Suboptimal selenium status in home parenteral nutrition patients with small bowel resections

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity^1–6 in industrial populations is associated with chronic diseases⁷, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.

Improved metagenome binning and assembly using deep variational autoencoders

Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .

A genomic catalog of Earth's microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Termite mounds contain soil-derived methanotroph communities kinetically adapted to elevated methane concentrations

Termite mounds have recently been confirmed to mitigate approximately half of termite methane (CH4) emissions, but the aerobic CH4 oxidising bacteria (methanotrophs) responsible for this consumption have not been resolved. Here, we describe the abundance, composition and CH4 oxidation kinetics of the methanotroph communities in the mounds of three distinct termite species sampled from Northern Australia. Results from three independent methods employed show that methanotrophs are rare members of microbial communities in termite mounds, with a comparable abundance but distinct composition to those of adjoining soil samples. Across all mounds, the most abundant and prevalent methane monooxygenase sequences were affiliated with upland soil cluster α (USCα), with sequences homologous to Methylocystis and tropical upland soil cluster (TUSC) also detected. The reconstruction of a metagenome-assembled genome of a mound USCα representative highlighted the metabolic capabilities of this group of methanotrophs. The apparent Michaelis-Menten kinetics of CH4 oxidation in mounds were estimated from in situ reaction rates. Methane affinities of the communities were in the low micromolar range, which is one to two orders of magnitude higher than those of upland soils, but significantly lower than those measured in soils with a large CH4 source such as landfill cover soils. The rate constant of CH4 oxidation, as well as the porosity of the mound material, were significantly positively correlated with the abundance of methanotroph communities of termite mounds. We conclude that termite-derived CH4 emissions have selected for distinct methanotroph communities that are kinetically adapted to elevated CH4 concentrations. However, factors other than substrate concentration appear to limit methanotroph abundance and hence these bacteria only partially mitigate termite-derived CH4 emissions. Our results also highlight the predominant role of USCα in an environment with elevated CH4 concentrations and suggest a higher functional diversity within this group than previously recognised.

Consequences of mutations and inborn errors of selenoprotein biosynthesis and functions

In its 200 years of history, selenium has been defined first as a toxic element and finally as a micronutrient. Selenium is incorporated into selenoproteins as selenocysteine (Sec), the 21st proteinogenic amino acid codified by a stop codon. Specific biosynthetic factors recode UGA stop codon as Sec. The significance of selenoproteins in human health is manifested through the identification of patients with inborn errors in selenoproteins or their biosynthetic factors. Selenoprotein N-related myopathy was the first disease identified due to mutations in a selenoprotein gene. Mutations in GPX4 were linked to Sedaghatian disease, characterized by bone and brain anomalies and cardiorespiratory failure. Mutations in TXNRD2 produced familial glucocorticoid deficiency (FGD) and dilated cardiomyopathy (DCM). Genetic generalized epilepsy was associated with mutations in TXNRD1 gene. Mutations in biosynthetic factors as SEPSECS, SECISBP2 and even tRNA^[Ser]Sec, have been also related to diseases. Thus, SEPSECS mutations produce a neurodegenerative disease called now pontocerebellar hypoplasia type 2D (PCH2D). SECISBP2 syndrome, caused by SECISBP2 mutations, is a multifactorial disease affecting mainly thyroid metabolism, bone, inner ear and muscle. Similar symptoms were reproduced in a patient carrying a mutation in tRNA^[Ser]Sec gene, TRU-TCA1-1. This review describes human genetic disorders caused by selenoprotein deficiency. Human phenotypes will be compared with mouse models to explain the pathologic mechanisms of lack of selenoproteins.

Understanding the importance of selenium and selenoproteins in muscle function

Selenium is an essential trace element. In cattle, selenium deficiency causes dysfunction of various organs, including skeletal and cardiac muscles. In humans as well, lack of selenium is associated with many disorders, but despite accumulation of clinical reports, muscle diseases are not generally considered on the list. The goal of this review is to establish the connection between clinical observations and the most recent advances obtained in selenium biology. Recent results about a possible role of selenium-containing proteins in muscle formation and repair have been collected. Selenoprotein N is the first selenoprotein linked to genetic disorders consisting of different forms of congenital muscular dystrophies. Understanding the muscle disorders associated with selenium deficiency or selenoprotein N dysfunction is an essential step in defining the causes of the disease and obtaining a better comprehension of the mechanisms involved in muscle formation and maintenance.

Antioxidant and immune status in active Crohn's disease. A possible relationship

BACKGROUND AND AIMS

As reactive oxygen has been demonstrated to participate in immune genes transcription, the aim of this study was to examine the relationship between systemic concentrations of several antioxidants and markers of inflammatory and immune activation in patients with Crohn's disease (CD).

