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The first chapter, “Pathogens and Parasites,” introduces the major helminthic, protozoal, viral, and bacterial intestinal disease agents, and it provides estimates of their current prevalence and contribution to the burden of human disease. The chapter discusses the biological and social determinants of infectious intestinal disease transmission, and it makes the point that, although a range of hygienic practices can have a significant influence on transmission, owing to a range of ecological and cultural variables, few universal rules apply. It discusses some recent findings from the microbiome project that provide new ways of thinking about infectious intestinal disease, and it makes the case that a deeper understanding of the historical epidemiology of infectious intestinal diseases can potentially improve the public health outcomes from contemporary interventions.
Contamination of raw milk by psychrotrophs can lead to the production of heat-resistant proteases and subsequent spoilage of UHT milk. Therefore, this research communication evaluated the effect of a pre-milking teat disinfectant (active components: L-(+)-lactic acid and salicylic acid) and a liner disinfectant (active components: peracetic acid and hydrogen peroxide) on the number of mesophilic and (proteolytic) psychrotrophic bacteria prior to milking. The teat orifices of 10 cows were sampled using a swabbing procedure before and after treatment with a pre-milking teat disinfectant on six subsequent days. On the teat orifices, there was a small but statistically significant decrease in the psychrotrophic bacterial counts between pre and post dipping. No differences were observed for the mesophilic bacterial counts and proteolytic active counts. Liners were also sampled using swabs pre and post disinfection. No statistically significant decrease in the bacterial counts was observed post liner disinfection, although there was a numerical decrease. Sixty-two percent of the proteolytic psychrotrophs were pseudomonads: 16.5% of which were P. fragi, 14.3% P. lundensis, 10.0% P. fluorescens and 2.9% P. putida. Trinitrobenzenesulfonic acid (TNBS) analysis revealed a wide variety in proteolytic activity (from 0 to 55 µmol glycine/ml milk) and the presence of high producers. It can be concluded that there was only a minor effect of teat and liner disinfection on the psychrotrophic bacterial counts indicating that the measures presented did not result in a reduction of the targeted bacteria on teat orifices and liners.
This review aims to familiarize the reader with research efforts on the cultivation media of lactic acid bacteria (LAB). We have also included a brief discussion on standard ingredients used in LAB media and chemically defined media as related to bacterial growth requirements. Recent research has focused on modifying standard media for the enumeration, differentiation, isolation, and identification of starter cultures and probiotics. Even though large numbers of these media have been developed to serve dairy microbial control, they have failed to provide consistent results. The research consequently points to the need to develop a reliable lactobacilli growth medium for the dairy industry.
The meadow spittlebug, Philaenus spumarius (Linnaeus) (Hemiptera: Aphrophoridae), is an important vector for the xylem-limited bacterium Xylella fastidiosa (Wells, Raju, Hung, Weisburg, Mandelco-Paul, and Brenner), which is associated with olive quick decline syndrome in southern Italy. The mouthparts of Hemiptera have important roles in host plant selection, feeding behavior and for vectoring pathogens that cause plant diseases. In this study, the functional morphology of the sensory structures located on the labium tip and precibarium of P. spumarius was investigated using scanning and transmission electron microscopy. The labium tip is composed of two symmetrical sensory complexes, each with five different types of sensilla: aporous sensilla trichodea type 1 and 2; uniporous sensilla chaetica type 1 and 2; and multiporous sensilla basiconica. The precibarium of P. spumarius has two kinds of sensory structures: bulbous sensilla and papillae sensilla. In particular, two groups of sensilla are located on the epipharynx: a distal group that consists of ten papillae sensilla and a proximal group composed of six papillae sensilla and two bulbous sensilla, while the hypopharynx has only two papillae sensilla. The involvement of these sensory structures in the context of feeding behavior and pathogen transmission is discussed.
