Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent

Optimizing bioreactor performance for organic matter removal can achieve sustainable and energy-efficient micropollutant removal in subsequent tertiary treatment. Bioreactor performance heavily depends on its resident microbial community; hence, a deeper understanding of community dynamics is essential. The microbial communities of three different bioreactors (biological activated carbon, moving bed biofilm reactor, sand filter), used for organic matter removal from wastewater treatment effluent, were characterized by 16S rRNA gene amplicon sequence analysis. An interdependency between bioreactor performance and microbial community profile was observed. Overall, Proteobacteria was the most predominant phylum, and Comamonadaceae was the most predominant family in all bioreactors. The relative abundance of the genus Roseococcus was positively correlated with organic matter removal. A generalized Lotka-Volterra (gLV) model was established to understand the interactions in the microbial community. By identifying microbial dynamics and their role in bioreactors, a strategy can be developed to improve bioreactor performance.

Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study

The infant gut microbiota affects childhood health. This pioneer microbiota may be vulnerable to antibiotic exposures, but could be supported by prebiotic oligosaccharides found in breast milk and some infant formulas. We sought to characterize the effects of several exposures on the neonatal gut microbiota, including human milk oligosaccharides (HMOs), galacto-oligosaccharides (GOS), and infant/maternal antimicrobial exposures. We profiled the stool microbiota of 1023 one-month-old infants from the KOALA Birth Cohort using 16S rRNA gene amplicon sequencing. We quantified 15 HMOs in breast milk from the mothers of 220 infants, using high-performance liquid chromatography-mass spectrometry. Both breastfeeding and antibiotic exposure decreased gut microbial diversity, but each was associated with contrasting shifts in microbiota composition. Other factors associated with microbiota composition included C-section, homebirth, siblings, and exposure to animals. Neither infant exposure to oral antifungals nor maternal exposure to antibiotics during pregnancy were associated with infant microbiota composition. Four distinct groups of breast milk HMO compositions were evident, corresponding to maternal Secretor status and Lewis group combinations defined by the presence/absence of certain fucosylated HMOs. However, we found the strongest evidence for microbiota associations between two non-fucosylated HMOs: 6'-sialyllactose (6'-SL) and lacto-N-hexaose (LNH), which were associated with lower and higher relative abundances of Bifidobacterium, respectively. Among 111 exclusively formula-fed infants, the GOS-supplemented formula was associated with a lower relative abundance of Clostridium perfringens. In conclusion, the gut microbiota is sensitive to some prebiotic and antibiotic exposures during early infancy and understanding their effects could inform future strategies for safeguarding a health-promoting infant gut microbiota.

Water and biofilm in drinking water distribution systems in the Netherlands

To keep the high quality of drinking water in the future for non-chlorinated drinking water systems, knowledge about the variables that most strongly affect this quality is necessary in order to know where to focus on and possibly even change aspects of drinking water production and distribution. Therefore, the aim of this study was to investigate which variables (source of drinking water, growth potential and pipe material type) have the biggest influence on bacterial community composition and biomass concentration of drinking water and biofilm in distribution systems. Ten different distribution systems were sampled for water and biofilm, obtained from four different pipe materials, throughout the Netherlands. The distribution systems are supplied either with drinking water produced from groundwater or surface water, and differ in drinking water quality parameters such as the growth potential. We found a significant relationship for growth potential and ATP concentration in water, but for the ATP in the biofilm none of the parameters showed a significant effect. Furthermore, the source of the drinking water and the pipe material did not significantly affect the ATP concentration in water and biofilm. The bacterial composition of in both water and biofilm was significantly different between distribution systems delivering water with low and high growth potential and between drinking water produced from groundwater or surface water. In contrast, the different pipe materials did not significantly affect composition of biofilm-associated communities. We conclude from these results that the growth potential of the treated water best explains the variation in biomass and bacterial composition in water and biofilm of non-chlorinated drinking water distribution systems followed by the drinking water source, whereas pipe materials seem to be of lesser importance.

Influence of pipe materials on the microbial community in unchlorinated drinking water and biofilm

Biodegradable compounds can cause undesired microbial growth in drinking water systems and these compounds can originate from the water or pipe materials used in drinking water systems. The aim of our study was to determine the influence of different pipe materials on the microbial populations in water and biofilm under semi-stagnant conditions. The microbial communities in biofilm and water, which were in contact with seven different materials, were characterized by determining ATP concentrations, microbial composition gene copy numbers of some specific microbial groups. The ATP concentration in water and biofilm varied between the different materials with glass (negative control) < copper < PVCC < PE-Xc < PE-Xb < PE-100 < PVC-P. Gene copy numbers of Legionella spp., Mycobacterium spp., Pseudomonas spp., Aeromonas spp., fungi and Vermamoeba vermiformis were also higher for PVC-P and PE than for glass, copper and PVCC. The bacterial community composition in water and biofilm varied between materials as well. PERMANOVA and CAP analysis demonstrated that copper and PVC-P are different when compared to the other materials. Furthermore, bacterial community composition and ATP concentrations in water and biofilm were similar after eight and 16 weeks incubation, but differed from results obtained after one week. Finally, the ATP, the specific microbial groups and the bacterial community composition also differed between water and biofilm on each material. We conclude from our study that pipe material is an important factor that influences the biomass concentration, abundance of specific microorganisms and the bacterial community composition in distribution systems with unchlorinated drinking water.

