Biology subjects

Ijaz, U. Z.

Publications and source records attributed to Ijaz, U. Z..

At least 19 recordsLinked to original sources

bioRxiv2024

Impact of commercial gut health interventions on caecal metagenome and broiler performance

BackgroundMaintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores as control against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use. ResultsUsing a binning strategy, 84 ([≥]75% completeness, [≤] 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European Poultry Efficiency Factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of Probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected abundance of microbial enzymes relating to carbohydrate and protein digestion, and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria including Rikenella microfusus and UBA7160 species. ConclusionsAll GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health.

microbiology↗

bioRxiv2023

Disease Resistance correlates with Core Microbiome Diversity in Cotton

Understanding the resident microbial communities and their above and below ground interactions with plants will provide necessary information for crop disease protection and stress management. In this study, we show how diversity of core microbiome varies with disease susceptibility of a crop. To test this hypothesis, we have focused on identifying the core microbial species of Cotton Leaf Curl Disease (CLCuD) susceptible Gossypium hirsutum and CLCuD resistant Gossypium arboreum under viral infestation. Derivation of core membership is challenging as it depends on an occupancy threshold of microbial species in a sampling pool, whilst accounting for different plant compartments. We have used an abundance-occupancy distribution approach where we dynamically assess the threshold for core membership, whilst marginalizing for occupancy in four compartments of the cotton plant, namely, leaf epiphyte, leaf endophyte, rhizosphere, and root endophyte. Additionally, we also fit a neutral model to the returned core species to split them into three groups, those that are neutral, those that are selected by the plant environment, and finally those that are dispersal limited. We have found strong inverse relationship between diversity of core microbiome and disease susceptibility. A deeper understanding of this association will aid in the development of biocontrol agents for improving plant immunity against biotrophic pathogens.

microbiology↗

bioRxiv2023

Balancing the scales: Impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities

Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome is unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: i) crop yields; ii) disease development (blackleg/common scab); and iii) soil microbial community dynamics. We used stocks of seed potatoes with varying Pectobacterium levels (Jelly [high load], Jelly [low load], and Estima [Zero - no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and harvest and advanced bioinformatic analyses were used to correlate microbes to treatments and disease symptoms. Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22-34%) but not in the zero stock (2-6%). Not irrigating increased common scab symptoms (2-5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea, and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted Anaerolinea as highly associated with blackleg symptoms in the field. We conclude that Pectobacterium pathogen load within seed stocks could have more substantial effects on soil communities than irrigation regimes.

microbiology↗

bioRxiv2023

Cotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated with Gossypium arboreum

The failure of breeding strategies has caused scientists to shift to other means where the new approach involves exploring the microbiome to modulate plant defense mechanisms against CLCuD. The cotton microbiome of CLCuD-resistant varieties may harbor a multitude of bacterial genera that significantly contribute to disease resistance and provide information on metabolic pathways that differ between the susceptible and resistant varieties. The current study aimed to explore the microbiome of CLCuD-susceptible Gossypium hirsutum and CLCuD-resistant Gossypium arboreum. Microbial community surveys performed using 16S rRNA gene amplification revealed that Pseudomonas inhabited the rhizosphere while Bacillus was predominantly found in the phyllosphere of CLCuV-tolerant G. arboreum. The study was done for the leaf endophyte, leaf epiphyte, rhizosphere, and root endophyte of the two cotton species. Furthermore, our disease incidence assay using pot experiments has revealed mechanistic insights through salicylic acid-producing Serratia spp. and Fictibacillus spp. isolated from CLCuD-resistant G. arboreum, which exhibited viral disease suppression and induced systemic resistance in CLCuD susceptible G. hirsutum.

plant biology↗

bioRxiv2023

intI1 primer selection for class 1 integron integrase gene and transcript quantification - validation and application for monitoring intl1 gene abundance within septic tanks in Thailand

