Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov., two novel species isolated from Sargassum, show genomic and physiological adaptations for a Sargassum-associated lifestyle.

The genus Tamlana from the Bacteroidota currently includes six validated species. Two strains designated PT2-4T and 62-3T were isolated from Sargassum abundant at the Pingtan island coast in the Fujian Province of China. 16S rRNA gene sequence analysis showed that the closest described relative of strains PT2-4T and 62-3T is Tamlana sedimentorum JCM 19808T with 98.40 and 97.98% sequence similarity, respectively. The 16S rRNA gene sequence similarity between strain PT2-4T and strain 62-3T was 98.68 %. Furthermore, the highest average nucleotide identity values were 87.34 and 88.97 % for strains PT2-4T and 62-3T, respectively. The highest DNA-DNA hybridization (DDH) value of strain PT2-4T was 35.2 % with strain 62-3T, while the DDH value of strain 62-3T was 37.7 % with T. sedimentorum JCM 19808T. Growth of strains PT2-4T and 62-3T occurs at 15-40 °C (optimum, 30 °C) with 0-4 % (w/v) NaCl (optimum 0-1 %). Strains PT2-4T and 62-3T can grow from pH 5.0 to 10.0 (optimum, pH 7.0). The major fatty acids of strains PT2-4T and 62-3T are iso-C15 : 0 and iso G-C15 : 1. MK-6 is the sole respiratory quinone. Genomic and physiological analyses of strains PT2-4T and 62-3T showed corresponding adaptive features. Significant adaptation to the growth environment of macroalgae includes the degradation of brown algae-derived diverse polysaccharides (alginate, laminarin and fucoidan). Notably, strain PT2-4T can utilize laminarin, fucoidan and alginate via specific carbohydrate-active enzymes encoded in polysaccharide utilization loci, rarely described for the genus Tamlana to date. Based on their distinct physiological characteristics and the traits of utilizing polysaccharides from Sargassum, strains PT2-4T and 62-3T are suggested to be classified into two novel species, Tamlana laminarinivorans sp. nov. and Tamlana sargassicola sp. nov. (type strain PT2-4T=MCCC 1K04427T=KCTC 92183T and type strain 62-3T=MCCC 1K04421T=KCTC 92182T).

Assessment of cardiovascular risk in patients with metabolic syndrome working in the agricultural sector.

INTRODUCTION: Cardiovascular diseases are the main death cause in Poland. Several clinical studies showed association between metabolic syndrome and higher prevalence of diabetes mellitus, cardiac events and mortality. The aim of the study was to estimate cardiovascular complications and death risk in subjects with metabolic syndrome (MS) working in agriculture. MATERIAL AND METHODS: The study included 332 people working in agriculture in Lodz voivodeship, 231 with MS and 101 healthy ones. Increased risk of cardiovascular complications was determined for pulse pressure (pp) >63 mmHg. Based on the SCORE index, 10-year death risk due to cardiovascular complications was estimated taking into account sex, age, smoking, systolic blood pressure and total cholesterol concentration. A value ≥5% was accepted as high risk of death within 10 years. RESULTS: Increased risk of cardiovascular complications (pulse pressure >63 mmHg) was found in 31.60% subjects with MS and 6.93% healthy ones. CONCLUSIONS: High risk of cardiovascular complications and death occurs statistically more frequently in subjects with MS than in the rest of the population.

Cultivable, Host-Specific Bacteroidetes Symbionts Exhibit Diverse Polysaccharolytic Strategies.