Protective effects of Lactobacillus plantarum strain P1 against toxicity of the environmental oestrogen di-n-butyl phthalate in rats

Phthalates are contaminants widely distributed in the food-chain, and they are considered as important environmental oestrogens in our lives. In the present study, eight strains of lactic acid bacteria were isolated for their ability to adsorb di-n-butyl-phthalate (DBP), and one of the strains, Lactobacillus plantarum strain P1, was selected for more detailed analyses of its phthalate adsorption capacity in vitro. This study also evaluated the in vivo protective effects of strain P1 against DBP toxicity in rats. Sixteen rats were divided into four groups, and animals received by oral gavage every other day for a period of one month saline with or without strain P1 at 2×10¹¹ cfu/kg followed by maize oil with or without DBP (50 mg/kg). Strain P1 could adsorb more DBP than saline alone, and the concentration of mono-n-butyl phthalate in urine was decreased in animals receiving P1. Furthermore, oestrogenic effects of the different treatments were assessed through counting of sperm and observation of testis, and strain P1 could protect the sexual organs of male rats. Our results suggested that P1 is effective against phthalate toxicity due to its ability to adsorb DBP in vivo and could be considered as a new dietary therapeutic strategy against environmental phtalate toxicity.

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs

Gastrointestinal helminth-microbiota associations are shaped by various ecological processes. The effect of the ecological context of the host on the bacterial microbiome and gastrointestinal helminth parasites has been tested in a number of ecosystems and experimentally. This study takes the important step to look at these two groups at the same time and to start to examine how these communities interact in a changing host environment. Fresh faecal samples (N = 335) from eight wild Eulemur populations were collected over 2 years across Madagascar. We used 16S ribosomal RNA gene sequencing to characterise the bacterial microbiota composition, and faecal flotation to isolate and morphologically identify nematode eggs. Infections with nematodes of the genera Callistoura and Lemuricola occurred in all lemur populations. Seasonality significantly contributed to the observed variation in microbiota composition, especially in the dry deciduous forest. Microbial richness and Lemuricola spp. infection prevalence were highest in a previously intensely logged site, whereas Callistoura spp. showed no such pattern. In addition, we observed significant correlations between gastrointestinal parasites and bacterial microbiota composition in these lemurs, with 0.4-0.7% of the variation in faecal bacterial microbiota composition being explained by helminth infections. With this study, we show effects of environmental conditions on gastrointestinal nematodes and bacterial interactions in wild lemurs and believe it is essential to consider the potential role of microbiome-parasite associations on the hosts' GI stability, health, and survival.

Domesticated equine species and their derived hybrids differ in their fecal microbiota

BACKGROUND

Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin the increased degradation of fiber in donkeys. Therefore, a study was conducted to assess if differences existed between the fecal microbiota of pony, donkey and hybrids derived from them (i.e. pony × donkey) when fed the same forage diet.

RESULTS

Fecal community composition of prokaryotes and anaerobic fungi significantly differed between equine types. The relative abundance of two bacterial genera was significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and 'probable genus 10' from the Lachnospiraceae family. The relative abundance of Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either of the other equine types. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals). The number of anaerobic fungal OTUs was also significantly higher in donkey than in the other two equine types, with no significant differences found between pony and pony × donkey. Equine types did not significantly differ with respect to prokaryotic alpha diversity, fecal dry matter content or fecal concentrations of bacteria, archaea and anaerobic fungi.

CONCLUSIONS

Donkey fecal microbiota differed from that of both pony and pony × donkey. These differences related to a higher relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggest that the hindgut microbiota plays a role. This offers novel opportunities for pony and pony × donkey to extract more energy from dietary fiber via microbial mediated strategies. This could potentially decrease the need for energy dense feeds which are a risk factor for gut-mediated disease.

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species

BACKGROUND

Equine gut microbiology studies to date have primarily focused on horses and ponies, which represent only one of the eight extant equine species. This is despite asses and mules comprising almost half of the world's domesticated equines, and donkeys being superior to horses/ponies in their ability to degrade dietary fiber. Limited attention has also been given to commensal anaerobic fungi and archaea even though anaerobic fungi are potent fiber degrading organisms, the activity of which is enhanced by methanogenic archaea. Therefore, the objective of this study was to broaden the current knowledge of bacterial, anaerobic fungal and archaeal diversity of the equine fecal microbiota to multiple species of equines. Core taxa shared by all the equine fecal samples (n = 70) were determined and an overview given of the microbiota across different equine types (horse, donkey, horse × donkey and zebra).

RESULTS

Equine type was associated with differences in both fecal microbial concentrations and community composition. Donkey was generally most distinct from the other equine types, with horse and zebra not differing. Despite this, a common bacterial core of eight OTUs (out of 2070) and 16 genus level groupings (out of 231) was found in all the fecal samples. This bacterial core represented a much larger proportion of the equine fecal microbiota than previously reported, primarily due to the detection of predominant core taxa belonging to the phyla Kiritimatiellaeota (formerly Verrucomicrobia subdivision 5) and Spirochaetes. The majority of the core bacterial taxa lack cultured representation. Archaea and anaerobic fungi were present in all animals, however, no core taxon was detected for either despite several taxa being prevalent and predominant.