Mycoplasma gallisepticum causes disease in poultry and emerged as a novel pathogen in house finches resulting in a mycoplasmal conjunctivitis epidemic across North America after a single successful host jump from poultry to house finches. The rapid spread of the epidemic across eastern North America, causing a decline in host abundance, has been documented. Once established, disease prevalence showed regular seasonal variation: a late summer/early autumn peak, a mid-December minimum, followed by a late winter peak and a breeding season minimum, which requires seasonal reproduction (providing an autumn pulse of naïve hosts) and winter social aggregation as well as partial immunity of recovered birds. Virulence evolved rapidly: in eastern populations it increased once the disease had become endemic. In western North America the established strain was of much lower virulence, but once established also increased in virulence. We show that virulence may evolve in opposite directions depending on selection pressures. A detailed study showed that disease decreased survival and mobility and a high proportion of birds recovered; also that re-observation rates of clinically diseased birds are often different from those of asymptomatic birds; only calculations which include this effect allow an accurate estimate of disease prevalence.
The present study aimed to evaluate the quality of fresh sushi in Egypt. Fifty samples of sushi (Salmo salar) were collected from restaurants in Alexandria, Egypt. Paraffin, semi-thin and ultra-thin sections were used for parasitological analysis by light and transmission electron microscopy. Bacteria were isolated by the dilution plate and direct plate methods and identified by a Vitek system. Twenty (40%) of the total examined samples showed microsporidia and helminth metacercariae infections. Histochemical stains showed distinct pinkish-red pyriform microspores embedded in muscular tissue stained with Gram, periodic acid-Schiff (PAS), and Ziehl–Neelsen (ZN) stains. Semi-thin sections showed double membrane xenoma-inducing granulomas containing spores at different developmental stages. Empty sporophorous vesicles and free spores were observed in the electron microscopic images. A bacteriological assay showed forty samples (80%) contaminated with human pathogenic bacteria with the average total bacterial counts ranging from 32 to 526 CFU/g. Four species of human pathogenic bacteria were identified in the examined samples, namely Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, and Serratia plymuthica in 40, 38, 11, and 6 samples, respectively. These constitute the first record of fresh sushi product in Egypt and indicate the potential pathogenicity associated with raw seafood products.
A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis, Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle.
Both short- and long-term effects of fertilizers on crops and soils are often studied only in arid or paddy soils, whereas less is known about the long-term effects in paddy-upland rotations, particularly with multiple crops and frequent tillage in subtropical areas. Therefore, an 18-year field experiment was initialized to assess the effects of different types of fertilization (no fertilizer; chemical fertilizer (CF); and manure in combination with CF (MCF)) on yield and soil chemical and microbial properties in a crop rotation involving rice (Oryza sativa L., summer), rapeseed (Brassica campestris L., winter), tobacco (Nicotiana tabacum L., the following summer), and hairy vetch (Vicia villosa Roth, the following winter). MCF caused higher yields of rapeseed grains and tobacco leaves than CF after 3 or 4 years of implementing the experiment, while rice yields varied little between MCF and CF, with one exception in 2011. Compared with the initial soil properties, providing soil with MCF increased organic matter (OM), while the opposite trend was found with CF. Higher microbial biomasses, enzyme activities, bacterial operational taxonomic units, and richness and diversity indexes of bacterial communities were found in soils receiving MCF, implying the improvement of soil microbial properties in the paddy-upland rotation system with multiple crops and frequent tillage. The experimental soils under varying fertilization were dominated by four bacterial phyla (Proteobacteria, Acidobacteria, Actinobacteria, and unclassified groups), which accounted for approximately 70% of the 16S rDNA sequences. Among the top 20 predominant bacteria, 14 were commonly found in all soil samples irrespective of which fertilizer treatment was implemented. Thus, the presence of those bacteria was stable in the soil and to some extent was influenced by fertilization. Most of them were facultative anaerobic bacteria, which can adapt to both anaerobic paddy soil and aerobic drylands. The dominant bacteria at various taxonomic levels found in soils might reflect multiple soil processes such as OM turnover, nutrient cycling, physical structure formation, and xenobiotic detoxification.
