Transmission and dynamics of mother-infant gut viruses during pregnancy and early life

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life. Using shotgun metagenomic sequencing applied to dsDNA extracted from Virus-Like Particles (VLPs) and bacteria, we generate 205 VLP metaviromes and 322 total metagenomes. With this data, we show that while the maternal gut virome composition remains stable during late pregnancy and after birth, the infant gut virome is dynamic in the first year of life. Notably, infant gut viromes contain a higher abundance of active temperate phages compared to maternal gut viromes, which decreases over the first year of life. Moreover, we show that the feeding mode and place of delivery influence the gut virome composition of infants. Lastly, we provide evidence of co-transmission of viral and bacterial strains from mothers to infants, demonstrating that infants acquire some of their virome from their mother's gut.

Lifelines NEXT: a prospective birth cohort adding the next generation to the three-generation Lifelines cohort study

Epidemiological research has shown there to be a strong relationship between preconceptional, prenatal, birth and early-life factors and lifelong health. The Lifelines NEXT is a birth cohort designed to study the effects of intrinsic and extrinsic determinants on health and disease in a four-generation design. It is embedded within the Lifelines cohort study, a prospective three-generation population-based cohort study recording the health and health-related aspects of 167,729 individuals living in Northern Netherlands. In Lifelines NEXT we aim to include 1500 pregnant Lifelines participants and intensively follow them, their partners and their children until at least 1 year after birth. Longer-term follow-up of physical and psychological health will then be embedded following Lifelines procedures. During the Lifelines NEXT study period biomaterials-including maternal and neonatal (cord) blood, placental tissue, feces, breast milk, nasal swabs and urine-will be collected from the mother and child at 10 time points. We will also collect data on medical, social, lifestyle and environmental factors via questionnaires at 14 different time points and continuous data via connected devices. The extensive collection of different (bio)materials from mother and child during pregnancy and afterwards will provide the means to relate environmental factors including maternal and neonatal microbiome composition) to (epi)genetics, health and developmental outcomes. The nesting of the study within Lifelines enables us to include preconceptional transgenerational data and can be used to identify other extended families within the cohort.

Capable and credible? Challenging nutrition science

Nutrition science has enriched our understanding of how to stay healthy by producing valuable knowledge about the interaction of nutrients, food, and the human body. Nutrition science also has raised societal awareness about the links between food consumption and well-being, and provided the basis for food regulations and dietary guidelines. Its collaborative and interdisciplinary research has accomplished much, scientifically and socially. Despite this, nutrition science appears to be in crisis and is currently confronted with a public reluctance to trust nutritional insights. Though deflating trust is a general phenomenon surrounding the scientific community, its impact on nutrition science is particularly strong because of the crucial role of nutrition in everyone’s daily life. We, a Dutch collective of nutritionists, medical doctors, philosophers and sociologists of science (http://www.nutritionintransition.nl), have diagnosed that nutrition science is meeting inherent boundaries. This hampers conceptual and methodological progress and the translation of novel insights into societal benefit and trust. In other words, nutrition science is facing limitations to its capability and credibility, impeding its societal value. We take up the challenge to halt the threatening erosion of nutrition science’s capability and credibility, and explore a way forward. We analyse limitations to capability and credibility, then argue that nutrition science is caught in a vicious circle, and end by offering some suggestions to transcend the limitations and escape the current deadlock. We invite nutritional experts as well as scholars from adjacent disciplines to engage in the discussion.

The production of intrinsically labeled milk and meat protein is feasible and provides functional tools for human nutrition research

Administration of labeled, free amino acids does not allow direct assessment of in vivo dietary protein digestion and absorption kinetics. Consequently, dietary protein sources with labeled amino acids incorporated within their protein matrix are required. The aim of the present study was to produce intrinsically L-[1-(13)C]phenylalanine-labeled milk and meat protein that would permit in vivo assessment of postprandial protein digestion and absorption kinetics in humans. One lactating dairy cow was continuously infused with 420 μmol of L-[1-(13)C]phenylalanine/min for 96 h, with plasma and milk being collected before, during, and after isotope infusion. Twenty-four hours after infusion, the cow was slaughtered to produce intrinsically labeled meat. Levels of L-[1-(13)C]phenylalanine enrichment as high as 40 mole percent excess (MPE) in milk and 1.5 MPE in meat protein were achieved. In a subsequent human proof-of-principle experiment, 2 healthy young males (25±1 yr; 66.2±5.2 kg) each ingested 135 g of L-[1-(13)C]phenylalanine intrinsically labeled minced beef, after which plasma samples were collected at regular time intervals. Plasma L-[1-(13)C]phenylalanine enrichments increased during the first 90 min following beef ingestion, reaching peak plasma enrichment levels of 0.61±0.04 MPE. Whole-body net protein balance, assessed by continuous infusion of L-[ring-(2)H(5)]phenylalanine and L-[ring-(2)H(2)]tyrosine, was higher in the postprandial period compared with basal values (6.4±0.1 vs. -4.5±0.1 μmol/kg per h). In conclusion, the production of intrinsically L-[1-(13)C]phenylalanine-labeled milk and meat protein is feasible and provides functional tools to investigate in vivo protein digestion and absorption kinetics in humans.