CONCLUSIONS

Whilst differences were observed between equine types, a core fecal microbiota existed across all the equines. This core was composed primarily of a few predominant bacterial taxa, the majority of which are novel and lack cultured representation. The lack of microbial cultures representing the predominant taxa needs to be addressed, as their availability is essential to gain fundamental knowledge of the microbial functions that underpin the equine hindgut ecosystem.

Modification of the equine gastrointestinal microbiota by Jerusalem artichoke meal supplementation

The objective of this study was to investigate the impact of natural prebiotic active compounds on the microbial composition in different regions of the equine gastrointestinal tract. Twelve adult horses (body weight [bwt] 534 ± 64.5 kg; age 14 ± 7.5 years) were randomly divided into two feeding groups. Six horses received a basal diet consisting of 1.5 kg hay/100 kg bwt x d^-1 and oat grains equal to 1.19 g starch/kg bwt x d^-1, supplemented with Jerusalem artichoke meal providing prebiotic fructooligosaccharides + inulin in a quantity of 0.15 g/kg bwt x d^-1. The remaining horses received a placebo added to the basal diet. The horses were fed for 21 d and euthanized at the end of the feeding period. Digesta samples from different parts of the gastrointestinal tract were taken, DNA extracted and the V1-V2 region of the 16S rRNA gene amplified. Supplementation with the prebiotic increased the relative abundance of Lactobacillus (P < 0.05), with a concurrent reduction of the relative abundance of Streptococcus mainly in the stomach (P < 0.05). In the hindgut, the supplemental prebiotic also increased the relative abundance of Lactobacillus but further reduced the relative abundance of fibrolytic bacteria, specifically the unclassified members of the families Lachnospiraceae (P < 0.05) and Ruminococcaceae. The relative abundance of the genus Ruminococcus increased solely in the caecum and colon transversum. Overall, the addition of the prebiotic significantly increased the diversity in nearly all parts of the gastrointestinal tract (P < 0.05). The feeding of this natural prebiotic compound to horses had an impact on the microbial community in the entire gastrointestinal tract. Furthermore, the effect on the bacterial community in the foregut (especially the stomach) was more pronounced in comparison to the effect in the hindgut. Therefore, the impact on stomach health should be carefully considered.

Legionella growth potential of drinking water produced by a reverse osmosis pilot plant

Treatment processes, such as membrane filtration with reverse osmosis (RO), are used to produce drinking water with a high degree of biostability. To our knowledge, the influence of RO water on biofilm formation and growth of L. pneumophila has not yet been investigated. Therefore, this study aimed (i) to determine the Legionella growth potential of (remineralised) RO-water produced by a pilot plant and to compare this to conventional treated groundwater, and (ii) to determine if different pipe materials, in contact with remineralised RO-water, can cause growth of L. pneumophila. The Legionella growth potential of water was determined with the boiler biofilm monitor (BBM) that mimics the flow of water in a premise plumbing system. The Legionella growth potential of materials in contact with remineralised RO-water was determined by using the biomass production potential (BPP)-test. ATP concentrations in the biofilm on the glass rings from the BBM fed with (remineralised) RO water fluctuated around 100 pg ATP cm^-2. In contrast, BBMs fed with conventionally treated water resulted in ten-fold higher ATP concentrations in the biofilm. Moreover, conventionally treated water had a Legionella growth potential that was 1000-fold higher than that of (remineralised) RO-water. Furthermore, glass, copper and PVC-C had the lowest biofilm concentrations and Legionella growth potential in the BPP-test, followed by PE-Xb, PE-Xc and PE-100. The highest biofilm concentration and Legionella growth potential were with PVC-P. Hence, our study demonstrated that remineralised RO-water did not enhance growth of L. pneumophila in the BBM that mimics the premises plumbing system. However, when PE or PVC-P materials are used growth of L. pneumophila can still occur in the premises plumbing system despite the high quality of the supplied remineralised RO-water.

Association between Psychosocial Stress and Fecal Microbiota in Pregnant Women

Maternal prenatal psychosocial stress is associated with altered child emotional and behavioral development. One potential underlying mechanism is that prenatal psychosocial stress affects child outcomes via the mother's, and in turn the child's, intestinal microbiota. This study investigates the first step of this mechanism: the relation between psychosocial stress and fecal microbiota in pregnant mothers. Mothers (N = 70) provided a late pregnancy stool sample and filled in questionnaires on general and pregnancy-specific stress and anxiety. Bacterial DNA was extracted and analysed by Illumina HiSeq sequencing of PCR-amplified 16 S ribosomal RNA gene fragments. Associations between maternal general anxiety and microbial composition were found. No associations between the other measured psychosocial stress variables and the relative abundance of microbial groups were detected. This study shows associations between maternal pregnancy general anxiety and microbial composition, providing first evidence of a mechanism through which psychological symptoms in pregnancy may affect the offspring.