Beneficial gut microbes can facilitate insect growth on diverse diets. The omnivorous American cockroach, Periplaneta americana (Insecta: Blattodea), thrives on a diet rich in plant polysaccharides and harbors a species-rich gut microbiota responsive to host diet. Bacteroidetes are among the most abundant taxa in P. americana and other cockroaches, based on cultivation-independent gut community profiling, and these potentially polysaccharolytic bacteria may contribute to host diet processing. Eleven Bacteroidetes isolates were cultivated from P. americana digestive tracts, and phylogenomic analyses suggest that they were new Bacteroides, Dysgonomonas, Paludibacter, and Parabacteroides species distinct from those previously isolated from other insects, humans, and environmental sources. In addition, complete genomes were generated for each isolate, and polysaccharide utilization loci (PULs) and several non-PUL-associated carbohydrate-active enzyme (CAZyme)-coding genes that putatively target starch, pectin, and/or cellulose were annotated in each of the isolate genomes. Type IX secretion system (T9SS)- and CAZyme-coding genes tagged with the corresponding T9SS recognition and export C-terminal domain were observed in some isolates, suggesting that these CAZymes were deployed via non-PUL outer membrane translocons. Additionally, single-substrate growth and enzymatic assays confirmed genomic predictions that a subset of the Bacteroides and Dysgonomonas isolates could degrade starch, pectin, and/or cellulose and grow in the presence of these substrates as a single sugar source. Plant polysaccharides enrich P. americana diets, and many of these gut isolates are well equipped to exploit host dietary inputs and potentially contribute to gut community and host nutrient accessibility.IMPORTANCE Gut microbes are increasingly being recognized as critical contributors to nutrient accessibility in animals. The globally distributed omnivorous American cockroach (Periplaneta americana) harbors many bacterial phyla (e.g., Bacteroidetes) that are abundant in vertebrates. P. americana thrives on a highly diverse plant-enriched diet, making this insect a rich potential source of uncharacterized polysaccharolytic bacteria. We have cultivated, completely sequenced, and functionally characterized several novel Bacteroidetes species that are endemic to the P. americana gut, and many of these isolates can degrade simple and complex polysaccharides. Cultivation and genomic characterization of these Bacteroidetes isolates further enable deeper insight into how these taxa participate in polysaccharide metabolism and, more broadly, how they affect animal health and development.

Biomass utilization by gut microbiomes.

Mammals rely entirely on symbiotic microorganisms within their digestive tract to gain energy from plant biomass that is resistant to mammalian digestive enzymes. Especially in herbivorous animals, specialized organs (the rumen, cecum, and colon) have evolved that allow highly efficient fermentation of ingested plant biomass by complex anaerobic microbial communities. We consider here the two most intensively studied, representative gut microbial communities involved in degradation of plant fiber: those of the rumen and the human large intestine. These communities are dominated by bacteria belonging to the Firmicutes and Bacteroidetes phyla. In Firmicutes, degradative capacity is largely restricted to the cell surface and involves elaborate cellulosome complexes in specialized cellulolytic species. By contrast, in the Bacteroidetes, utilization of soluble polysaccharides, encoded by gene clusters (PULs), entails outer membrane binding proteins, and degradation is largely periplasmic or intracellular. Biomass degradation involves complex interplay between these distinct groups of bacteria as well as (in the rumen) eukaryotic microorganisms.

Polysaccharide Utilization Loci: Fueling Microbial Communities.

The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fueling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species and are of critical importance in competitive environments. In Bacteroidetes bacteria, these systems are organized as polysaccharide utilization loci (PULs), which are strictly regulated, colocalized gene clusters that encode enzyme and protein ensembles required for the saccharification of complex carbohydrates. This review provides historical perspectives and summarizes key findings in the study of these systems, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function. The ecological implications of dynamic PUL deployment by key species in the human gastrointestinal tract are explored, as well as the wider distribution of these systems in other gut, terrestrial, and marine environments.

[Questions of terminology, systematization and grading of complications of contact ureteral lithotripsy].