METHODS

In 26 CD patients and 15 controls we compared plasma selenium and zinc concentrations, erythrocyte glutathione peroxidase (GSHPx) and superoxide dismutase activities, as well as erythrocyte sedimentation rate (ESR), C-reactive protein, tumor necrosis factor-alpha, interleukin-6, blood neopterin and soluble receptors of interleukin-2 (sIL-2R), and examined the link between these parameters.

RESULTS

Selenium concentration and GSHPx activity were decreased in CD patients (54.5 +/- 3.2 vs 79 &plusmn 2.2 microg/l, P<< 0.05; 28 +/- 1.6 vs 38 +/- 2.6 IU/g Hb, P<< 0.05) and positively correlated to each other's (r= 0.59, P<< 0.01). TNF-alpha was significantly increased in patients (18 +/- 2.6 vs 5 +/- 0.6 pg/ml;P<< 0.001), negatively correlated to GSHPx activity (r= -0.56, P<< 0.05) and selenium concentration (r= -0.72, P<< 0.001), and positively to neopterin and sIL-2R concentrations. Selenium showed negative correlation with sIL-2R (r= -0.83, P<< 0.0001) and ESR.

CONCLUSIONS

In CD patients low selenium concentration may participate in reduced GSHPx activity facilitating inflammatory and immune activation. In these patients, selenium monitoring and, if needed, supplementation may be of therapeutical interest.

Selenium depletion in patients with gastrointestinal diseases: are there any predictive factors?

BACKGROUND

Patients with intestinal disease are at risk of developing selenium deficiency due to impaired intestinal absorption. The aim of the present study was to evaluate selenium status and to identify predictive factors of selenium depletion in patients with gastrointestinal disease.

METHODS

The concentration of selenium and the activity of glutathione peroxidase in plasma and erythrocytes were measured by fluorometry and by spectrophotometry. Eighty-six patients with Crohn's disease, 40 patients with ulcerative colitis, and 39 patients with various other gastrointestinal diseases were studied. Twenty-seven patients (16%) received home parenteral nutrition. Stool mass, faecal fat, and vitamin B12 absorption were analysed in 100 patients.

RESULTS

The plasma selenium concentration was decreased in 85% of the patients receiving supplementary parenteral nutrition and in 20% of the patients receiving oral nutrition, among them in 26% of the patients with Crohn's disease. Almost all patients with ulcerative colitis had normal selenium levels. A statistically significant correlation was found between plasma selenium and vitamin B12 absorption, stool mass, faecal fat excretion, body mass index, P-albumin, P-zinc, and the length of the remaining small bowel. Stepwise regression analyses showed that the strongest predictors of selenium deficiency were stool mass, vitamin B12 absorption, and the length of the small-bowel resection.

CONCLUSION

Selenium deficiency is common in patients with severe gastrointestinal disorders. The deficiency is mainly related to malabsorption, and a low selenium level was almost invariably present in patients who needed parenteral supplementation due to gut failure.

Trace elements in clinical nutrition

Although the nearly 20 essential trace elements in humans constitute a small fraction of total body weight (less than 4%), the effect of their presence on well-being is enormous. Enteral nutrition, whether oral or by tube, is fraught with problems that influence nutrient absorption, distribution, metabolism, and ultimately, excretion. Parenteral nutrition, although delivered to the intravascular milieu, carries with it no guarantee that the trace mineral will indeed reach the target site for action. With the questionable nature of dietary histories and their unavailability in the setting of relatively emergent nutrition therapy, it behooves the clinician to begin complete nutrition and to include recommended trace elements early on. The clinician must also be ever vigilant about delivering sufficient full-strength commercially available enteral formula to provide the recommended dietary allowances of trace minerals.

Principles of nutrition therapy for short-bowel syndrome

Short-bowel syndrome is characterized by maldigestion, malabsorption, dehydration, electrolyte abnormalities, and both macronutrient and micronutrient deficiencies. Nutritional and hydration status are difficult to maintain without the provision of specialized nutrition support when more than 75% of the small intestine has been resected. Each patient's response to small-bowel resection is unique; therefore, the type of therapy must be tailored to each individual's bowel resection, complications that ensue, and specific nutrient needs. Clinical management should be guided by principles of nutrition assessment and treatment of nutrient deficiencies as well as routine monitoring of the patient's clinical course and response to therapy.

Short-bowel syndrome: a review of the role of nutrition support

Advances in long-term venous access devices and in parenteral nutrition solutions have made it possible for patients with severe short bowel syndrome to survive and to live in our society. The spectrum of this disease is such that some patients may be able to lessen their dependence or even become free from parenteral therapy. This review will discuss the role of nutrition support in the patient with short bowel syndrome.