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut

Animal health benefits from a stable intestinal homeostasis, for which proper development and functioning of the intestinal microbiota and immune system are essential. It has been established that changes in microbial colonization in early life (the first 2 wk post hatch) impacts the functioning of the adult gut and the associated crosstalk between microbiota and intestinal mucosal cells. The aim of the present study was to study the effect of the administration of antibiotics later in life (d 15 to 20 post hatch) on microbiota and immune parameters. For this purpose, chickens received from 15 d post hatch during 5 d amoxicillin or enrofloxacin through their drinking water. Before and at 6, 16, and 27 d after start of the administration of antibiotics, the composition of the microbiota in the jejunum was determined using a 16S ribosomal RNA gene-targeted DNA microarray, the CHICKChip. At 6 d after the start of the administration of the antibiotics, the composition and diversity of the microbiota were affected significantly (P < 0.05), but this change was small and observed only temporarily since differences disappeared at 16 d after initiating treatment with amoxillin and at 27 d after starting treatment with enrofloxacin. Intestinal morphology and development were not visibly affected since there were no differences between villus/crypt ratios and numbers of PAS+ and PCNA+ cells in the duodenum and jejunum at any time point. At 16 d after the start of antibiotic administration, the number of CD4+ T-cells and CD8+ T-cells in the duodenum was lower compared to the control animals; however, this difference was not significant. At some time points, significant differences (P < 0.05) were observed among the groups to locally expressed IL-8, IL-1β, IFN-γ, IL-2, and IL-4 mRNA. However, this effect was not long lasting, as differences that were observed at 16 d after starting the treatment had disappeared at 27 d after treatment was started. The results of this study indicate that later in the broiler's life, antibiotics only temporarily affect intestinal microbial and immune parameters.

Long-term effects of early life microbiota disturbance on adaptive immunity in laying hens

Due to an interplay between intestinal microbiota and immune system, disruption of intestinal microbiota composition during immune development may have consequences for immune responses later in life. The present study investigated the effects of antibiotic treatment in the first weeks of life on the specific antibody response later in life in chickens. Layer chicks received an antibiotic cocktail consisting of vancomycin, neomycin, metronidazole, and amphotericin-B by oral gavage every 12 h, and ampicillin and colistin in drinking water for the first week of life. After the first week of life, chicks received ampicillin and colistin in drinking water for two more weeks. Control birds received no antibiotic cocktail and plain drinking water. Fecal microbiota composition was determined during antibiotic treatment (d 8 and 22), two weeks after cessation of antibiotic treatment (d 36), and at the end of the experimental period at d 175 using a 16S ribosomal RNA gene targeted microarray, the Chicken Intestinal Tract Chip (ChickChip). During antibiotic treatment fecal microbiota composition differed strongly between treatment groups. Fecal microbiota of antibiotic treated birds consisted mainly of Proteobacteria, and in particular E.coli, whereas fecal microbiota of control birds consisted mainly of Firmicutes, such as lactobacilli and clostridia. Two weeks after cessation of antibiotic treatment fecal microbiota composition of antibiotic treated birds had recovered and was similar to that of control birds. On d 105, 12 weeks after cessation of antibiotic treatment, chicks of both treatment groups received an intra-tracheal lipopolysaccharide (LPS)/human serum albumin (HuSA) challenge. Antibody titers against LPS and HuSA were measured 10 days after administration of the challenge. While T cell independent antibody titers (LPS) were not affected by antibiotic treatment, antibiotic treated birds showed lower T cell dependent antibody titers (HuSA) compared with control birds. In conclusion, intestinal microbial dysbiosis early in life may still have effects on the specific antibody response months after cessation of antibiotic treatment and despite an apparent recovery in microbiota composition.

In vitro fermentation of prebiotic carbohydrates by intestinal microbiota in the presence of Lactobacillus amylovorus DSM 16998

The aim of this study was to evaluate the assimilation of the prebiotics fructooligosaccharides (FOS), galactooligosaccharides (GOS), and Konjac glucomannan oligosaccharides (KGMO) by three human (H1, H2 and H3) and pig (P1, P2 and P3) faecal microbiotas in the presence of the potentially probiotic strain Lactobacillus amylovorus DSM 16698, using an in vitro batch fermentation model. Total bacteria and L. amylovorus populations were quantified using qPCR and biochemical features (pH, production of short chain fatty acids (SCFA), lactate, ammonia, and carbohydrate assimilation) were determined. L. amylovorus did not have a competitive advantage under in vitro conditions, reflected by its reduced relative abundance during fermentation despite the carbohydrate sources added. Pig microbiota sustained more stable probiotic counts. Intermittently produced lactate was possibly assimilated by the microbiota and converted to other SCFA as the carbohydrates were assimilated, with H3 probably having a methanogenic metabolism with high lactate and acetate consumption except in the presence of FOS, which assimilation resulted in the highest total SCFA for this volunteer. Addition of FOS also resulted in lower pH and ammonia, which might have been used as nitrogen source by pig microbiota. KGMO needed longer fermentation periods to be completely assimilated by both human and porcine faecal microbiotas. Overall, our results reinforce the notion that care must be taken when generalising the effects claimed for a given probiotic or potentially probiotic strain, including the combination with different prebiotic substrates, since they may vary considerably among individuals, which is important when studying potentially pro- and prebiotic combinations for application as functional foods and feed ingredients.

