Journal: bioRxiv

Article Title: Oral Actinobacteria sense and defend against parasitic epibionts

doi: 10.64898/2026.09.08.750141

Figure Lengend Snippet: A) Growth of TM7-008 (fold change) achieved on the indicated S. odontolytica F0309 strains. OBNOAD_01965 encodes a candidate Esx substrate sharing protein sequence-level homology with AesB. Data represent mean±SD, n=3 biological replicates. *p≤0.05; one-way ANOVA with multiple comparisons to the wild-type mean. B) Level of AesA and AesB detected in cell-free culture supernatant of the indicated So F0309 strains. SC, spectral counts. Data represent the mean ± s.d. (n = 3 technical replicates). C) IUPred3 prediction of disordered regions in AesB . The relative positions of the N- and C-terminal domains are depicted in the schematic above the graph. The dashed line represents a disorder probability of 50%.

Article Snippet: To obtain a closed reference genome to be employed in subsequent analyses, we sequenced the genome of S. odontolytica F0309 wild-type strain using the Standard Bacterial Genome Sequencing with Extraction service by Plasmidsaurus (Eugene, OR, USA).

Techniques: Sequencing

Journal: bioRxiv

Article Title: Oral Actinobacteria sense and defend against parasitic epibionts

doi: 10.64898/2026.09.08.750141

Figure Lengend Snippet: A) Unrooted maximum likelihood phylogeny of AesB homologs identified by iterative PSI-BLAST searching of the clustered NR database . Proteins found in So F0309 indicated with blue circles. B) Relative conservation at each residue position of AesB, coloured according to the scale at bottom left. Conservation was calculated using the multiple sequence alignment assembled in (A). C) Sequence log deriving from an alignment of the C-terminal region of AesB. The grey wedge indicates the position of the conserved C-terminal charged region. Residues experimentally tested for their importance in inhibiting replication of TM7-008 are highlighted in pink.

Article Snippet: To obtain a closed reference genome to be employed in subsequent analyses, we sequenced the genome of S. odontolytica F0309 wild-type strain using the Standard Bacterial Genome Sequencing with Extraction service by Plasmidsaurus (Eugene, OR, USA).