AIM: To investigate the advantages and disadvantages of the current variants of systematization and grading of complications of contact ureteral lithotripsy (CULT) and develop a working classification of CULT complications. MATERIALS AND METHODS: The study analyzed results of 545 fluoroscopy-guided endoscopic procedures performed at the MRRCI Clinic of Urology from 2008 to 2015 in 506 patients with ureterolithiasis. RESULTS: The proposed and implemented classification and terminology of CULT complications unifies the diagnostic and management algorithm. This tool is more systematic and structured than the classical classification and universal methods of systematization and grading of CULT complications (classifying CULT complications in "major" and "minor", PULS scale, Satava and Clavien-Dindo grading systems). Given the lack of clear grading of ureteral rupture, it was divided into amputation (two-level rupture) and avulsion (one-level rupture). Using such term as extravasation of the contrast media and/or migration of the stone outside of the ureter is groundless because these complications occur only after the perforation of the ureteral wall. Therefore, these conditions are complications not of CULT, but of the ureteral wall perforation. The ureteral perforation was classified into macro- and micro-perforation. CONCLUSION: The existing terminology, classification and grading of the CULT complications should undergo a more detailed analysis. None of the existing classifications of CULT complications afford them to be fully staged and systematized. The working classification of complications of CULT developed at the M.F. Vladimirsky MRRCI Clinic of Urology warrants a multi-center prospective study to validate it and investigate its effectiveness.

An overview of microbial enzymatic approaches for pectin degradation.

Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and ß-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.

Bacteroides thetaiotaomicron metabolic activity decreases with polysaccharide molecular weight.

The human colon hosts hundreds of commensal bacterial species, many of which ferment complex dietary carbohydrates. To transform these fibers into metabolically accessible compounds, microbes often express a series of dedicated enzymes homologous to the starch utilization system (Sus) encoded in polysaccharide utilization loci (PULs). The genome of Bacteroides thetaiotaomicron (Bt), a common member of the human gut microbiota, encodes nearly 100 PULs, conferring a strong metabolic versatility. While the structures and functions of individual enzymes within the PULs have been investigated, little is known about how polysaccharide complexity impacts the function of Sus-like systems. We here show that the activity of Sus-like systems depends on polysaccharide size, ultimately impacting bacterial growth. We demonstrate the effect of size-dependent metabolism in the context of dextran metabolism driven by the specific utilization system PUL48. We find that as the molecular weight of dextran increases, Bt growth rate decreases and lag time increases. At the enzymatic level, the dextranase BT3087, a glycoside hydrolase (GH) belonging to the GH family 66, is the main GH for dextran utilization, and BT3087 and BT3088 contribute to Bt dextran metabolism in a size-dependent manner. Finally, we show that the polysaccharide size-dependent metabolism of Bt impacts its metabolic output in a way that modulates the composition of a producer-consumer community it forms with Bacteroides fragilis. Altogether, our results expose an overlooked aspect of Bt metabolism that can impact the composition and diversity of microbiota. IMPORTANCE: Polysaccharides are complex molecules that are commonly found in our diet. While humans lack the ability to degrade many polysaccharides, their intestinal microbiota contain bacterial commensals that are versatile polysaccharide utilizers. The gut commensal Bacteroides thetaiotaomicron dedicates roughly 20% of their genomes to the expression of polysaccharide utilization loci for the broad range utilization of polysaccharides. Although it is known that different polysaccharide utilization loci are dedicated to the degradation of specific polysaccharides with unique glycosidic linkages and monosaccharide compositions, it is often overlooked that specific polysaccharides may also exist in various molecular weights. These different physical attributes may impact their processability by starch utilization system-like systems, leading to differing growth rates and nutrient-sharing properties at the community level. Therefore, understanding how molecular weight impacts utilization by gut microbe may lead to the potential design of novel precision prebiotics.

Simulated operations (SOs) apply mechanical support to structures to confirm symptom causation.

Simulated operations (SOs) are a direct application of the Integral Theory (IT) mantras, "structure and function are related" and "restore the structure and you will improve the function". SOs performed in a clinic setting, are the most effective way possible to test the validity of the IT predictions: stress urinary incontinence (SUI) and urge are mainly caused by laxity in the vagina or its supporting ligaments. The SUI prediction of the IT is validated if a hemostat applied vaginally in the position of the midurethra to mechanically support the pubourethral ligament (PUL) immediately stops urine loss on coughing. The urge and chronic pelvic pain (CPP) predictions of the IT are similarly validated if a patient states her urge and pain symptoms are relieved by insertion of the bottom blade of a bivalve speculum which supports the uterosacral ligaments (USLs). An important use of SOs is to preoperatively assess (by the hemostat test) whether sling surgery for SUI is likely to cure the patient. Similarly, the speculum is very useful for diagnosing whether severe urge or pain symptoms in a woman with minimal prolapse are originating from weak USLs. If digital support of a cystocele relieves urge symptoms, the patient can reasonably be informed that a cystocele repair should improve the urge as well her cystocele prolapse. Used intraoperatively under spinal anesthesia, SOs can determine whether a sling is sufficiently tight to reverse the loose PUL which is causing the SUI. Approximating both cardinal ligaments (CLs) intraoperatively can result in a remarkable disappearance of a transverese defect cystocele; approximating USLs intraoperatively can give an indication of how effective a USL plication would be surgically.

Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes.

Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like ß-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.

The model polysaccharide potato galactan is actually a mixture of different polysaccharides.

Commercially-supplied potato galactan (PG) is widely used as a model polysaccharide in various bioactivity studies. However, results using this galactan are not always consistent with the stated composition. Here, we assessed its composition by fractionating this commercial PG and purified its primary components: PG-A, PG-B and PG-Cp with weight-averaged molecular weights of 430, 93, and 11.3 kDa, respectively. PG-Cp consists of free ß-1,4-galactan chains, whereas PG-A and PG-B are type I rhamnogalacturonans with long ß-1,4-galactan side chains of up to 80 Gal residues and short ß-1,4-galactan side chains of 0 to 3 Gal residues that display a "trees in lawn" pattern. Structures of these polysaccharides correlate well with their activities in terms of galectin-3 binding and gut bacterial growth assays. Our study clarifies the confusion related to commercial PG, with purified fractions serving as better model polysaccharides in bioactivity investigations.

A pectic polysaccharide isolated from Achyranthes bidentata is metabolized by human gut Bacteroides spp.

Achyranthes bidentata (A. bidentata) is a famous traditional Chinese medicine (TGM) for treatment osteoporosis. Polysaccharides, a major factor for shaping the gut microbiota, are the primary ingredients of A. bidentata. However, bioactivity of A. bidentata polysaccharide on human gut microbiota (HGM) remains unknown. Here, a homogeneous pectic polysaccharide A23-1 with average molecular weight of 93.085 kDa was extracted and purified from A. bidentata. And A23-1 was compsed of rhamnose, glucuronic acid, galacturonic acid, glucose, galactose and arabinose in a molar ratio of 7.26: 0.76: 5.12: 2.54: 23.51: 60.81. GC-MS, partial acid hydrolysis and NMR results indicated the backbone of A23-1 was composed of 1, 2, 4-Rhap and 1, 4-GlapA, while the branches were composed of galactose, arabinose, glucose and glucuronic acid. Further, A23-1 was found to be degraded into monosaccharides and fragments. Taking Bacteroides thetaiotaomicron (BT) as a model, we suggested three polysaccharide utilization loci (PULs) might be involved in the A23-1 degradation. Degraded products generated by BO might not support the growth of probiotics. Besides, acetate and propionate as the main end products were generated by Bacteroides spp. and probiotics utilizing A23-1. These findings suggested A23-1 was possible one of food sources of human gut Bacteroides spp.

Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative ß-agarase.

Marine microbes, particularly Bacteroidetes, are a rich source of enzymes that can degrade diverse marine polysaccharides. Aquimarina sp. ERC-38, which belongs to the Bacteroidetes phylum, was isolated from seawater in South Korea. It showed agar-degrading activity and required an additional carbon source for growth on marine broth 2216. Here, the genome of the strain was sequenced to understand its agar degradation mechanism, and 3615 protein-coding sequences were predicted, which were assigned putative functions according to their annotated functional feature categories. In silico genome analysis revealed that the ERC-38 strain has several carrageenan-degrading enzymes but could not degrade carrageenan because it lacked genes encoding κ-carrageenanase and S1_19A type sulfatase. Moreover, the strain possesses multiple genes predicted to encode enzymes involved in agarose degradation, which are located in a polysaccharide utilization locus. Among the enzymes, Aq1840, which is closest to ZgAgaC within the glycoside hydrolase 16 family, was characterized using a recombinant enzyme expressed in Escherichia coli BL21 (DE3) cells. An enzyme assay revealed that recombinant Aq1840 mainly converts agarose to NA4. Moreover, recombinant Aq1840 could weakly hydrolyze A5 into A3 and NA2. These results showed that Aq1840 is involved in at least the initial agar degradation step prior to the metabolic pathway that uses agarose as a carbon source for growth of the strain. Thus, this enzyme can be applied to development and manufacturing industry for prebiotic and antioxidant food additive. Furthermore, our genome sequence analysis revealed that the strain is a potential resource for research on marine polysaccharide degradation mechanisms and carbon cycling.