Toxicity of homologous series of organic solvents for the gram-positive bacteria Arthrobacter and Nocardia Sp. and the gram-negative bacteria Acinetobacter and Pseudomonas Sp

The toxicity of homologous series of organic solvents has been investigated for the gram-positive bacteria, Arthrobacter sp. and Nocardia sp., and the gram-negative bacteria, Acinetobacter sp. and Pseudomonas sp. The hydrophobicity of the solvent, expressed by its logP(octanol), proves to be a good measure for the toxicity of solvents in a two-phase system. The transition from toxic to nontoxic solvents occurs between logP(octanol) 3 and 5 and depends on the homologous series. No correlation has been found between the hydrophobicity of the substituent on the alkyl backbone of the solvent and the location of the transition point in toxicity. The logP(octanol), above which all solvents are nontoxic, is used to express the solvent tolerance of the bacteria. In general, the solvent tolerance of gram-negative bacteria is found to be slightly higher than that of gram-positive bacteria, but this does not hold for all homologous series of organic solvents investigated.Because the toxicity effects of organic solvents in a two-phase system can be ascribed to molecular as well as phase toxicity effects, molecular toxicity effects were investigated separately in a one-phase system with subsaturating amounts of organic solvent. The solvent concentration in the aqueous phase, at which 50% of the metabolic activity of the bacteria is lost, is used to express solvent toxicity. This concentration is found to be similar for the gram-positive Arthrobacter and the gram-negative Acinetobacter. Assuming the critical membrane concentration theory (G. J. Osborne et al. Enzyme Microb. Technol. 1990, 12: 281-291) to be valid, it can be concluded that differences in solvent tolerance between these two bacteria, cannot be ascribed to differences in response to molecular toxicity. Prediction of the toxicity of any solvent, using the critical membrane theory, appears to be possible in the case of alkanols or alkyl acetates. However, prediction of the toxicity of ethers appears to be impossible.

Influence of ions on growth and production of exopolysaccharides by Lactobacillus delbrueckii subsp. bulgaricus NCFB 2772

Several lactic acid bacteria produce exopolysaccharides (EPS), either attached to the cell wall or excreted into the environment as slime material. EPS produced by Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) and Streptococcus thermophilus play an important role in improving the texture and stability of yogurt and preventing syneresis (Cerning, 1990; Nakajima et al. 1990). The amount and composition of the EPS produced by lactic acid bacteria are dependent on a number of factors, such as temperature, initial pH, carbon source and the availability of minerals, vitamins and other medium components.

In previous work it was shown that the production and sugar composition of the EPS from Lb. bulgaricus NCFB2772 are affected by the carbohydrate source (Grobben et al. 1995, 1996). In a simplified defined medium, from which several vitamins and trace elements were omitted, EPS production by Lb. bulgaricus significantly increased, although growth of the strain was reduced (Grobben et al. 1998).

Identification of biosynthetic intermediates of the extracellular polysaccharide viilian in Lactococcus lactis subspecies cremoris SBT 0495

Lactococcus lactis subspecies cremoris SBT 0495 produces the phosphopolysaccharide viilian, which consists of the repeating unit beta-D-glucosyl-(1-->4)-(alpha-L-rhamnosyl-(1-->2))-(alpha-D-galac tose-1- phosphoryl-(-->3)-beta-galactosyl-(1-->4)-beta-D-glucose. A lipid extract was prepared from cells in the late exponential phase of growth and was hydrolyzed by hydrochloric acid under mild conditions to split lipid-linked intermediates in the extract into lipid and sugar moieties. Both moieties were purified by chromatographic techniques and were characterized to identify intermediates of the viilian biosynthetic pathway. A polyisoprenoid isolated from the chloroform-soluble fraction of the hydrolyzed lipid extract was identified by mass spectrometry as undecaprenol. Saccharides isolated from the water-soluble fraction of the hydrolyzed lipid extract by anion-exchange chromatography, were characterized by glycosidic linkage analysis to discriminate sugar moieties of intermediates of viilian biosynthesis from compounds liberated from cell wall components. Some oligosaccharide analogues contain a glycerol residue, suggesting that these are fragments of glycosylglycerides and/or lipoteichoic acid. Three fragments were identified to be glucose, galactosyl-(1-->4)-glucose, and rhamnosyl-(1-->2)-galactosyl-(1-->4)-glucose, which are in agreement with the structure of the repeating unit of viilian. These saccharides most likely represent the first three steps of the sequential assembly of the repeating unit of the undecaprenol assembly.