Techniques: Residue, Sequencing

Journal: bioRxiv

Article Title: Oral Actinobacteria sense and defend against parasitic epibionts

doi: 10.64898/2026.09.08.750141

Figure Lengend Snippet: A) Differential expression of S. meyeri W712 proteins between W712– TM7-008 co-cultures and W712 mono-cultures. Protein levels represent averaged, normalized LFQ values as described in . Proteins are grouped and colored in the same way as in and (other Esx-related and pyrimidine synthesis proteins are not shown). Data represent the mean ± s.d. for proteins in the indicated category, n = 3 technical replicates. *p≤0.05, one sample t test comparing mean with value 0. B) EsrG1 T263 phosphorylation in S. meyeri W712 wild-type grown in mono-cultures (Control) or co-cultures with TM7-008 or TM7- 074, based on MaxQuant phosphor (STY) analysis of whole cell proteome datasets. The line indicates the mean. n = 3 technical replicates. Values are raw MS1 intensities (arbitrary units). C) Unrooted phylogenetic tree depicting the distribution of Esr pathways across the class Actinomycetes. Each leaf represents a taxonomic family, colored according to the number of Esr pathways identified among members of that family. Orders containing greater than one family are highlighted in grey. An additional blue circle denotes families containing species that have been experimentally shown to support the growth of Saccharibacteria. Tree is based on an concatenated alignment of 120 conserved proteins, derived from the Genome Taxonomy Database . D) Schematic depicting representative examples of genetically linked Esr and Esx gene clusters. Genes are colored according to functional modules as in . E) Schematic depicting the domain architectures of diverse EsrG proteins and their relative frequencies. The experimentally determined phosphorylation sites on EsrG proteins from S. odontolytica and S. meyeri are depicted as yellow circles. F) Relative levels (SC ratio) of the indicated proteins in cell-free supernatant of the indicated So F0309 strains, normalized to wild-type values. Data represent the mean ± s.d, n = 3 technical replicates. G) Fold-change in levels of TM7-008 after 40 hours of growth on the indicated So F0309 strains. Data represent mean ± SD (n = 3 biological replicates). * p≤0.05, one-way ANOVA with Šidák correction for multiple comparisons to the mean of the wild-type strain; H) Model depicting the potential modes of Esr pathway function, with Esr components colored to reflect relative sequence diversity. The sequence diversity of the linker domain of EsrA, which can be comprised of different classes of repeats, could not be readily compared across proteins and is thus colored grey. In both Esr1-like (left) and Esr2-like pathways (right), sensing of diverse threat signals via the sequence-divergent β-propeller domains of EsrA proteins activates a signaling cascade that proceeds through conserved MoxR and vWA proteins and a kinase/phosphatase pair to affect the phosphorylation state of a divergent FHA protein. Upon phosphorylation, the variable domain architectures of these FHA proteins permit a variety of responses, including transcription of defensive genes through direct (zinc finger domain-mediated) and indirect mechanisms (left) and post- translational activation of defensive pathways such as the Esx secretion system (right). Alongside canonical EsxA-EsxB dimers (grey), these Esx systems secrete AesB-like effectors (green) that promote defense against the threat imposed by Saccharibacteria. PPL1, pseudophosphatase-like; Zn, zinc finger.

Article Snippet: To obtain a closed reference genome to be employed in subsequent analyses, we sequenced the genome of S. odontolytica F0309 wild-type strain using the Standard Bacterial Genome Sequencing with Extraction service by Plasmidsaurus (Eugene, OR, USA).

Techniques: Quantitative Proteomics, Phospho-proteomics, Control, Derivative Assay, Functional Assay, Sequencing, Activation Assay

Journal: bioRxiv

Article Title: Identification of soil microbes associated with real-time plastic degradation using in situ conductivity sensors

doi: 10.64898/2026.08.16.745074

Figure Lengend Snippet: Step 1 ) The sensors are printed with biodegradable PHBV, poly(3-hydroxybutuyrate- co -3-hydroxyvalerate), on one side and non-biodegradable PMMA, poly(methyl methacrylate) on the other side as a control. Step 2 ) UV-sterilized sensors are inserted into soil mesocosms and monitor PHBV degradation in real-time as an increase in resistance, which we normalize to the non-degraded PMMA. Step 3 ) At the end of the mesocosm incubation, the sensors are removed and we can summarise the PHBV degradation signal to identify which soils have the highest capacity to degrade PHBV. Step 4 ) PHBV and PMMA material from sensors incubated in the highest PHBV-degrading soils are scraped off and used as starting material for culture-independent ( Step 5 , left panel) and culture-dependent ( Step 6 , right panel) approaches to identify novel PHBV degraders. Step 5, left ) We used the PHBV and PMMA material from high degrading soils for 16S rRNA and ITS marker gene sequencing to identify microbes enriched on degraded PHBV compared to non-degraded PMMA from each in situ sensor. Step 5, right ) We also used the PHBV material from high degrading soils to isolate novel PHBV degraders on agar plates with a PHBV overlay (inset). Isolates that formed clearing zones on plates were cultured in liquid media to measure their continued capacity to degrade PHBV. We also measured the respiration rates of isolates growing with PHBV as their sole carbon source to confirm PHBV catabolism.

Article Snippet: DNA aliquots from two of our isolates, Streptomyces sp. [2CO Garden Isolate], Lysinibacillus sp. [2CO Garden Isolate] were sequenced by Plasmidsaurus using their bacterial genome sequencing service.

Techniques: Control, Incubation, Marker, Sequencing, In Situ, Cell Culture