Determination of selenium in blood components by X-ray emission spectrometry. Procedures, concentration levels, and health implications

Sampling, storing, sample pretreatment, and experimental conditions for selenium (Se) determination in human serum, plasma, and whole blood by X-ray emission spectrometric (XRS) methods are described. Concentration levels in these biological fluids, found by this technique, are discussed and compared to values found by other techniques for the same healthy population group in the same area. XRS analysis of blood from patients with various pathological conditions is reviewed, with special attention to the relation of Se with the concentration level of other essential or nonessential trace elements.

Selenium: clinical significance and analytical concepts

Selenium is an essential trace element in humans and animals. Its only established function in humans is the antioxidant activity of glutathione peroxidase, a selenoenzyme. Severe prolonged deficiency may cause a fatal cardiomyopathy. Iatrogenic causes of selenium deficiency include parenteral and enteral nutrition. Low plasma selenium is also found in malabsorption, cystic fibrosis, rheumatoid arthritis, neoplasia, and other varied clinical disorders. Death has resulted from a single massive ingestion of selenium, while chronic excessive intake causes skin, nail, and hair pathology. Extreme geographical variation in population blood and urine selenium levels and a marked age-specific variation in population reference intervals are important factors in understanding selenium nutrition. Nutritional requirements, biological availability, and metabolism are discussed in relation to geographical, age, and method variability. Sampling, processing procedures, and methods for selenium quantitation are reviewed. Selenium content in different biological matrices and reference values for pediatric, adult, and obstetric populations are provided.

Plasma vitamin and mineral status in home parenteral nutrition patients

Home parenteral nutrition (HPN) provides long-term nutritional support for persons whose absorptive capacity is compromised by a variety of intestinal malabsorption problems. However, the presence of vitamin and mineral deficiency syndromes that normally would not have time to develop in the hospitalized patient receiving total parenteral nutrition has been reported in patients receiving HPN. This study entails a longitudinal survey of plasma concentrations of vitamins A, E, and 1,25-dihydroxyvitamin D, as well as the minerals zinc, copper, and selenium, in patients receiving HPN. Plasma samples from eight patients who had been on HPN for 1-92 months before the study began were obtained once a month over a 12-month period. The blood was drawn immediately before their evening infusion of TPN in order to approximate fasting plasma nutrient concentrations. Patient values were compared to fasting control values and to published norms. Values for vitamin A, 1,25-dihydroxyvitamin D, and zinc all were within the normal range, and there was no evidence of metabolic bone disease. Plasma vitamin E and copper concentrations exceeded the normal range for most of the 12-month period. Of all of the nutrients studied, only plasma selenium concentrations were consistently in the low-normal to below-normal range. Selenium levels in patients on HPN should be monitored regularly, and supplementation may be necessary if clinical conditions warrant.

A key to the literature of total parenteral nutrition: update 1987

This comprehensive bibliography is intended to enhance the education of the practitioner, student, and academician in the area of parenteral nutrition. This bibliography is not all-inclusive but serves as an update from the original published in 1983. Of particular note in this work is the addition of topics that reflect a growing interest in medical specialties with regard to patient nutritional status and support.

Prediction of whole blood selenium levels in patients on long-term parenteral nutrition

In an attempt to define clinical variables which might predict the whole blood selenium level prior to supplementation, whole blood selenium levels were determined in 21 home parenteral nutrition patients who were not receiving selenium supplementation. These levels were examined for possible correlations by single and multivariant analysis with the following clinical parameters: age at initiation of home parenteral nutrition, months of home parenteral nutrition received, hematocrit, albumin, estimated length of remaining small bowel, kilocalories per kilogram actual body weight infused per day, grams protein per kilogram actual body weight infused per day, and multiple of ideal body weight. Of all the combinations of variables examined, the best correlation obtained was between whole blood selenium levels and the total kilocalories per kilogram body weight per day delivered intravenously (r = -0.89, p less than 0.001). A statistically significant correlation (r = -0.67, p less than 0.01) was also observed between selenium levels and the grams protein per kilogram actual body weight infused per day. However, inclusion of this or additional variables did not increase the predictive value of the equation describing whole blood selenium levels as a function of the calories delivered. The implication of this study is that patients requiring more intensive nutritional support develop lower selenium levels during the course of treatment. Despite these correlations, no single clinical parameter or combination of parameters, however, was of sufficient predictive value to preclude laboratory determination of whole blood selenium values in deciding which patients might benefit from selenium supplementation.