Antimicrobial resistance (AMR) poses serious global public health threat and wastewater treatment (WWT), including septic tanks, are a significant source of AMR genes to the environment. Environmental monitoring of broad-range AMR genes remains a challenge. The class-1 integron-integrase (intI1) gene has been proposed as a proxy for overall AMR abundance, but there is no consensus on the qPCR primer set to use. A systematic review of the literature found 65 primer sets. The coverage and specificity of each, including newly designed MGB-TaqMan primer-probe, was evaluated against a database of clinical and environmental intl1, intl1-like and non-intl1 sequences. Three primer sets were selected, laboratory validated for DNA and mRNA quantification and used to quantity intl1 gene abundance from household and healthcare conventional septic tanks (CST) and novel household Solar Septic Tanks (SST) in Thailand. Specificity of the intl1 septic tank amplicons showed that no primer set could distinguish between intl1 and intl-1 like sequences. Each primer set showed the same trends across septic tanks, with highest gene abundance in influent>sludge>effluent. There was no statistical difference between the same sample quantified by the three primer sets. However, when comparing gene abundances from the same primer set across septic tanks, statistical differences between different sample types were observed for one primer set but not the others. This may lead to different interpretation of risk associated with each reactor in spreading intl1 to the environment. Comparing reactor types, intI1 abundance in the effluent was lowest in the SST-household<CST-household<CST-healthcare. Depending on primer set used, 31 to 42% of intI1 was removed from effluent of the CST-household tank with accessible influent. Our study provided insight into the importance of intl1 primer choice. We propose the use of the validated set (F3-R3) for optimal intI1 quantification and towards the goal of achieving standardisation across environmental studies.

molecular biology↗

bioRxiv2023

CViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

We have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The software provides a single platform to give statistical inference, and employs algorithms, some borrowed from numerical ecology literature to allow exploratory as well as hypothesis driven analyses. The end product is a highly interactive toolkit with multiple document interface, that makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant hypotheses. As a proof-of-concept, we have used CViewer to explore two distinct metagenomics datasets: a dietary intervention study to understand Crohns disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean.

bioinformatics↗

bioRxiv2022

Cross-sectional study of antimicrobial resistance and ecology in gastrointestinal and oral microbial communities of urban Pakistani adults

Background and AimsAntimicrobial resistance (AMR) is one of the most serious global public health threats affecting lower-middle-income countries (LMICs) due to lack of awareness, inadequate healthcare and sanitation infrastructure, plus other environmental factors. In this study, we aimed to link microbial assembly and covariates (body mass index, smoking, use of antibiotics) to gut microbiome structure and correlate AMR gene prevalence. MethodsWe examined the gastrointestinal and oral microbial profiles of healthy adults in Pakistan through 16S rRNA gene sequencing with a focus on different ethnicities, antibiotic usage, drinking water type, smoking, and other demographic measures. We then utilised a suite of innovative statistical tools, driven by numerical ecology and machine learning, to address the above aims. ResultsWe observed tap water as the main contributor for development of AMR in the Pakistani cohort. In addition, microbial niche breadth analysis based on null modelling procedures highlighted an aberrant gut microbial signature of smokers with increased age. ConclusionsDrinking water plays a more important role in AMR spread in Pakistan rather than other factors considered. Moreover, covariates such as smoking, and age impact the human microbial community structure in this Pakistani cohort. To the best of our knowledge, this is one of the first studies that provide a snapshot of the microbiomes of healthy individuals in Pakistan and considers AMR profiles with an emphasis on potential sources of AMR prevalence. Background and ContextPakistan is categorized as a low-and-middle-income country by the World Bank where misuse of antibiotics is widespread, and multidrug resistance is prevalent. Thus, it is imperative that we understand antimicrobial resistance and the drivers of human microbiomes in Pakistan. New FindingsIn a healthy Pakistani cohort, individuals that consumed Tap Water had almost 6-fold more associations with AMRs. Therefore, drinking water source could be a strong driver in the spread of AMR. LimitationsA limitation is the use of predictive functional profiles. However, shotgun metagenomics may be prohibitively costly for LMICs given the urgent need for AMR surveillance. Clinical Research RelevanceOur research shows strong associations of key microbial taxa with covariates such as age, BMI, and gender. Additionally, we show correlations between specific outlier taxa that are present both in the gut and oral communities, highlighting potential future feasibility for use of the oral microbiome as a proxy to gut dysbiosis in some cases. Basic Research RelevanceWe have applied recent advancements in analytical tools to link both AMR prevalence and human microbiome composition with factors such as age, BMI, gender, ethnicity, smoking status, use of antibiotics, and drinking water source. Additionally, we use null modelling to show that the microbial communities are subject to strong environmental pressure and dispersal limitation. Lay SummaryWe analysed gut and oral microbes from healthy individuals in Pakistan and found that the potential for antibiotic resistance was increased in those who drank tap water.

