Fontibacterium africanum


Citation

Formal styling
Fontibacterium africanum Fernandes et al., 2025
Effective publication
Fernandes et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:gnukuc44 (validated)
Canonical URL
https://seqco.de/i:49874

Nomenclature

Rank
Species
Syllabication
a.fri.ca'num
Etymology
N.L. neut. adj. africanum, pertaining to the isolation source of the MAG (Lake Malawi) and a prevalence in the African Great Lakes
Nomenclatural type
NCBI Assembly: GCA_965235885.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type genome is Fontibacterium africanum N-Mw6-13nov23-081 (GCA_965235885.1), a metagenome-assembled genome (MAG) assembled from 50 m depth from Lake Malawi, Malawi (date: 2023-11-13). N-Mw6-13nov23-081 has a genome size of 1.1 Mbp with a genomic GC content of 30%, contains 1 rRNA gene (5S rRNA) and 28 tRNAs. The genome is of high quality, consisting of 7 contigs, with a completeness of 95.2%, contamination of 0% and strain heterogeneity of 0% as assessed with checkM. The metagenome was assembled with FLYE from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Metagenomic fragment recruitment of >600 samples from five continents indicate that the species is present only in the African Great Lakes Malawi, Tanganyika, and Kivu. The closest cultivated relatives are Fontibacterium commune, syn. ‘Candidatus Fonsibacter ubiquis’ LSUCC0530 (GCF_002688585.1; later reclassified to ‘Ca. Allofontibacter communis’), with an average amino acid identity of 68.64 % and average nucleotide identity of 71.78 % and another newly proposed species, Fontibacterium abundans MiE-29 (GCA_965235095.1), with an AAI of 68.51 % and an ANI of 71.6 %. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Fonsibacter; s__Fonsibacter sp016882225.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Pelagibacterales » Pelagibacteraceae » Fontibacterium » Fontibacterium africanum
Parent
Fontibacterium

Genomics

Accession
NCBI Assembly:GCA_965235885.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 95.2%
  • Contamination: 0.0%
  • Quality: 95.2
Ribosomal and transfer RNA genes
  • 0 16S rRNAs
  • 0 23S rRNAs
  • tRNAs for 17 amino acids
Sequencing depth
167.0 ×
Source
Other features
  • G+C Content: 30.0%
  • Coding Density: 93.1%
  • Codon Table: 11
  • N50: 170,168 bp
  • Contigs: 7
  • Largest Contig: 300,879 bp
  • Assembly Length: 1,027,849 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
This is a metagenome-assembled genome (MAG) that was assembled with FLYE v2.9.1-b1780 (settings: --nano-corr –meta –no-alt-contigs) from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Contigs ≥3 kbp were used for hybrid binning (tetranucleotide frequencies and coverage data using cross-mapping of reads gained from the same lake, i.e., 12 samples in the case of Lake Malawi) using MaxBin-2.2.7, MetaBAT and MetaBAT2 and DAS Tool-1.1.3 to combine their predictions. Bins were manually curated and CheckM v1.1.3 was used to estimate bin completeness, contamination, and strain heterogeneity. rRNA genes were predicted with barrnap v0.9, tRNA genes were predicted with tRNAscan v1.4. Although the fragmentation of this long-read MAG is low (it consists of only 7 contigs), and it is highly complete (95.2%) it contains only a 5S rRNA gene, but no 16S or 23S rRNA genes. 
Automated checks
Complete

Last modified 4 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
8 months ago by Salcher, Michaela M
Submitted
3 months ago by Salcher, Michaela M
Curators
Validated
2 months ago by Rodriguez-R, Luis M
Date of priority
2025-08-28 03:13 PM (UTC)

Publications
1

Citation Title
Fernandes et al., 2025, Nature Microbiology Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
Effective publication



© 2022-2025 The SeqCode Initiative
  All information contributed to the SeqCode Registry is released under the terms of the Creative Commons Attribution (CC BY) 4.0 license
seqco.de/r:gnukuc44