Mastitis is one of the most prevalent and costly diseases in dairy cattle. Key components for adequate mastitis control are the detection of early stages of infection, as well as the selection of appropriate management interventions and therapies based on the causal pathogens associated with the infection. The objective was to characterize the pattern of electrical conductivity (EC) in milk during intramammary infection, considering specific mastitis-causing pathogen groups involvement. Cows (n = 200) identified by an in-line mastitis detection system with a positive deviation ≥15% in the manufacturer’s proprietary algorithm for EC (high electrical conductivity (HEC)) were considered cases and enrolled in the study at the subsequent milking. One control (CON) cow, within normal ranges for EC, was matched to each case. A composite milk sample was collected aseptically from each cow for bacteriological culture. Milk yield (MY) and EC were recorded for each milking during ±7 days relative to enrollment. Milk cultures were categorized into gram positive (GP), gram negative (GN), other (OTH) and no growth (NOG). Data were submitted for repeated-measures analysis with EC as the dependent variable and EC status at day −1, bacteriological culture category, parity number, stage of lactation and days relative to sampling as main independent variables. Average (± standard error (SE)) EC was greater in HEC than in CON cows (12.5 ± 0.5 v. 10.8 ± 0.5 mS/cm) on the day of identification (day −1). Milk yield on day −1 was greater in CON than in HEC (37.6 ± 5.1 v. 33.5 ± 5.2 kg). For practical management purposes, average EC on day −1 was similar for the different bacteriological culture categories: 11.4 ± 0.6, 11.7 ± 0.5, 12.3 ± 0.8 and 11.7 ± 0.5 mS/cm in GN, GP, OTH and NOG, respectively. Parity number was only associated with day −1 EC in HEC group, with the greatest EC values in parity 3 (12.3 ± 0.3 mS/cm), followed by parity 2 (11.9 ± 0.2 mS/cm), parity >3 (11.6 ± 0.5 mS/cm) and primiparous cows (11.2 ± 0.2 mS/cm). An effect on EC for the interaction of day relative to identification by pathogen gram category was observed. The same interaction effect was observed on daily MY. Overall, the level of variation for MY and EC between- and within-cows was substantial, and as indicated by the model diagnostic procedures, the magnitude of the variance in the cows in the CON group resulted in deviations from normality in the residuals. We concluded that characteristic temporal patterns in EC and MY in particular pathogen groups may provide indications for differentiation of groups of mastitis-causing pathogens. Further research to build detection models including EC, MY and cow-level factors is required for accurate differentiation.
The evidence supporting the efficacy of antibiotic therapy in the treatment of chronic rhinosinusitis is not compelling. A limited number of studies show that the changes in the nasal microbiome in patients following drug therapy are unpredictable and variable. The evidence for the impact of oral antibiotics on the gut microbiota is stronger, possibly as a result of differences in drug distribution to various sites around the body. There are few studies on sinus mucosal and mucus levels of oral antibiotics used in the treatment of chronic rhinosinusitis. The distribution dependent effects of antibiotics on the sinonasal microbiome is unclear.
This review highlights that relative drug concentrations and their efficacy on microbiota at different sites is an important subject for future studies investigating chronic rhinosinusitis.