microbiology↗

bioRxiv2021

Microbiomes in drinking water treatment and distribution: a critical review and meta-analysis from source to tap

A meta-analysis of existing and available Illumina 16S rRNA datasets from drinking water source, treatment and drinking water distribution systems (DWDS) were collated to compare changes in abundance and diversity throughout. Samples from bulk water and biofilm were used to assess principles governing microbial community assembly and the value of amplicon sequencing to water utilities. Individual phyla relationships were explored to identify competitive or synergistic factors governing DWDS microbiomes. The relative importance of stochasticity in the assembly of the DWDS microbiome was considered to identify the significance of source and treatment in determining communities in DWDS. Treatment of water significantly reduces overall species abundance and richness, with chlorination of water providing the most impact to individual taxa relationships. The assembly of microbial communities in the bulk water of the source, primary treatment process and DWDS is governed by more stochastic processes, as is the DWDS biofilm. DWDS biofilm is significantly different from bulk water in terms of local contribution to beta diversity, type and abundance of taxa present. Water immediately post chlorination has a more deterministic microbial assembly, highlighting the significance of this process in changing the microbiome, although elevated levels of stochasticity in DWDS samples suggest that this may not be the case at customer taps. 16S rRNA sequencing is becoming more routine, and may have several uses for water utilities, including: detection and risk assessment of potential pathogens such as those within the genera of Legionella and Mycobacterium; assessing the risk of nitrification in DWDS; providing improved indicators of process performance and monitoring for significant changes in the microbial community to detect contamination. Combining this with quantitative methods like flow cytometry will allow a greater depth of understanding of the DWDS microbiome.

microbiology↗

bioRxiv2021

Deploying an in vitro gut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-Mos(R) on the Atlantic salmon (Salmo salar) gut microbiome.

Mannose-oligosaccharide (MOS) pre-biotics are widely deployed in animal agriculture as immunomodulators as well as to enhance growth and gut health. Their mode of action is thought to be mediated through their impact on host microbial communities and the associated metabolism. Bio-Mos is a commercially available pre-biotic currently used in the agri-feed industry. To assess Bio-Mos for potential use as a prebiotic growth promotor in salmonid aquaculture, we have modified an established Atlantic salmon in vitro gut model, SalmoSim, to evaluate its impact on the host microbial communities. Inoculated from biological triplicates of adult farmed salmon pyloric caeca compartments, the microbial communities were stabilised in SalmoSim followed by a twenty-day exposure to the prebiotic and in turn followed by an eight day wash out period. Dietary inclusion of MOS resulted in a significant increase in formate (p=0.001), propionate (p=0.037) and isovalerate (p=0.024) levels, correlated with increased abundances of several, principally, anaerobic microbial genera (Fusobacterium, Agarivorans, Pseudoalteromonas). DNA metabarcoding with the 16S rDNA marker confirmed a significant shift in microbial community composition in response to MOS supplementation with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggests that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to augment in vivo trials of microbiome modulators. ImportanceIn this paper we report the results of the impact of prebiotic (MOS supplementation) on microbial communities within recently developed Atlantic salmon gut microbiome in vitro simulator. Our data suggest that Bio-Mos may be of value in salmonid production as it enhances volatile fatty acid production in the Atlantic salmon gut and correlates with a significant shift in microbial community composition with observed increase in lactic acid producing Carnobacterium. In conjunction with previous in vivo studies linking enhanced volatile fatty acid production alongside MOS supplementation to host growth and performance, our data suggest that Bio-Mos may be of value in salmonid production. Furthermore, our data highlights the potential role of in vitro gut models to augment in vivo trials of microbiome modulators.

