Complex History of Aerobic Respiration and Phototrophy in the Chloroflexota Class Anaerolineae Revealed by High-Quality Draft Genome of Ca. Roseilinea mizusawaensis AA3_104.

Roseilinea is a novel lineage of Chloroflexota known only from incomplete metagenome-assembled genomes (MAGs) and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophs in the Chloroflexia class such as Chloroflexus and Roseiflexus. Here, we present a high-quality MAG of a member of Roseilinea, improving our understanding of the metabolic capacity and phylogeny of this genus, and resolving the multiple instances of horizontal gene transfer that have led to its metabolic potential.

Expanded Genomic Sampling Refines Current Understanding of the Distribution and Evolution of Sulfur Metabolisms in the .

The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolutionary histories, perform two drastically different metabolisms. Here, we aim at shedding some light on the distribution, diversity, and evolutionary histories of MSR and MSD, with a focus on the as a test case.

Changes in ATP Sulfurylase Activity in Response to Altered Cyanobacteria Growth Conditions.

We investigated variations in cell growth and ATP Sulfurylase (ATPS) activity when two cyanobacterial strains-Synechocystis sp. PCC6803 and Synechococcus sp. WH7803-were grown in conventional media, and media with low ammonium, low sulfate and a high CO/low O atmosphere.

The Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core.

Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats.

Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales.

Genome-resolved metagenomic sequencing approaches have led to a substantial increase in the recognized diversity of microorganisms; this included the discovery of novel metabolic pathways in previously recognized clades, and has enabled a more accurate determination of the extant distribution of key metabolisms and how they evolved over Earth history. Here, we present metagenome-assembled genomes of members of the Chloroflexota (formerly Chloroflexi or Green Nonsulfur Bacteria) order Aggregatilineales (formerly SBR1031 or Thermofonsia) discovered from sequencing of thick and expansive microbial mats present in an intertidal lagoon on Little Ambergris Cay in the Turks and Caicos Islands. These taxa included multiple new lineages of Type 2 reaction center-containing phototrophs that were not closely related to previously described phototrophic Chloroflexota-revealing a rich and intricate history of horizontal gene transfer and the evolution of phototrophy and other core metabolic pathways within this widespread phylum.

Clinical impact of subclonal EGFR T790M mutations in advanced-stage EGFR-mutant non-small-cell lung cancers.

Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). Here we show that the size of the EGFR T790M-positive clone impacts response to osimertinib. T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M-positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients.

Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer.

Photosynthesis-both oxygenic and more ancient anoxygenic forms-has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria.

Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen.

We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species-here proposed as Candidatus Anthektikosiphon siderophilum-that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.

Genomic sequence analysis of SH388 and proposed reassignment to fam. nov.

Here, we report the draft genome sequence of SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the phylum . Additionally, comparative genomic and phylogenetic analyses contextualize the convergent evolution of sulfur disproportionation and potential extracellular electron transfer in this organism relative to other members of the .

Draft Genome Sequence of Desulfobacter hydrogenophilus DSM 3380, a Psychrotolerant Sulfate-Reducing Bacterium.

Here, we describe the genome of DSM 3380, a bacterium that belongs to the The genome of this strictly anaerobic bacterium capable of sulfate reduction expands our understanding of microbial sulfate reduction in a wide range of environmental conditions.

Draft Genome Sequence of Desulfovibrio sulfodismutans ThAc01, a Heterotrophic Sulfur-Disproportionating Member of the .

Here, we describe the genome of ThAc01, a member first isolated from freshwater mud and the first strain reported to be capable of growth via sulfur disproportionation. As such, this genome expands our understanding of the diversity of sulfur-disproportionating microorganisms.

Draft Genome Sequence of subsp. DSM 14055, a Moderately Thermophilic Sulfate Reducer.

Here, we describe the genome of subsp. DSM 14055, a member of the that is capable of sulfate reduction coupled to the oxidation of propionate, lactate, pyruvate, and H/CO This genome expands our understanding of microbial sulfate reduction (MSR) in anaerobic methanogenic environments.

Draft Genome Sequence of Acidianus ambivalens DSM 3772, an Aerobic Thermoacidophilic Sulfur Disproportionator.