Adaptation of faecal microbiota in sows after diet changes and consequences for in vitro fermentation capacity

In vitro gas production studies are routinely used to assess the metabolic capacity of intestinal microbiota to ferment dietary fibre sources. The faecal inocula used during the in vitro gas production procedure are most often obtained from animals adapted to a certain diet. The present study was designed to assess whether 19 days of adaptation to a diet are sufficient for faecal inocula of pigs to reach a stable microbial composition and activity as determined by in vitro gas production. Eighteen multiparous sows were allotted to one of two treatments for three weeks: a diet high in fibre (H) or a diet low in fibre (L). After this 3-week period, the H group was transferred to the low fibre diet (HL-treatment) while the L group was transferred to the diet high in fibre (LH-treatment). Faecal samples were collected from each sow at 1, 4, 7, 10, 13, 16 and 19 days after the diet change and prepared as inoculum used for incubation with three contrasting fermentable substrates: oligofructose, soya pectin and cellulose. In addition, inocula were characterised using a phylogenetic microarray targeting the pig gastrointestinal tract microbiota. Time after diet change had an effect (P<0.05) on total gas production for the medium-fast fermentable substrates; soya pectin and oligofructose. For the more slowly fermentable cellulose, all measured fermentation parameters were consistently higher (P<0.05) for animals in the HL-treatment. Diet changes led to significant changes in relative abundance of specific bacteria, especially for members of the Bacteroidetes and Bacilli, which, respectively, increased or decreased for the LH-treatment, while changes were opposite for the HL-treatment. Changing the diet of sows led to changes in fermentation activity of the faecal microbiota and in composition of the microbiota over time. Adaptation of the microbiota as assessed by gas production occurred faster for LH-animals for fast fermentable substrates compared with HL-animals. Overall, adaptation of the large intestinal microbiota of sows as a result of ingestion of low and high fibre diets seems to take longer than 19 days, especially for the ability to ferment slowly fermentable substrates.

Molecular ecological tools to decipher the role of our microbial mass in obesity

After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota

The human intestinal microbiota is responsible for various health-related functions, and its diversity can be readily mapped with the 16S ribosomal RNA targeting Human Intestinal Tract (HIT) Chip. Here we characterise distal gut samples from chimpanzees, gorillas and marmosets, and compare them with human gut samples. Our results indicated applicability of the HITChip platform can be extended to chimpanzee and gorilla faecal samples for analysis of microbiota composition and enterotypes, but not to the evolutionary more distant marmosets.

Effects of a simple or a complex starter microbiota on intestinal microbiota composition in caesarean derived piglets

The present study was designed to develop a model in piglets that allows the investigation of the effects of postnatal association with a simple or a complex microbiota on gut health and development. Thirty piglets from 2 sows were obtained by caesarean delivery (day 0) and were equally divided over 2 treatment groups housed in separate clean, nonsterile rooms. All piglets received orally a simple microbiota consisting of Lactobacillus amylovorus, Clostridium glycolicum, and Parabacteroides spp. on days 1, 2, and 3 after birth. On day 3 and 4 the piglets received either a complex microbiota by providing them with a fecal inoculant of an adult sow [complex association (CA)] or a placebo inoculant [simple association (SA)]. Fecal microbiota composition, as determined by denaturing gradient gel electrophoresis and by pig intestinal tract chip (PITChip) analysis of 16S rRNA genes (days 3, 5, 7, 14, and 28), was less diverse in the SA group compared to the CA group. A difference in fecal microbiota composition between treatments persisted until the end of the study. It was concluded that the composition of microbiota in feces of cesarean delivery-derived piglets is influenced by bacterial association in the first days after birth. Differences in fecal microbiota composition between piglets exposed to a simple or complex inoculum at early age persisted for at least 3 wk.

Rearing environment affects development of the immune system in neonates

Early-life exposure to appropriate microbial flora drives expansion and development of an efficient immune system. Aberrant development results in increased likelihood of allergic disease or increased susceptibility to infection. Thus, factors affecting microbial colonization may also affect the direction of immune responses in later life. There is a need for a manipulable animal model of environmental influences on the development of microbiota and the immune system during early life. We assessed the effects of rearing under low- (farm, sow) and high-hygiene (isolator, milk formula) conditions on intestinal microbiota and immune development in neonatal piglets, because they can be removed from the mother in the first 24 h for rearing under controlled conditions and, due to placental structure, neither antibody nor antigen is transferred in utero. Microbiota in both groups was similar between 2 and 5 days. However, by 12-28 days, piglets reared on the mother had more diverse flora than siblings reared in isolators. Dendritic cells accumulated in the intestinal mucosa in both groups, but more rapidly in isolator piglets. Importantly, the minority of 2-5-day-old farm piglets whose microbiota resembled that of an older (12-28-day-old) pig also accumulated dendritic cells earlier than the other farm-reared piglets. Consistent with dendritic cell control of T cell function, the effects on T cells occurred at later time-points, and mucosal T cells from high-hygiene, isolator pigs made less interleukin (IL)-4 while systemic T cells made more IL-2. Neonatal piglets may be a valuable model for studies of the effects of interaction between microbiota and immune development on allergy.