Utility of Post-ureteroscopy Lesion Scale (PULS) in Per-operative Decision-Making for the Need of Double J Stent.

OBJECTIVES: To assess the applicability of the post ureteroscopy lesion scale (PULS) as an objective measure to define the need for double J (DJ) stent placement after ureterorenoscopy (URS). METHODS: Between June and December 2020 a cross-sectional study was conducted at a university hospital. All patients fulfilling the inclusion criteria undergoing URS for renal or ureteric stones were included. At the completion of procedures, the ureter was carefully inspected for injury. Lesions were classified using PULS scoring by the operating surgeon, another consultant, and the resident. The primary outcome was to validate the PULS score against the surgeon's decision for postoperative stenting and to assess its reliability.  Results: A total of 126 patients were included with a mean age of 43.42±15.3 years. The mean stone size was 9.42±3.60mm. DJ stents were placed in 81 cases (62.4%). All of the 38 (30.1%) patients with a significant residual fragment were stented. Ureteric injury of grade 1 was observed in 66 patients (52.3%), of which 22 (33%) had DJ stenting. PULS grade 2 injuries were observed in 22 patients (17.4%), and 95% were stented. With a PULS score of > 2 almost all (97.8%) were stented. Inter-rater reliability of PULS scoring was high among the consultants (Kendall's W=0.89, p<0.005). CONCLUSION: DJ stent placement was observed in 33%, 95%, and 98% of patients with PULS grade 1, 2, and >2 injury respectively. In patients with no residual fragment, the need for DJ stenting can be objectively defined using the PULS scoring system as it has high specificity and good interrater reliability.

Complete genome sequence and Carbohydrate Active Enzymes (CAZymes) repertoire of Gilvimarinus sp. DA14 isolated from the South China Sea.

Gilvimarinus sp. DA14, a putative new species isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an aerobic and heterotrophic agar degrading bacterium. Here, we present the complete genome sequence of strain DA14, which comprises 3.96 Mb sequences with 53.39% GC content. In total, 3391 CDSs, 6 rRNA genes and 44 tRNA genes were obtained. Genomic analysis of strain DA14 revealed that 218 CAZymes classes were identified and they were organized in 371 CAZymes in PULs involved in polysaccharides degradation, transport and regulation. Further, we performed the genome comparison among Gilvimarinus strains and analysis the diversity of CAZymes and PULs. Meanwhile, ability of agar and alginate degradation in strain DA14 were analyzed. This study represents a thorough genomic characterization of CAZymes repertoire of Gilvimarinus, provides insight into diversity of polysaccharide degrading enzymes existing in Gilvimarinus sp. DA14 and their biotechnological applications.

Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans.

BACKGROUND: Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes. RESULTS: We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/ß-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs. CONCLUSIONS: The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.

Crowdsourcing Evaluation of Ureteroscopic Videos Using the Post-Ureteroscopic Lesion Scale to Assess Ureteral Injury.