Here, we describe the genome sequence of DSM 3772, an archaeon belonging to the order that was first isolated from continental solfataric fields. This thermoacidophile was sequenced because it utilizes a unique sulfur disproportionation pathway that enables this metabolism under aerobic conditions, in contrast to obligately anaerobic bacterial sulfur disproportionators.

Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs.

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing.

Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Eremiobacterota (WPS-2).

Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2.

Follow the Oxygen: Comparative Histories of Planetary Oxygenation and Opportunities for Aerobic Life.

Aerobic respiration-the reduction of molecular oxygen (O) coupled to the oxidation of reduced compounds such as organic carbon, ferrous iron, reduced sulfur compounds, or molecular hydrogen while conserving energy to drive cellular processes-is the most widespread and bioenergetically favorable metabolism on Earth today. Aerobic respiration is essential for the development of complex multicellular life; thus the presence of abundant O is an important metric for planetary habitability. O on Earth is supplied by oxygenic photosynthesis, but it is becoming more widely understood that abiotic processes may supply meaningful amounts of O on other worlds.

The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time.

The fixation of inorganic carbon species like CO to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated.

Podoplanin regulates the migration of mesenchymal stromal cells and their interaction with platelets.

Mesenchymal stromal cells (MSCs) upregulate podoplanin at sites of infection, chronic inflammation and cancer. Here, we investigated the functional consequences of podoplanin expression on the migratory potential of MSCs and their interactions with circulating platelets. Expression of podoplanin significantly enhanced the migration of MSCs compared to MSCs lacking podoplanin.

Comparative adhesive and migratory properties of mesenchymal stem cells from different tissues.

Background: Mesenchymal stem cells (MSC) are used in therapy, often by injection into the blood.

Objective: We aimed to compare the adhesive and migratory properties of MSC from umbilical cords (UCMSC), bone marrow (BMMSC) or trabecular bone (TBMSC), which might influence delivery to injured tissue.

Methods: MSC were perfused through glass capillaries coated with matrix proteins, collagen or fibronectin, or albumin.

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch.

Background: Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored.

Results: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands.

Mesenchymal Stem Cells as Endogenous Regulators of Inflammation.

This chapter discusses the regulatory role of endogenous mesenchymal stem cells (MSC) during an inflammatory response. MSC are a heterogeneous population of multipotent cells that normally contribute towards tissue maintenance and repair but have garnered significant scientific interest for their potent immunomodulatory potential. It is through these physicochemical interactions that MSC are able to exert an anti-inflammatory response on neighbouring stromal and haematopoietic cells.

MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes.

Summary: Genome-resolved metagenomics allows the construction of draft microbial genomes from short-read shotgun metagenomics (Metagenome-Assembled Genomes, or MAGs); however, even high-quality MAGs are typically somewhat incomplete and contain a small amount of contaminant sequence, making accurate prediction of metabolic potential challenging. Here, we describe MetaPOAP, an algorithm for probabalistic assessment of the statistical likelihoods for the presence or absence of metabolic pathways in MAGs.

Availability And Implementation: MetaPOAP is available as Python scripts on GitHub or from the Fischer lab webpage, https://github.

Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer.

The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs.

Origin-Specific Adhesive Interactions of Mesenchymal Stem Cells with Platelets Influence Their Behavior After Infusion.

We investigated the adhesive behavior of mesenchymal stem cells (MSC) in blood, which might influence their fate when infused as therapy. Isolated human bone marrow MSC (BMMSC) or umbilical cord MSC (UCMSC) adhered efficiently from flow to the matrix proteins, collagen, or fibronectin, but did not adhere to endothelial selectins. However, when suspended in blood, BMMSC no longer adhered to collagen, while UCMSC adhered along with many aggregated platelets.

Draft Genome Sequence of sp. CP2_5A, a Phototrophic Member of the Phylum Recovered from a Japanese Hot Spring.

The phylum contains a single known phototrophic member, , which was recovered from a hot spring metagenome from Yellowstone National Park. Here, we expand the diversity of the genus with a genome recovered from a hot spring in Japan, extending the known range of this lineage to a new continent.