The effects of selected probiotic strains on the development of eczema (the PandA study)

BACKGROUND

Modification of the intestinal microbiota by administration of probiotic bacteria may be a potential approach to prevent allergic disease. We aimed to study primary prevention of allergic disease in high-risk children by pre- and postnatal supplementation of selected probiotic bacteria.

METHODS

In a double-blind, randomized, placebo-controlled trial, a mixture of probiotic bacteria selected by in-vitro experiments (Bifidobacterium bifidum, Bifidobacterium lactis, and Lactococcus lactis; Ecologic Panda) was prenatally administered to mothers of high-risk children (i.e. positive family history of allergic disease) and to their offspring for the first 12 months of life.

RESULTS

Parental-reported eczema during the first 3 months of life was significantly lower in the intervention group compared with placebo, 6/50 vs 15/52 (P = 0.035). After 3 months, the incidence of eczema was similar in both groups. Cumulative incidence of parental-reported eczema at 1 and 2 years was 23/50 (intervention) vs 31/48 (placebo) and 27 (intervention) vs 34 (placebo), respectively. The number needed to treat was 5.9 at age 3 and 12 months and 6.7 at age 2 years. The intervention group was significantly more frequently colonized with higher numbers of Lc. lactis. Furthermore, at age 3 months, in vitro production of IL-5 (146 pg/ml vs 72 pg/ml; P = 0.04) was decreased in the probiotic-group compared with the placebo-group.

CONCLUSIONS

This particular combination of probiotic bacteria shows a preventive effect on the incidence of eczema in high-risk children, which seems to be sustained during the first 2 years of life. In addition to previous studies, the preventive effect appears to be established within the first 3 months of life.

Resilience of Microbial Systems Towards Disturbances

In this paper we aim at summarizing the current definitions of resilience in systems ecology with particular attention towards microbial systems. The recent advances of biomolecular techniques have provided scientists with new tools to investigate these systems in greater detail and with higher resolution. Therefore existing concepts and hypotheses have been revisited and discussed with respect to their applicability for ecosystems ruled by microbial processes. This review has also led to some reflections on the suitability of the term "resilience" as a general goal in environmental policies.

Diversity of the Lactobacillus group in breast milk and vagina of healthy women and potential role in the colonization of the infant gut

AIMS

To evaluate the diversity of the Lactobacillus group in breast milk and the vagina of healthy women and understand their potential role in the infant gut colonization using the 16S rRNA gene approaches.

METHODS AND RESULTS

Samples of breast milk, vaginal swabs and infant faeces were aseptically collected from five mothers whose neonates were born by vaginal delivery and another five that had their babies by caesarean section. After polymerase chain reaction (PCR) amplification using Lactobacillus group-specific primers, amplicons were analysed by denaturing gradient gel electrophoresis (DGGE). Clone libraries were constructed to describe the Lactobacillus group diversity. DGGE fingerprints were not related to the delivery method. None of the species detected in vaginal samples were found in breast milk-derived libraries and only few were detected in infant faeces.

CONCLUSIONS

The bacterial composition of breast milk and infant faeces is not related to the delivery method.

SIGNIFICANCE AND IMPACT OF THE STUDY

It has been suggested that neonates acquire lactobacilli by oral contamination with vaginal strains during delivery; subsequently, newborns would transmit such bacteria to the breast during breastfeeding. However, our findings confirm, at the molecular level that in contrast to the maternal vagina, breast milk seems to constitute a good source of lactobacilli to the infant gut.

Anaerobic microbial LCFA degradation in bioreactors

This paper reviews recent results obtained on long-chain fatty acids (LCFA) anaerobic degradation. Two LCFA were used as model substrates: oleate, a mono-unsaturated LCFA, and palmitate, a saturated LCFA, both abundant in LCFA-rich wastewaters. 16S rRNA gene analysis of sludge samples submitted to continuous oleate- and palmitate-feeding followed by batch degradation of the accumulated LCFA demonstrated that bacterial communities were dominated by members of the Clostridiaceae and Syntrophomonadaceae families. Archaeal populations were mainly comprised of hydrogen-consuming microorganisms belonging to the genus Methanobacterium, and acetate-utilizers from the genera Methanosaeta and Methanosarcina. Enrichment cultures growing on oleate and palmitate, in the absence or presence of sulfate, gave more insight into the major players involved in the degradation of unsaturated and saturated LCFA. Syntrophomonas-related species were identified as predominant microorganisms in all the enrichment cultures. Microorganisms clustering within the family Syntrophobacteraceae were identified in the methanogenic and sulfate-reducing enrichments growing on palmitate. Distinct bacterial consortia were developed in oleate and palmitate enrichments, and observed differences might be related to the different degrees of saturation of these two LCFA. A new obligately syntrophic bacterium, Syntrophomonas zehnderi, was isolated from an oleate-degrading culture and its presence in oleate-degrading sludges detected by 16S rRNA gene cloning and sequencing.

