A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead−based platforms (KingFisher, epMotion, and ...Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for
gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.
Abstract
To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio ...dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.
Alternatives to effectively mitigate methane emissions of beef cattle are needed. This experiment investigated the dietary inclusion of ruminal probiotics as a potential anti-methanogenic feed additive and its effect on the growth performance of beef cattle.
Lay Summary
Greenhouse gas emissions are a major concern in the beef industry. This study examined the effects of supplementation with ruminal probiotics consisting of three native ruminal microbes (NRM) for their influence on methane reduction and growth performance of beef cattle. Eighty Angus × SimAngus-crossbred cattle were grouped by sex and weight, randomly assigned to a treatment group, control or NRM supplementation, and subsequently fed commercially relevant diets for at least 134 d with or without NRM supplementation until they reached a target finishing weight. Methane emissions and growth performance metrics were recorded at regular intervals. Cattle-fed diets with NRM had a greater average daily gain during most part of the experimental period, required fewer days to reach the finishing weight, and emitted less methane than cattle in the control treatment. Supplementing NRM can be a viable method to reduce greenhouse gas emissions while improving the performance of beef cattle-fed concentrates-based diets.
Background Engaging older adults in clinical communication is an essential aspect of high-quality elder care, patient safety and satisfaction in hospitals and GP clinics. However, the factors that ...influence older adults' participation during their appointments with health professionals from the older patient's perspective remain under-investigated. Objectives We aimed to fill this knowledge gap by reviewing research articles that have examined older patients' involvement in clinical communication. In doing so, we hope to assist healthcare professionals and institutions in developing new strategies to improve older patients' participation and engagement in clinical communication. Methods A systematic review of nine databases was conducted for studies reporting identified influences on older patients' participation in clinical communication published from 2010. These studies were then subjected to thematic analysis for stratification. Results Twenty-one articles with a total of 36,797 participants were included and highlighted three major themes that influenced older patients' participation in the clinical communication. The first theme identified includes accessibility to appointments, support, health information and person-centred care, highlighting that access to appointments, person centred care and health information significantly influences clinical communication participation. Relevant and understandable healthcare information identified that communication factors i.e. tailored health information, health literacy and patient language barriers, and communication impairments influences older patients' participation. Older Patient perceptions of HCP credibility and trustworthiness highlighted how patient's perceptions of health professionals influence their willingness to participate in clinical communications. Conclusions and implications This review demonstrates that there are several factors that contribute to insufficient or no participation of older patients in clinical communication in hospitals and GP clinics. These include accessibility to relevant and understandable health information, and the perceived health professional credibility and trustworthiness. Identifying ways to address these factors may improve patient participation, doctor-patient collaboration and overall health outcomes for older patients.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Recent studies suggest that variation in diet across time and space results in changes in the mammalian gut microbiota. This variation may ultimately impact host ecology by altering nutritional ...status and health. Wild animal populations provide an excellent opportunity for understanding these interactions. However, compared to clinical studies, microbial research targeting wild animals is currently limited, and many published studies focus only on a single population of a single host species. In this study we utilize fecal samples from two species of howler monkey (Alouatta pigra and A. palliata) collected at four sites to investigate factors influencing the gut microbiota at three scales: taxonomic (host species), ecosystemic (forest type), and local (habitat disturbance/season). The results demonstrate that the effect of host species on the gut microbiota is stronger than the effect of host forest type, which is stronger than the effect of habitat disturbance or seasonality. Nevertheless, within host species, gut microbiota composition differs in response to forest type, habitat disturbance, and season. Variations in the effect size of these factors are associated both with host species and environment. This information may be beneficial for understanding ecological and evolutionary questions associated with Mesoamerican howler monkeys, as well as determining conservation challenges facing each species. These mechanisms may also provide insight into the ecology of other species of howler monkeys, non-human primates, and mammals.
Abstract
The objective of this study was to evaluate the effects of two rumen-native microbial feed supplements (MFS) on milk production, milk composition, and feed efficiency. A total of 90 ...multiparous cows between 40 and 60 d in milk were enrolled in a randomized block design study. Within each block (baseline milk yield), cows were randomly assigned to: control (no microbial feed supplementation), MFS1 (0.33 g/kg total mixed ration TMR of an MFS containing a minimum of Clostridium beijerinckii at 2 × 106 CFU/g and Pichia kudriavzevii at 2 × 107 CFU/g), or MFS2 (0.33 g/kg TMR of a MFS containing a minimum of C. beijerinckii at 2 × 106 CFU/g, P. kudriavzevii at 2 × 107 CFU/g, Ruminococcus bovis at 2 × 107 CFU/g, and Butyrivibrio fibrisolvens at 2 × 107 CFU/g). Cows were housed in a single group and fed the study diets ad libitum for 270 d. Individual milk yield was recorded using electronic milk meters, and milk fat and protein were measured using optical in-line analyzers at each of two daily milkings. Treatment and treatment by time effects were assessed through multiple linear regression analyses. Treatment effects were observed for milk and energy-corrected milk (ECM) yields, milk fat and protein yields and concentrations, dry matter intake (DMI), and feed efficiency; those effects were conditional to time for milk yield, DMI, and feed efficiency. Overall, milk, ECM, fat, and protein yields were higher for MFS2 compared with control cows (+3.0, 3.7, 0.12, and 0.12 kg/d, respectively). Compared with MFS1, milk yield was higher and protein yield tended to be higher for MFS2 cows (+2.9 and 0.09 kg/d, respectively). In contrast, MFS1 cows produced 0.17 and 0.08 units of percentage per day more fat and protein than MFS2 cows, and 0.07 units of percentage per day more protein than control cows. Dry matter intake and feed efficiency were higher for MFS2 cows compared with MFS1 cows (+1.3 kg/d and 0.06, respectively), and feed efficiency was higher for MFS2 cows compared with control cows (+0.04). Where observed, treatment by time effects suggest that the effects of MFS2 were more evident as time progressed after supplementation was initiated. No effects of microbial supplementation were observed on body weight, body condition score, somatic cell count, or clinical mastitis case incidence. In conclusion, the supplementation of MFS2 effectively improved economically important outcomes such as milk yield, solids, and feed efficiency.