We investigated a large multistate outbreak that occurred in the United States in 2015–2016. Epidemiologic, laboratory, and traceback studies were conducted to determine the source of the infections. We identified 907 case-patients from 40 states with illness onset dates ranging from July 3, 2015 to March 2, 2016. Sixty-three percent of case-patients reported consuming cucumbers in the week before illness onset. Ten illness sub-clusters linked to events or purchase locations were identified. All sub-clusters investigated received cucumbers from a single distributor which were sourced from a single grower in Mexico. Seventy-five cucumber samples were collected, 19 of which yielded the outbreak strain. Whole genome sequencing performed on 154 clinical isolates and 19 cucumber samples indicated that the sequenced isolates were closely related genetically to one another. This was the largest US foodborne disease outbreak in the last ten years and the third largest in the past 20 years. This was at least the fifth multistate outbreak caused by contaminated cucumbers since 2010. The outbreak is noteworthy because a recall was issued only 17 days after the outbreak was identified, which allowed for the removal of the contaminated cucumbers still available in commerce, unlike previous cucumber associated outbreaks. The rapid identification and response of multiple public health agencies resulted in preventing this from becoming an even larger outbreak.
The prevalence of antimicrobial resistance (AMR) varies significantly among different patient populations. We aimed to summarise AMR prevalence data from screening studies in different patient settings in Switzerland and to identify surveillance gaps. We performed a systematic review, searching Pubmed, MEDLINE, Embase (01/2000–05/2017) and conference proceedings for Swiss studies reporting on carbapenemase-producing Enterobacteriaceae (CPE), extended-spectrum beta-lactamases (ESBL), mobilised colistin-resistance, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) within different patient settings. We identified 2345 references and included 46 studies. For acute care patients, most screening data come from admission screenings, whereas AMR prevalence among hospitalised patients is largely unknown. Universal admission screenings showed ESBL-prevalences of 5–8% and MRSA-prevalences of 2–5%. For targeted screening, ESBL-prevalence ranged from 14–21%; MRSA-prevalence from 1–4%. For refugees, high ESBL (9–24%) and MRSA (16–24%) carriage rates were reported; returning travellers were frequently (68–80%) colonised with ESBL. Screening data for other pathogens, long-term care facility (LTCF) residents and pediatric populations were scarce. This review confirms high ESBL- and MRSA-carriage rates for risk populations in Switzerland. Emerging pathogens (CPE and VRE) and certain populations (inpatients, LTCF residents and children) are understudied. We encourage epidemiologists and public health authorities to consider these findings in the planning of future surveillance studies.
Microbial parasites adapted to thrive at mammalian mucosal surfaces have evolved multiple times from phylogenetically distant lineages into various extracellular and intracellular life styles. Their symbiotic relationships can range from commensalism to parasitism and more recently some host–parasites interactions are thought to have evolved into mutualistic associations too. It is increasingly appreciated that this diversity of symbiotic outcomes is the product of a complex network of parasites–microbiota–host interactions. Refinement and broader use of DNA based detection techniques are providing increasing evidence of how common some mucosal microbial parasites are and their host range, with some species being able to swap hosts, including from farm and pet animals to humans. A selection of examples will illustrate the zoonotic potential for a number of microbial parasites and how some species can be either disruptive or beneficial nodes in the complex networks of host–microbe interactions disrupting or maintaining mucosal homoeostasis. It will be argued that mucosal microbial parasitic diversity will represent an important resource to help us dissect through comparative studies the role of host–microbe interactions in both human health and disease.
The micro-organisms which inhabit the human gut (i.e. the intestinal microbiota) influence numerous human biochemical pathways and physiological functions. The present review focuses on two questions, ‘Are intestinal microbiota effects measurable and meaningful?’ and ‘What research methods and variables are influenced by intestinal microbiota effects?’. These questions are considered with respect to doubly labelled water measurements of energy expenditure, heat balance calculations and models, measurements of RMR via indirect calorimetry, and diet-induced energy expenditure. Several lines of evidence suggest that the intestinal microbiota introduces measurement variability and measurement errors which have been overlooked in research studies involving nutrition, bioenergetics, physiology and temperature regulation. Therefore, we recommend that present conceptual models and research techniques be updated via future experiments, to account for the metabolic processes and regulatory influences of the intestinal microbiota.