Effects of yeast culture on performance, gut integrity, and blood cell composition of weanling pigs

An experiment was conducted to determine the effects of yeast culture (YC) and modified yeast culture [YC + cell wall product (CWP) containing mannan oligosaccharides] in pig diets on the performance, gut integrity, and blood cell composition of weanling pigs and to determine whether these dietary supplements could replace antimicrobial growth promoters (AGP) in pig diets. A total of 480 weanling pigs (27 d old and 7.8 +/- 0.1 kg of BW) were assigned to 1 of 4 experimental treatments: 1) diets without AGP or YC (control diet); 2) control + AGP; 3) control + 0.125% YC; and 4) control + 0.125% YC + 0.2% CWP. Piglets were fed experimental diets for 5 wk after weaning. Blood samples were collected from 8 piglets at weaning and from 8 piglets per treatment on d 14 and 35 after weaning for blood cell composition. These piglets were slaughtered for measurement of villous length and crypt depth in the jejunal mucosa and microbial profiling on the intestinal digesta. Average daily gain (P = 0.06) and G:F (P = 0.02) were improved for piglets that were fed the supplemented diets compared with piglets that were fed the control diet. Average daily feed intake was unaffected by dietary treatment. Performance was similar in piglets fed diets supplemented with AGP, YC, and YC + CWP. Blood cell composition, villous length, crypt depth, and microbial composition in the gut were unaffected by dietary treatment, but they were affected by time after weaning. Red blood cells, hemoglobin, hematocrit value, mean cell volume, mean cell hemoglobin, percentage of lymphocytes in the leukocyte population, villous length, and crypt depth were greater (P < 0.05) at 5 wk after weaning than at 2 wk after weaning. Eosinophils (P = 0.06) in the leukocyte population tended to be greater at 5 wk after weaning. Concentration of neutrophils in the leukocyte population and percentages of CD4 and CD8 cells were lower (P < 0.02) at 5 wk after weaning. The CD4:CD8 ratio (P = 0.07) tended to be lower at 5 wk after weaning. Results suggest that yeast culture could be an alternative to AGP in the diets of weanling pigs and that addition of CWP to diets containing YC would not improve the performance or health of weanling pigs above that of YC alone. Thus, more insight into the mode of action of YC is needed.

Degradation of methanethiol by methylotrophic methanogenic archaea in a lab-scale upflow anaerobic sludge blanket reactor

In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30 degrees C to H2S, CO2, and CH4. At a hydraulic retention time of 9 h, a maximum influent concentration of 6 mM MT was applied, corresponding to a volumetric loading rate of 16.5 mmol liter-1 day-1. The archaeal community within the reactor was characterized by anaerobic culturing and denaturing gradient gel electrophoresis analysis, cloning, and sequencing of 16S rRNA genes and quantitative PCR. Initially, MT-fermenting methanogenic archaea related to members of the genus Methanolobus were enriched in the reactor. Later, they were outcompeted by Methanomethylovorans hollandica, which was detected in aggregates but not inside the granules that originated from the inoculum, the microbial composition of which remained fairly unchanged. Possibly other species within the Methanosarcinacaea also contributed to the fermentation of MT, but they were not enriched by serial dilution in liquid media. The archaeal community within the granules, which was dominated by Methanobacterium beijingense, did not change substantially during the reactor operation. Some of the species related to Methanomethylovorans hollandica were enriched by serial dilutions, but their growth rates were very low. Interestingly, the enrichments could be sustained only in the presence of MT and did not utilize any of the other typical substrates for methylotrophic methanogens, such as methanol, methyl amine, or dimethylsulfide.

Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays

Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.

Clostridium beijerinckii cells expressing Neocallimastix patriciarum glycoside hydrolases show enhanced lichenan utilization and solvent production

Growth and the production of acetone, butanol, and ethanol by Clostridium beijerinckii NCIMB 8052 on several polysaccharides and sugars were analyzed. On crystalline cellulose, growth and solvent production were observed only when a mixture of fungal cellulases was added to the medium. On lichenan growth and solvent production occurred, but this polymer was only partially utilized. To increase utilization of these polymers and subsequent solvent production, the genes for two new glycoside hydrolases, celA and celD from the fungus Neocallimastix patriciarum, were cloned separately into C. beijerinckii. To do this, a secretion vector based on the pMTL500E shuttle vector and containing the promoter and signal sequence coding region of the Clostridium saccharobutylicum NCP262 eglA gene was constructed and fused either to the celA gene or the celD gene. Stable C. beijerinckii transformants were obtained with the resulting plasmids, pWUR3 (celA) and pWUR4 (celD). The recombinant strains showed clear halos on agar plates containing carboxymethyl cellulose upon staining with Congo red. In addition, their culture supernatants had significant endoglucanase activities (123 U/mg of protein for transformants harboring celA and 78 U/mg of protein for transformants harboring celD). Although C. beijerinckii harboring either celA or celD was not able to grow, separately or in mixed culture, on carboxymethyl cellulose or microcrystalline cellulose, both transformants showed a significant increase in solvent production during growth on lichenan and more extensive degradation of this polymer than that exhibited by the wild-type strain.