Multi-drug resistant (MDR)
is a major nosocomial pathogen causing a wide range of clinical conditions with significant mortality rates.
strains are equipped with a multitude of antibiotic resistance ...mechanisms, rendering them resistant to most of the currently available antibiotics. Thus, there is a critical need to explore novel strategies for controlling antibiotic resistance in
. This study investigated the efficacy of two food-grade, plant-derived antimicrobials (PDAs), namely
-cinnamaldehyde (TC) and eugenol (EG) in decreasing
's resistance to seven β-lactam antibiotics, including ampicillin, methicillin, meropenem, penicillin, aztreonam, amoxicillin, and piperacillin. Two MDR
isolates (ATCC 17978 and AB 251847) were separately cultured in tryptic soy broth (∼6 log CFU/ml) containing the minimum inhibitory concentration (MIC) of TC or EG with or without the MIC of each antibiotic at 37°C for 18 h.
strains not exposed to the PDAs or antibiotics served as controls. Following incubation,
counts were determined by broth dilution assay. In addition, the effect of PDAs on the permeability of outer membrane and efflux pumps in
was measured. Further, the effect of TC and EG on the expression of
genes encoding resistance to β-lactam antibiotics (
), efflux pumps (
), and multi-drug resistant protein (
) was studied using real-time quantitative PCR (RT-qPCR). The experiment was replicated three times with duplicate samples of each treatment and control. The results from broth dilution assay indicated that both TC and EG in combination with antibiotics increased the sensitivity of
to all the tested antibiotics (
< 0.05). The two PDAs inhibited the function of
efflux pump, (AdeABC), but did not increase the permeability of its outer membrane. Moreover, RT-qPCR data revealed that TC and EG down-regulated the expression of majority of the genes associated with β-lactam antibiotic resistance, especially
and
(
< 0.05). The results suggest that TC and EG could potentially be used along with β-lactam antibiotics for controlling MDR
infections; however, their clinical significance needs to be determined using
studies.
Although genetic approaches are the standard in microbiome analysis, proteome-level information is largely absent. This discrepancy warrants a better understanding of the relationship between gene ...copy number and protein abundance, as this is crucial information for inferring protein-level changes from metagenomic data. As it remains unknown how metaproteomic systems evolve during dynamic disease states, we leveraged a 4.5-year fecal time series using samples from a single patient with colonic Crohn's disease. Utilizing multiplexed quantitative proteomics and shotgun metagenomic sequencing of eight time points in technical triplicate, we quantified over 29,000 protein groups and 110,000 genes and compared them to five protein biomarkers of disease activity. Broad-scale observations were consistent between data types, including overall clustering by principal-coordinate analysis and fluctuations in Gene Ontology terms related to Crohn's disease. Through linear regression, we determined genes and proteins fluctuating in conjunction with inflammatory metrics. We discovered conserved taxonomic differences relevant to Crohn's disease, including a negative association of
and a positive association of
with calprotectin. Despite concordant associations of genera, the specific genes correlated with these metrics were drastically different between metagenomic and metaproteomic data sets. This resulted in the generation of unique functional interpretations dependent on the data type, with metaproteome evidence for previously investigated mechanisms of dysbiosis. An example of one such mechanism was a connection between urease enzymes, amino acid metabolism, and the local inflammation state within the patient. This proof-of-concept approach prompts further investigation of the metaproteome and its relationship with the metagenome in biologically complex systems such as the microbiome.
A majority of current microbiome research relies heavily on DNA analysis. However, as the field moves toward understanding the microbial functions related to healthy and disease states, it is critical to evaluate how changes in DNA relate to changes in proteins, which are functional units of the genome. This study tracked the abundance of genes and proteins as they fluctuated during various inflammatory states in a 4.5-year study of a patient with colonic Crohn's disease. Our results indicate that despite a low level of correlation, taxonomic associations were consistent in the two data types. While there was overlap of the data types, several associations were uniquely discovered by analyzing the metaproteome component. This case study provides unique and important insights into the fundamental relationship between the genes and proteins of a single individual's fecal microbiome associated with clinical consequences.
•Calcifying fibrous tumours of the pleura (CFTP) are rare, with 34 cases reported.•CFTP diagnosis challenges: radiological similarity to other benign thoracic tumours.•Definitive CFTP identification ...requires excision and immunohistological analysis.•Nine-year post-surgical follow-up showed no recurrence.•CFTP's aetiology and progression remain uncertain, and further research is needed.
Calcifying fibrous tumours of the pleura (CFTPs) are extremely rare benign tumours with uncertain aetiology, with only 34 cases, including this one, reported worldwide to date. CFTPs commonly originate from subcutaneous and deep soft tissues of the gastrointestinal tract and pleura. It is essential to differentiate CFTP from other pleural intrathoracic masses that present similarly but are challenging with radiological imaging alone. As a result, excision via surgical intervention alongside immunohistological and histological assessment is the current best method for definitive diagnosis. Due to the significantly low incidence of CFTP, extensive sample studies for further research are currently not possible. As a result, all cases of CFTP should be reported to help improve future research in diagnostic accuracy and understanding of pathogenicity and aetiology. We are reporting a case of an incidentally detected CFTP on CT in a 30-year-old female.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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