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Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell-cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.

Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.

Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~10³ cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator. [ABSTRACT FROM AUTHOR]

Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein- coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.

Background: Emergency abdominal surgery is associated with significant postoperative morbidity and mortality. The delivery of standardized pathways in this setting may have the potential to transform clinical care and improve patient outcomes. Methods: The OVID SP versions of MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials were searched between January 1950 and October 2022. All randomized and non-randomized cohort studies comparing protocolized care streams with standard care protocols in adult patients (>18 years old) undergoing major emergency abdominal surgery with 30-day follow-up data were included. Studies were excluded if they reported on standardized care protocols in the trauma or elective setting. Outcomes assessed included length of stay, 30-day postoperative morbidity, 30-day postoperative mortality and 30-day readmission and reoperations rates. Risk of bias was assessed using ROBINS-I for non-randomized studies and RoB-2 for randomized controlled trials. Meta-analysis was performed using random effects modelling. Results: Seventeen studies including 20 927 patients were identified, with 12 359 patients undergoing protocolized care pathways and 8568 patients undergoing standard care pathways. Thirteen unique protocolized pathways were identified, with a median of eight components (range 6–15), with compliance of 24–100%. Protocolized care pathways were associated with a shorter hospital stay compared to standard care pathways (mean difference −2.47, 95% c.i. −4.01 to −0.93, P = 0.002). Protocolized care pathways had no impact on postoperative mortality (OR 0.87, 95% c.i. 0.41 to 1.87, P = 0.72). A reduction in specific postoperative complications was observed, including postoperative pneumonia (OR 0.42 95% c.i. 0.24 to 0.73, P = 0.002) and surgical site infection (OR 0.34, 95% c.i. 0.21 to 0.55, P < 0.001). Discussion: Protocolized care pathways in the emergency setting currently lack standardization, with variable components and low compliance; however, despite this they are associated with short-term clinical benefits. The delivery of postoperative care following emergency laparotomy is highly variable and significantly impacts postoperative outcomes. Protocolized postoperative pathways in emergency laparotomy are compared to standard care by meta-analysis to determine their impact on postoperative clinical outcomes. This meta-analysis identified 13 unique protocolized care pathways that were associated with a reduction in length of stay, morbidity and mortality. [ABSTRACT FROM AUTHOR]

Background Overall survival rates for locally recurrent rectal cancer (LRRC) continue to improve but the evidence concerning health-related quality of life (HrQoL) remains limited. The aim of this study was to describe the short-term HrQoL differences between patients undergoing surgical and palliative treatments for LRRC. Methods An international, cross-sectional, observational study was undertaken at five centres across the UK and Australia. HrQoL in LRRC patients was assessed using the European Organisation for Research and Treatment of Cancer (EORTC) QLQ-CR29 and functional assessment of cancer therapy – colorectal (FACT-C) questionnaires and subgroups (curative versus palliative) were compared. Secondary analyses included the comparison of HrQoL according to the margin status, location of disease and type of treatment. Scores were interpreted using minimal clinically important differences (MCID) and Cohen effect size (ES). Results Out of 350 eligible patients, a total of 95 patients participated, 74.0 (78.0 per cent) treated with curative intent and 21.0 (22.0 per cent) with palliative intent. Median time between LRRC diagnosis and HrQoL assessments was 4 months. Higher overall FACT-C scores denoting better HrQoL were observed in patients undergoing curative treatment, demonstrating a MCID with a mean difference of 18.5 (P < 0.001) and an ES of 0.6. Patients undergoing surgery had higher scores denoting a higher burden of symptoms for the EORTC CR29 domains of urinary frequency (P < 0.001, ES 0.3) and frequency of defaecation (P < 0.001, ES 0.4). Higher overall FACT-C scores were observed in patients who underwent an R0 resection versus an R1 resection (P = 0.051, ES 0.6). EORTC CR29 scores identified worse body image in patients with posterior/central disease (P = 0.021). Patients undergoing palliative chemoradiation reported worse HrQoL scores with a higher symptom burden on the frequency of defaecation scale compared with palliative chemotherapy (P = 0.041). Conclusion Several differences in short-term HrQoL outcomes between patients undergoing curative and palliative treatment for LRRC were documented. Patients undergoing curative surgery reported better overall HrQoL and a higher burden of pelvic symptoms. [ABSTRACT FROM AUTHOR]

Background Undertaking randomized clinical trials (RCTs) in emergency surgical settings is associated with methodological and practical challenges. This study explored patients' and clinicians' perspectives associated with the conduct of an RCT comparing laparoscopic and open colorectal surgery in the acute setting. Methods All eligible patients screened and enrolled for the 'Laparoscopic versus open colorectal surgery in the acute setting (LaCeS)' multicentre, randomized clinical feasibility trial in five UK NHS Trusts were invited to respond to a survey. Patients and healthcare professionals were also invited to take part in semi-structured interviews. Survey and interviews explored the acceptability of the feasibility trial. Interviews were audio recorded, transcribed verbatim, and analysed using thematic analysis. Survey data were analysed descriptively to assess patient views of the trial and intervention. Results Out of 72 patients enrolled for the LaCeS RCT, survey data were collected from 28 patients (38.9 per cent), and interviews were conducted with 16 patients and 14 healthcare professionals. Thirteen out of 28 patients (46 per cent) had treatment preferences but these were not strong enough to deter participation. Twelve of the patients interviewed believed that their surgeon preferred laparoscopic surgery, but this did not deter them from participating in the trial. Half of the surgeons interviewed expressed the view that laparoscopic surgery was of benefit in this setting, but recognized that the need for research evidence outweighed their personal treatment preferences. Eight of the 14 recruiters reported that the emergency setting affected recruitment, especially in centres with fewer recruiting surgeons. Interviewees reported that recruitment was helped significantly by using surgical trainees to consent patients. Conclusion This study identified specific challenges for the LaCeS trial design to address and adds significant insights to our understanding of recruiting to emergency surgical trials more broadly. [ABSTRACT FROM AUTHOR]

Background: Medical technologies have the potential to improve quality and efficiency of healthcare. The design of clinical trials should consider participants' perspectives to optimise enrolment, engagement and satisfaction. This study aims to assess patients' perceptions of their involvement in medical device trials, to inform the designs of future medical technology implementation and evaluation.Methods: Four focus groups were undertaken with a total of 16 participants who had participated in a study testing hospital inpatient remote monitoring devices. Interviews were audio-recorded, transcribed verbatim and underwent thematic analysis.Results: Four main themes emerged: patients' motivations for participating in medical device research; patients' perceptions of technology in medicine; patients' understanding of trial methodology; and patients' perceptions of the benefits of involvement in medical device trials. The appeal of new technology is a contributing factor to the decision to consent, although concerns remain regarding risks associated with technology in healthcare settings. Perceived benefits of participating in device trials include extra care, social benefits and comradery with other participants seen using the devices, although there is a perceived lack of confidence in using technology amongst older patients.Conclusion: Future device trials should prioritise information sharing with participants both before and after the trial. Verbal and written information alongside practical demonstrations can help to combat a lack of confidence with technology. Randomised trials and those with placebo- or sham-controlled arms should not be considered as barriers to participation. Study results should be disseminated to participants in lay format as soon as possible, subject to participant permission. [ABSTRACT FROM AUTHOR]

Author(s): Kathryn M. Kauffman [1]; Fatima A. Hussain [1]; Joy Yang [1]; Philip Arevalo [1]; Julia M. Brown [2]; William K. Chang [2]; David VanInsberghe [1]; Joseph Elsherbini [1]; Radhey [...]