Enhancement of Exopolysaccharide Production by Lactobacillus delbrueckii subsp. bulgaricus NCFB 2772 with a Simplified Defined Medium

The aim of this work was to investigate the medium requirements for growth and production of exopolysaccharides by Lactobacillus delbrueckii subsp. bulgaricus NCFB 2772. The strain was grown in batch cultures on a chemically defined medium, and the technique of single omission of medium components was applied to determine the nutritional requirements. The omission of aspartic acid, glutamic acid, or glycine affected growth only slightly, and the omission of glutamine, asparagine, or threonine resulted in a stronger reduction of the growth. All the other amino acids were essential. Multiple omissions of amino acids caused an almost complete loss of growth. L. delbrueckii subsp. bulgaricus required only riboflavin, calcium pantothenate, and nicotinic acid as individual vitamins. Surprisingly, when only these vitamins were present in the medium and other vitamins were not, less growth was observed than in the complete medium but the amount of exopolysaccharide produced was significantly greater. These observations were studied in more detail with a simplified defined medium in which L. delbrueckii subsp. bulgaricus was able to grow and produce exopolysaccharides. Although the final optical density in the simplified medium was lower, the production of exopolysaccharides was about twofold higher than in the complete medium.

Mechanisms of membrane toxicity of hydrocarbons

Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.

Mechanisms of membrane toxicity of hydrocarbons

Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.

Interactions of cyclic hydrocarbons with biological membranes

Many cyclic hydrocarbons, e.g. aromatics, cycloalkanes, and terpenes, are toxic to microorganisms. The primary site of the toxic action is probably the cytoplasmic membrane, but the mechanism of the toxicity is still poorly understood. The effects of cyclic hydrocarbons were studied in liposomes prepared from Escherichia coli phospholipids. The membrane-buffer partition coefficients of the cyclic hydrocarbons revealed that these lipophilic compounds preferentially reside in the membrane. The partition coefficients closely correlated with the partition coefficients of these compounds in a standard octanol-water system. The accumulation of hydrocarbon molecules resulted in swelling of the membrane bilayer, as assessed by the release of fluorescence self-quenching of fluorescent fatty acid and phospholipid analogs. Parallel to the expansion of the membrane, an increase in membrane fluidity was observed. These effects on the integrity of the membrane caused an increased passive flux of protons and carboxyfluorescein. In cytochrome c oxidase containing proteoliposomes, both components of the proton motive force, the pH gradient and the electrical potential, were dissipated with increasing concentrations of cyclic hydrocarbons. The dissipating effect was primarily the result of an increased permeability of the membrane for protons (ions). At higher concentrations, cytochrome c oxidase was also inactivated. The effective concentrations of the different cyclic hydrocarbons correlated with their partition coefficients between the membrane and aqueous phase. The impairment of microbial activity by the cyclic hydrocarbons most likely results from hydrophobic interaction with the membrane, which affects the functioning of the membrane and membrane-embedded proteins.

Metabolism of tetralin (1,2,3,4-tetrahydronaphthalene) in Corynebacterium sp. strain C125

Corynebacterium sp. strain C125, originally isolated on o-xylene, was selected for its ability to grow on tetralin (1,2,3,4-tetrahydronaphthalene) as the sole source of carbon and energy. The catabolism of tetralin in Corynebacterium sp. strain C125 was shown to proceed via initial hydroxylation of the benzene nucleus at positions C-5 and C-6, resulting in the formation of the corresponding cis-dihydro diol. Subsequently, the dihydro diol was dehydrogenated by a NAD-dependent dehydrogenase to 5,6,7,8-tetrahydro-1,2-naphthalene diol. The aromatic ring was cleaved in the extradiol position by a catechol-2,3-dioxygenase. The ring fission product was subject to a hydrolytic attack, resulting in the formation of a carboxylic acid-substituted cyclohexanone. This is the first report of the catabolism of tetralin via degradation of the aromatic moiety.

Effects of the membrane action of tetralin on the functional and structural properties of artificial and bacterial membranes

Tetralin is toxic to bacterial cells at concentrations below 100 mumol/liter. To assess the inhibitory action of tetralin on bacterial membranes, a membrane model system, consisting of proteoliposomes in which beef heart cytochrome c oxidase was reconstituted as the proton motive force-generating mechanism, and several gram-positive and gram-negative bacteria were studied. Because of its hydrophobicity, tetralin partitioned into lipid membranes preferentially (lipid/buffer partition coefficient of tetralin is approximately 1,100). The excessive accumulation of tetralin caused expansion of the membrane and impairment of different membrane functions. Studies with proteoliposomes and intact cells indicated that tetralin makes the membrane permeable for ions (protons) and inhibits the respiratory enzymes, which leads to a partial dissipation of the pH gradient and electrical potential. The effect of tetralin on the components of the proton motive force as well as disruption of protein-lipid interaction(s) could lead to impairment of various metabolic functions and to low growth rates. The data offer an explanation for the difficulty in isolating and cultivating microorganisms in media containing tetralin or other lipophilic compounds.