Mars is considered to be one of the most favourable places in the Solar System to search for past and present life. In the past Mars was warmer and wetter, so terrestrial halophiles can be regarded as analogues of hypothetical ancient Martian halophiles. In this study we used microorganisms from unique Altai region (Russia) to estimate the capability of terrestrial bacteria and archaea to survive at low temperatures and high concentration of salts and metals, similar to the Martian environment. The current report demonstrates that both halophilic archaea and halotolerant bacteria from saline lakes of the Altai region may be considered as analogues of ancient Martian organisms, since they are able to withstand conditions that hypothetically existed in subsurface layers of the early Mars (low temperatures, salt solutions with a high content of NaCl) with only slight decrease in viability. We also found that the studied microorganisms can use some organic substances found in meteorites. We consider that transfer of unicellular halophiles from Earth to Mars was possible, and, moreover, they could successfully survive and grow on early Mars. Adjusting our growth media to the chemical composition of the lakes, from which the studied strains were isolated, resulted in significant increase in survival and growth rates. Certain strains could survive several freeze–thaw cycles at −70 °C typical for Martian nights.
Intake in sugar-rich diets can be limited either via rumen fill or excessive rumen fermentation and source of non-fibre carbohydrate (NFC) in the diet can affect both factors. The aim of the current study was to quantify the effect of partially replacing ground maize (GM) with steam-rolled maize (SRM) or pelleted citrus pulp (PCP) at two concentrate levels in sugarcane-based diets on digestibility, rumen ecosystem and metabolism of Nellore steers. Six rumen-cannulated steers were assigned to a 6 × 6 Latin square, replicated in time, in a 2 × 3 factorial arrangement of treatments with two levels of concentrate (600 or 800 g concentrate/kg dry matter [DM]) and three NFC sources. Each steer within a period was considered an experimental unit. Feeding more concentrate increased total tract digestibility of organic matter and decreased fibre intake and passage rate. It also reduced rumen populations of Fibrobacter succinogenes and Streptococcus bovis and increased Ruminococcus flavefaciens. Substituting PCP for GM increased rumen pH, acetic acid and organic matter digestibility. Feeding PCP also reduced R. flavefaciens and R. amylophilus rumen populations. Substituting SRM for GM increased starch digestibility and rumen propionic acid, but decreased rumen ammonia concentration. Feeding SRM increased rumen populations of Megasphaera elsdenii with the high-concentrate diet but reduced Ruminococcus albus populations at both concentrate levels. In conclusion, partial replacement of GM by PCP decreased intake in sugar-rich diets, while increasing total tract neutral detergent fibre digestibility. Replacement of GM with SRM increases rumen fermentation and total tract digestibility of starch.
Nowadays, there is much legislation in the world devoted to restrict the use of synthetic antibiotics in the poultry industry, which could reduce performance rate and production profits. Various phyto-biotic growth promoters have been proposed to serve as antibiotic alternatives with emphasis on plant extracts and essential oils. This study was conducted to assess the impacts of using the oregano essential oil (OEO) (comprised of 5% thymol and 65% carvacrol) and Enviva essential oil (EEO) (4.5% cinnamaldehyde and 13.5% thymol) as phytobiotic feed additives (PFA) on growth performance, cecal microbiota and serum biochemicals of growing ducks. In total, 800 11-day-old ducklings, housed in 20 floor pens, were allotted randomly into five dietary treatments: (i) A basal diet (BD) (control), (ii.) BD+50 mg EEO/kg, (iii.) BD+100 mg EEO/kg, (iv.) BD+150 mg OEO/kg and (v.) BD+300 mg OEO/kg diet. The growth performance traits were studied between 11 and 42 days of age. At the experiment end, 40 ducks were slaughtered (eight/ treatment) and cecal digesta and blood samples were collected to estimate the cecal bacterial populations and serum blood biochemicals. The results indicated that the tested levels of OEO and EEO did not display any significant effect (P>0.05) on the duck’s final BW, BW gain, growth rate, feed intake, feed conversion ratio or survivability rate. Besides, the different levels of EEO and OEO decreased the cecal populations of Coliforms (P<0.01), total aerobes (P<0.01) and lactose-negative Enterobacteria (P<0.05) in comparison with those of the control group. Finally, the tested EEO and OEO levels did not show any significant effect on the serum variables; in terms of total protein, albumin, globulin, total cholesterol, triglycerides, alanine aminotransferase and aspartate aminotransferase. In conclusion, the antimicrobial effect of the OEO and EEO against the cecal microbiota has been proven, while they did not display significant effects on the growth performance or blood variables of growing ducks.
