 2023). T4P are known to mediate host recognition, adhesion, and DNA uptake, thereby potentially compensating for their limited metabolic repertoire (Méheust et al., 2019). Transmission and scanning electron microscopic observations have consistently revealed the presence of pili-like structures, further supporting T4P being a shared feature across this phylum (Kuroda et al., 2022a, 2022b; Xie et al., 2022; Yakimov et al., 2022). Furthermore, isolate TM7i was shown to use pili for host attachment via twitching-like motility (Xie et al., 2022). In addition, in N. lyticus TM7x, it has been experimentally demonstrated that two functionally distinct type IV pili are produced, with one mediating initial attachment to the host‍ ‍bacterium and the other driving twitching motility (Grossman et al., 2025). Therefore, T4P-based episymbiotic relationships appear to be common within the phylum Minisyncoccota. In contrast, flagellar-related genes were not detected, and consistent with previous findings, they appear to be largely absent in the phylum Minisyncoccota (Castelle et al., 2018). Collectively, these findings indicate that T4P play a crucial role in motility and host interactions within this lineage.

Host-associated lifestyles are common in the phylum Minisyncoccota. In contrast, a distinct genomic feature has been identified in the “Ca. Gracilibacteria”/JAEDAM01 lineage. While UGA functions as a stop codon in the standard genetic code, UGA-to-glycine recoding has been reported in this lineage (Rinke et al., 2013). Single-cell genomic anal­yses revealed that in the lineage formerly known as SR1, many genes contained UGA codons at positions conserved for glycine residues, and also that a specialized tRNA^Gly_UCA was aminoacylated with glycine by glycyl-tRNA synthetase (Campbell et al., 2013). Large-scale metagenomic anal­yses have further demonstrated that UGA-to-glycine recoding is restricted to the “Ca. Gracilibacteria”/JAEDAM01 lineage, with its origin being traceable to their last common ancestor (Ivanova et al., 2014).

Conclusions

We herein provided an overview of current knowledge of the phylum Minisyncoccota, with a focus on historical transitions in its phylogenetic classification. We also summarized findings on PCR primer design, FISH probe development, metabolic features, phylogenetic diversity, and parasitic relationships. Members of Minisyncoccota exhibit extremely limited metabolic capacities, with the majority of central metabolic and cofactor biosynthetic pathways being absent or incomplete. Consistent with MAG-based metabolic inferences from both environmental samples and cultivated strains, they are generally unable to survive independently and are considered to adopt epibiotic lifestyles that are dependent on other microorganisms. T4P, frequently observed across this lineage, appear to mediate host recognition and attachment and may also contribute to DNA uptake, potentially facilitating survival through host interactions despite restricted metabolic repertoires. These findings suggest that Minisyncoccota are not merely metabolically constrained bacteria, but instead represent organisms that fulfill dependent or interdependent roles within microbial communities. Overall, our understanding of microbial diversity and evolution has been expanded by the phylum Minisyncoccota, and its existence provides insights into the “hidden” division of labor within microbial ecosystems. Future efforts, particularly the isolation of additional uncultivated strains and experimental validation, will be essential to further elucidate the functional roles and symbiotic mechanisms of Minisyncoccota.

Citation

Fujii, N., Nakajima, M., Narihiro, T., Kuroda, K., and Kindaichi, T. (2026) Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota. Microbes Environ 41: ME25084.

https://doi.org/10.1264/jsme2.ME25084

Acknowledgements

This work was supported by JSPS KAKENHI Grant Numbers JP16H04833, JP20H02287, JP23KJ1642, and JP25K00043. FISH observations using a confocal laser scanning microscope (LSM700) were conducted at the Department of Gene Science, Integrated Experimental Support/Research Division, Natural Science Center for Basic Research and Development, Hiroshima University.

Conflicts of Interest

The authors declare that there are no conflicts of interest.

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