Development of a gene cloning and inactivation system for halorespiring Desulfitobacterium dehalogenans

Efficient host-vector systems have been developed for the versatile, strictly anaerobic, halo- and fumarate-respiring gram-positive bacterium Desulfitobacterium dehalogenans. An electroporation-based transformation procedure resulting in approximately 10(3) to 10(4) transformants per microg of the cloning vector pIL253 was developed and validated. The broad-host-range vector pG+host9 was shown to replicate at a permissive temperature of 30 degrees C, whereas the replicon was not functional at 40 degrees C. The D. dehalogenans frdCAB operon, predicted to encode a fumarate reductase, was cloned, characterized, and targeted for insertional inactivation by pG+host9 carrying a 0.6-kb internal frdA fragment. Single-crossover integration at the frdA locus occurred at a frequency of 3.3 x 10(-4) per cell and resulted in partially impaired fumarate reductase activity. The gene cloning and inactivation systems described here provide a solid basis for the further elucidation of the halorespiratory network in D. dehalogenans and allow for its further exploitation as a dedicated degrader.

Transcriptional regulation of the cpr gene cluster in ortho-chlorophenol-respiring Desulfitobacterium dehalogenans

To characterize the expression and possible regulation of reductive dehalogenation in halorespiring bacteria, a 11.5-kb genomic fragment containing the o-chlorophenol reductive dehalogenase-encoding cprBA genes of the gram-positive bacterium Desulfitobacterium dehalogenans was subjected to detailed molecular characterization. Sequence analysis revealed the presence of eight designated genes with the order cprTKZEBACD and with the same polarity except for cprT. The deduced cprC and cprK gene products belong to the NirI/NosR and CRP-FNR families of transcription regulatory proteins, respectively. CprD and CprE are predicted to be molecular chaperones of the GroEL type, whereas cprT may encode a homologue of the trigger factor folding catalysts. Northern blot analysis, reverse transcriptase PCR, and primer extension analysis were used to elucidate the transcriptional organization and regulation of the cpr gene cluster. Results indicated halorespiration-specific transcriptional induction of the monocistronic cprT gene and the biscistronic cprBA and cprZE genes. Occasional read-through at cprC gives rise to a tetracistronic cprBACD transcript. Transcription of cprBA was induced 15-fold upon addition of the o-chlorophenolic substrate 3-chloro-4-hydroxyphenylacetic acid within 30 min with concomitant induction of dehalogenation activity. Putative regulatory protein binding motifs that to some extent resemble the FNR box were identified in the cprT-cprK and cprK-cprZ intergenic regions and the promoter at cprB, suggesting a role for FNR-like CprK in the control of expression of the cprTKZEBACD genes.

Random transposition by Tn916 in Desulfitobacterium dehalogenans allows for isolation and characterization of halorespiration-deficient mutants

To allow for the molecular analysis of halorespiration by the strictly anaerobic gram-positive bacterium Desulfitobacterium dehalogenans, halorespiration-deficient mutants were selected and characterized following insertional mutagenesis by the conjugative transposon Tn916. To facilitate rapid screening of transconjugants, a highly efficient method for the growth of single colonies on solidified medium has been developed. A streptomycin-resistant mutant of D. dehalogenans was isolated and mated with Enterococcus faecalis JH2-2 carrying Tn916. Insertion of one or two copies of Tn916 into the chromosome of D. dehalogenans was observed. From a total of 2,500 transconjugants, 24 halorespiration-deficient mutants were selected based upon their inability to use 3-chloro-4-hydroxyphenylacetic acid as an electron acceptor. Physiological characterization led to the definition of three phenotypic classes of mutants that differed in their ability to use the additional terminal electron acceptors nitrate and fumarate. The activities of hydrogenase and formate dehydrogenase were determined, and the transposon insertion sites in selected mutants representing the different classes were analyzed on the sequence level following amplification by inverse PCR. The results of the molecular characterization as well as the pleiotropic phenotypes of most mutants indicate that genes coding for common elements shared by the different respiratory chains present in the versatile D. dehalogenans have been disrupted.

Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans

ortho-Chlorophenol reductive dehalogenase of the halorespiring Gram-positive Desulfitobacterium dehalogenans was purified 90-fold to apparent homogeneity. The purified dehalogenase catalyzed the reductive removal of a halogen atom from the ortho position of 3-chloro-4-hydroxyphenylacetate, 2-chlorophenol, 2,3-dichlorophenol, 2,4-dichlorophenol, 2,6-dichlorophenol, pentachlorophenol, and 2-bromo-4-chlorophenol with reduced methyl viologen as electron donor. The dechlorination of 3-chloro-4-hydroxyphenylacetate was catalyzed by the enzyme at a Vmax of 28 units/mg protein and a Km of 20 microM. The pH and temperature optimum were 8.2 and 52 degrees C, respectively. EPR analysis indicated one [4Fe-4S] cluster (midpoint redox potential (Em) = -440 mV), one [3Fe-4S] cluster (Em = +70 mV), and one cobalamin per 48-kDa monomer. The Co(I)/Co(II) transition had an Em of -370 mV. Via a reversed genetic approach based on the N-terminal sequence, the corresponding gene was isolated from a D. dehalogenans genomic library, cloned, and sequenced. This revealed the presence of two closely linked genes: (i) cprA, encoding the o-chlorophenol reductive dehalogenase, which contains a twin-arginine type signal sequence that is processed in the purified enzyme; (ii) cprB, coding for an integral membrane protein that could act as a membrane anchor of the dehalogenase. This first biochemical and molecular characterization of a chlorophenol reductive dehalogenase has revealed structural resemblance with haloalkene reductive dehalogenases.