bioengineering↗

bioRxiv2021

ASSEMBLY AND DYNAMICS OF MICROBIAL COMMUNITIES IN GRANULAR, FIXED-BIOFILM AND PLANKTONIC METHANOGENIC MICROBIOMES VALORIZING LONG CHAIN FATTY ACID (LCFA)-RICH WASTEWATER

Distinct microbial assemblages are engineered in anaerobic digestion (AD) reactors to drive sequential conversions of organics to methane. The spatio-temporal development of three such assemblages (granules, biofilms, planktonic) derived from the same inoculum was studied in replicated bioreactors treating long-chain fatty acids (LCFA)-rich wastewater at 20{degrees}C at hydraulic retention times (HRTs) of 12-72 h. We found granular, biofilm and planktonic assemblages differentiated by diversity, structure, and assembly mechanisms; demonstrating a spatial compartmentalisation of the microbiomes from the initial community reservoir. Our analysis linked abundant Methanosaeta and Syntrophaceae-affiliated taxa (Syntrophus and uncultured) to their putative, active roles in syntrophic LCFA bioconversion. LCFA loading rates (stearate, palmitate), and HRT, were significant drivers shaping microbial community dynamics and assembly. This study of the archaea and syntrophic bacteria actively valorising LCFAs at short HRTs and 20{degrees}C will help uncover the microbiology underpinning anaerobic bioconversions of fats, oil and grease. HighlightsO_LIGranular, biofilm and planktonic assemblages developed from the same seed reservoir C_LIO_LIThree assemblages forming metacommunity differed in diversity and composition C_LIO_LIMultiple null models applied to quantify deterministic and stochastic mechanisms C_LIO_LIDominant, active role of acetoclastic Methanosaeta confirmed in granules and biofilm C_LIO_LIDynamic, non-core-microbiome taxa correlated with environmental variables C_LI

microbiology↗

bioRxiv2020

Use of null models to compare the assembly of northeast Atlantic bacterial community in the presence of crude oil with either chemical dispersant or biosurfactant

The compositions of marine microbial communities in response to crude oil in the presence of biosurfactant or synthetic dispersants have been extensively studied in the last decade. Assembly processes, however, in such communities are poorly understood. In this study, we used seven different but complementing null model approaches, such as elements of metacommunity structure, Raup-Crick beta-diversity, normalised stochasticity ratio, Tuckers null model, quantitative process estimates, lottery assembly, and phylogenetic dispersion models, to quantify the relative importance of ecological process that drive the community assembly. We found that the presence of chemical dispersant in the oil-amended microcosms induced significant temporal changes in the assembly processes that were different from the oil-only or biogenic dispersant-amended microcosms. The assembly processes in all microcosms were neither purely deterministic nor stochastic, but increasingly deterministic in dispersant-amended microcosms. Furthermore, the relative importance of determinisms varied over time and was strongest during the middle phase of incubation. Tuckers null model revealed that phylogenetically distinct taxa might have shaped the bacterial community assembly in the different microcosms towards more niche or neutral processes. Moreover, there was faster recruitment of phylogenetically distant species in the dispersant-amended community. Drift, homogenising selection and dispersal limitation were the dominant assembly processes in all microcosms, but variable selection was only important in dispersant-amended microcosms. In conclusion, our study highlights that the assembly processes in marine bacterial communities are not static but rather dynamic, and the chemical dispersant can cause significantly different patterns of community assembly compared to non-amended or biosurfactant-amended microcosms. ImportanceThe null model strategy is designed to intentionally exclude an ecological or evolutionary process of interest and create a beta diversity pattern that would be expected in the absence of this particular process - i.e. the community structure is random in respect to the process being tested. Recent advancements of bioinformatics and statistical tools have made it possible to apply theoretical macroecological concepts to microbial metagenomics in order to better understand and quantify the mechanisms and patterns controlling the complexity of microbial ecology. The conclusions from the null models can help predict the changes in microbial biodiversity and ecosystem services in oil polluted environments and therefore assist in making effective decisions with regards to what would be the best oil spill response option for similar environmental conditions.