The aim of the study was to investigate any association between extrauterine growth restriction (EUGR) and intestinal flora of <30-week-old preterm infants. A total of 59 preterm infants were assigned to EUGR (n=23) and non-EUGR (n=36) groups. Intestinal bacteria were compared by using high-throughput sequencing of bacterial rRNA. The total abundance of bacteria in 344 genera (7568 v. 13,760; P<0.0001) and 456 species (10,032 v. 18,240; P<0.0001) was significantly decreased in the EUGR group compared with the non-EUGR group. After application of a multivariate logistic model and adjusting for potential confounding factors, as well as false-discovery rate corrections, we found four bacterial genera with higher and one bacterial genus with lower abundance in the EUGR group compared with the control group. In addition, the EUGR group showed significantly increased abundances of six species (Streptococcus parasanguinis, Bacterium RB5FF6, two Klebsiella species and Microbacterium), but decreased frequencies of three species (one Acinetobacter species, Endosymbiont_of_Sphenophorus_lev and one Enterobacter_species) compared with the non-EUGR group. Taken together, there were significant changes in the intestinal microflora of preterm infants with EUGR compared to preterm infants without EUGR.
Eight ruminally-fistulated wethers were used to examine the temporal effects of afternoon (PM; 1600h) v. morning (AM; 0800 h) allocation of fresh spring herbage from a perennial ryegrass (Lolium perenne L.)-based pasture on fermentation and microbial community dynamics. Herbage chemical composition was minimally affected by time of allocation, but daily mean ammonia concentrations were greater for the PM group. The 24-h pattern of ruminal fermentation (i.e. time of sampling relative to time of allocation), however, varied considerably for all fermentation variables (P⩽0.001). Most notably amongst ruminal fermentation characteristics, ammonia concentrations showed a substantial temporal variation; concentrations of ammonia were 1.7-, 2.0- and 2.2-fold greater in rumens of PM wethers at 4, 6 and 8h after allocation, respectively, compared with AM wethers. The relative abundances of archaeal and ciliate protozoal taxa were similar across allocation groups. In contrast, the relative abundances of members of the rumen bacterial community, like Prevotella 1 (P=0.04), Bacteroidales RF16 group (P=0.005) and Fibrobacter spp. (P=0.008) were greater for the AM group, whereas the relative abundance of Kandleria spp. was greater (P=0.04) for the PM group. Of these taxa, only Prevotella 1 (P=0.04) and Kandleria (P<0.001) showed a significant interaction between time of allocation and time of sampling relative to feed allocation. Relative abundances of Prevotella 1 were greater at 2h (P=0.05), 4h (P=0.003) and 6h (P=0.01) after AM allocation of new herbage, whereas relative abundances of Kandleria were greater at 2h (P=0.003) and 4h (P<0.001) after PM allocation. The early post-allocation rise in ammonia concentrations in PM rumens occurred simultaneously with sharp increases in the relative abundance of Kandleria spp. and with a decline in the relative abundance of Prevotella. All measures of fermentation and most microbial community composition data showed highly dynamic changes in concentrations and genus abundances, respectively, with substantial temporal changes occurring within the first 8h of allocating a new strip of herbage. The dynamic changes in the relative abundances of certain bacterial groups, in synchrony with a substantial diurnal variation in ammonia concentrations, has potential effects on the efficiency by which N is utilised by the grazing ruminant.