INTRODUCTION AND OBJECTIVES: We hypothesized that crowdsourcing assessments could be applied to the Postureteroscopic Lesion Scale (PULS) for ureteral injury. METHODS: At a single institution, we prospectively digitally recorded 14 ureters at the terminal portion of standard ureteroscopic procedures. Each recording was reviewed by 10 global experts to determine a mean PULS score. Following training, the Crowd-Sourced Assessment of Technical Skills, C-SATS® (C-SATS, Inc., Seattle, WA) platform was used to obtain crowd-based reviews. The mean crowd PULS scores was determined using the linear mixed-effects (LME) model. The intraclass correlation coefficient (ICC) was calculated to measure the agreement among experts. Spearman's rank correlation (rho) was used to quantify the strength of the relationship between the crowd LME mean and the experts. RESULTS: Ten expert's reviews and 2100 layman reviews were obtained in 21 days and 49 hours, respectively. The ICC for the 10 experts was 0.68 (95% confidence interval 0.49, 0.86). When the expert mean PULS was <1, the crowd scored those recordings at 1 or greater. The highest scored recording by the experts was a 3.2, which the crowd scored at 2.25. The correlation between the crowd LME means and expert means across all videos was 0.70 (p = 0.0056) indicative of moderately strong agreement. CONCLUSION: In this initial application of crowd-sourced evaluation of ureteral injury, there was a moderately strong correlation between crowd and expert ratings. Refinement of the training, through exposure to the nuances of ureteral injuries, in particular for PULS <1 or ≥3, may lead to better crowd/expert correlation. Compared to expert review, crowd data can be collected with much greater efficiency.

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment.

To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron-sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.

BACKGROUND: The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood. RESULTS: In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample. CONCLUSIONS: Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.

Controle de enchentes no lote por poço de infiltração de água pluvial sob nova concepção / Stormwater source control with infiltration wells under a new conception

RESUMO O objetivo deste trabalho foi avaliar uma nova concepção de poço de infiltração como técnica de controle de drenagem pluvial na fonte. Esse poço, denominado P-GHidro, possui furos na parede dos anéis de concreto, camada de brita externa aos anéis para melhorar a distribuição de água, pré-filtro de geotêxtil na tampa e filtros adicionais no fundo e na lateral, entre a brita e o solo. Usou-se como referência o poço de infiltração comumente empregado em São Carlos, São Paulo (P-SC), cuja construção foi realizada com anéis de concreto justapostos ao solo sem furos laterais e sem pré-filtro. Foram realizados seis ensaios de chuvas simuladas para cada poço de infiltração. Os dados experimentais de vazão de água infiltrada foram modelados pelo método de Puls. A condutividade hidráulica, constante ou variada, foi empregada como parâmetro de calibração do modelo aos dados experimentais; o ajuste foi avaliado por meio dos coeficientes de determinação (R2) e de Nash-Sutcliffe (NS). O P-GHidro apresentou melhor desempenho na infiltração de água pluvial, com volume armazenado 25% menor e tempos de esvaziamento 4% menores que os do P-SC. A modelagem apresentou boa representatividade dos dados experimentais para condutividade hidráulica constante (média de R2 de 0,92 e de NS de 0,56) e melhor ainda para condutividade hidráulica variada (média de R2 de 0,97 e de NS de 0,97).

ABSTRACT The objective of this study was to evaluate a new concept of infiltration well as in loco stormwater drainage source control. This infiltration well, namely P-GHidro, has holes in the wall of the concrete rings, layer of gravel external to the rings in order to improve the water distribution, a geotextile prefilter on the cover, and additional filters on the bottom and on the sides between the gravel and the soil. An infiltration well common in San Carlos (P-SC), São Paulo, Brazil, was used as reference, and its construction uses concrete rings juxtaposed to the soil without side holes or prefilter. Six tests of simulated rain were performed for each design infiltration well. The experimental data of infiltrated water flow were modeled by Puls method. The hydraulic conductivity, constant or variable, was used as a model adjustment parameter to the experimental data, and the adjustment was assessed using the coefficients of determination (R2) and Nash-Sutcliffe (NS). P-GHidro had a better performance in the stormwater infiltration, with stored volume and emptying times smaller than the P-SC. The modeling showed good adjustments to the experimental data for constant hydraulic conductivity (average R2 = 0.92 and NS = 0.56) and even better adjustments for variable hydraulic conductivity (average R2 = 0.97 and NS = 0.97).