We review recent insights into the #ecology and #biogeography of the oral #microbiome, especially those regarding less well-understood members such as fungi, archaea, viruses, and #saccharibacteria / #patescibacteria

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples | mSystems Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput, manual ...

New publication is live today! Obtaining complete bacterial genomes from saliva samples using @nanopore sequencing.

#microbiology #nanopore #dentistry #genomics #Bioinformatics #saccharibacteria #actinomyces
@JCVenterInst @UCSDMedSchool @mSystemsJ

journals.asm.org/doi/10.1128/ms…

Complete Genome Sequence of “Candidatus Nanosynbacter” Strain HMT-348_TM7c-JB, a Member of Saccharibacteria Clade G1 | Microbiology Resource Announcements Saccharibacteria are abundant and diverse members of the human oral microbiome; however, they are poorly understood and appear to exhibit an epibiont/parasitic lifestyle dependent on host bacteria. Here, a complete metagenome-assembled genome (MAG) ...

New publication:I used @nanopore sequencing and Polypolish to get the first complete genome of the G1 Saccharibacteria, HMT-348, one of the most prevalent Saccharibacteria clades in the human microbiome.
#saccharibacteria #microbiology #dentistry

journals.asm.org/doi/10.1128/mr…

Guess I'm on a roll this week. Also coming very soon...
#microbiology #dentistry #saccharibacteria #nanopore #metagenomics #genomics #microbiome

Another first-in-clade complete #Saccharibacteria genome is about to be released (Clade G1, HMT-348). Assembled using both @nanopore and @illumina on a rainy San Diego day in late December.
#Microbiology
#dentistry

Excited to attend this symposium in-person and present a poster on my clade G6 #saccharibacteria genomes in 2 weeks!

x.com/ForsythResearc…

Yesterday, I shared some of my recent research on #saccharibacteria at the2021 @CedIadr Oral Health Research Congress. The work is also published in @mSphereJ
#dentistry
#microbiology
#microbiome

Complete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle | mSphere ABSTRACT Saccharibacteria (formerly TM7) have reduced genomes and a small cell size and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of Saccharibacteria inhabiting the human oral cavity, ...

New manuscript is live:#microbiology
#microbiome
#saccharibacteria
#dentistry

journals.asm.org/doi/10.1128/mS…

Complete Genome Sequence of Strain JB001, a Member of Saccharibacteria Clade G6 (“Candidatus Nanogingivalaceae”) | Microbiology Resource Announcements At least 6 highly diverse clades of Saccharibacteria inhabit the human oral cavity. However, all oral Saccharibacteria strains with currently available complete genome sequences or cultured isolates belong to clade G1, leaving clades G2 through G6 poorly ...

The first complete genome of a clade G6 Saccharibacteria is now available, representing one of the smallest naturally occurring bacterial genomes. Completed using @nanopore
#dentistry #microbiology #Saccharibacteria #TM7 #microbiome #nanopore

journals.asm.org/doi/10.1128/MR…

#Saccharibacteria clade G6: 1 year ago, there was only 1 available genome from this group. Now, there are 11, representing at least 3-5 distinct species and 3 complete genomes. We still know almost nothing about them.#dentistry
#microbiology
#Tm7

ow.ly/dplw50F2DRc

Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle Saccharibacteria (formerly TM7) have reduced genomes, a small size, and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of Saccharibacteria inhabiting the human oral cavity, cultured isolates or complete genomes of oral Saccharibacteria have been previously limited to the G1 clade. In this study, nanopore sequencing was used to obtain three complete genome sequences from clade G6. Phylogenetic analysis suggested the presence of at least 3-5 distinct species within G6, with two discrete taxa represented by the 3 complete genomes. G6 Saccharibacteria were highly divergent from the more well-studied clade G1, and had the smallest genomes and lowest GC-content of all Saccharibacteria. Pangenome analysis showed that although 97% of shared pan-Saccharibacteria core genes and 89% of G1-specific Core Genes had putative functions, only 50% of the 244 G6-specific Core Genes had putative functions, highlighting the novelty of this group. Compared to G1, G6 encoded divergent metabolic pathways. G6 genomes lacked an F1F0 ATPase, the pentose phosphate pathway, and several genes involved in nucleotide metabolism, which were all core genes for G1. G6 genomes were also unique compared to G1 in that they encoded lactate dehydrogenase, adenylate cyclase, limited glycerolipid metabolism, a homolog to a lipoarabinomannan biosynthesis enzyme, and the means to degrade starch. These differences at key metabolic steps suggest a distinct lifestyle and ecological niche for clade G6, possibly with alternative hosts and/or host-dependencies, which would have significant ecological, evolutionary, and likely pathogenic, implications. IMPORTANCE Saccharibacteria are ultrasmall, parasitic bacteria that are common members of the oral microbiota and have been increasingly linked to disease and inflammation. However, the lifestyle and impact on human health of Saccharibacteria remains poorly understood, especially for the 5 clades (G2-G6) with no complete genomes or cultured isolates. Obtaining complete genomes is of particular importance for Saccharibacteria, because they lack many of the “essential” core genes used for determining draft genome completeness and few references exist outside of clade G1. In this study, complete genomes of 3 G6 strains, representing two candidate species, were obtained and analyzed. The G6 genomes were highly divergent from G1, and enigmatic, with 50% of the G6 core genes having no putative functions. The significant difference in encoded functional pathways is suggestive of a distinct lifestyle and ecological niche, probably with alternative hosts and/or host-dependencies, which would have major implications in ecology, evolution, and pathogenesis. ### Competing Interest Statement The authors have declared no competing interest.

The preprint of my next paper is live!
#microbiology
#saccharibacteria
#tm7
#dentistry
#nanopore

biorxiv.org/content/10.110…

My first paper focusing on Saccharibacteria (and first single-author paper 😎) will be live very soon. Another genome completed with @nanopore / Oxford Nanopore Technologies.
#saccharibacteria
#microbiome
#microbiology
#tm7
#nanopore