ecology↗

bioRxiv2020

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants.

BackgroundAlthough synthetic dispersants are effective in dispersing crude oil, they can alter the natural microbial response to oil and potentially hinder its biodegradation. Biosurfactants, however, are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. This study investigated the microbial community dynamics, ecological drivers, functional diversity, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52. ResultsWe found the microbial community composition and diversity were markedly different in the rhamnolipid-amended treatment compared to that with Finasol, with key aromatic hydrocarbon-degrading bacteria like Cycloclasticus being suppressed in the Finasol treatment but not in oil-only and rhamnolipid-amended treatments. Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment and Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Vibrio abundance increased substantially in treatments receiving Finasol, suggesting a potentially important role for these organisms in degrading dispersant components. In fact, Finasol was linked with a negative impact on alpha diversity. Deterministic environmental filtering played a dominant role in regulating the community assembly in all treatments but was strongest in the dispersant-amended treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment. ConclusionOverall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants affect the natural marine microbial community, supporting their potential application in oil spills.

genomics↗

bioRxiv2020

Deploying and in vitro gut model to assay the impact of a mannan-oligosaccharide prebiotic, Bio-MOS(R) on the Atlantic salmon (Salmo salar) gut microbiome.

microbiology↗

bioRxiv2020

Development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities: SalmoSim

Atlantic salmon are a species of major economic importance. Intense innovation is underway to improve salmon feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the industry. Several gut models targeted at monogastric vertebrates are now in operation. Here we report progress in the development of an Atlantic salmon in vitro gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum and mid gut) and associated microbial communities. The artificial gut model was established in a series of linked bioreactors seeded with biological material derived for adult marine phase salmon. In biological triplicate, the response of the in vitro system to two distinct dietary formulations (fish meal and fish meal free) was compared to a parallel in vivo trial over forty days. 16S rDNA sequencing, qPCR, ammoniacal nitrogen and volatile fatty acid measurements were undertaken to survey microbial community dynamics and function. SalmoSim communities were indistinguishable (p=0.230) from their founding inocula at 20 days and most abundant genera (e.g. Psycrobacter, Staphylococcus, Pseudomonas) proliferated the in vitro system. Real salmon and SalmoSim responded similarly to the introduction of the novel feed, with most taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa was affected non-identically across both systems. Consistent with a low impact of the novel feed on microbial community function, VFA profiles were not significantly different in SalmoSim pre and post the switch feed. This study represents an important first-step in the development of an in vitro gut system as a tool for the improvement of salmon nutrition.

microbiology↗

bioRxiv2020

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae.

BackgroundAquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod (Gadus morhua) is modest in comparison to market demand. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack (Ascophyllum nodosum) or sea lettuce (Ulva rigida) macroalgae in a 12-week trial. ResultsThe results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the U. rigida supplemented fish group and the control group at any time-point. This contrasts with the A. nodosum treatment. Fish within this group were further categorised as either Normal or Lower Growth. Lower Growth individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders Vibrionales (Vibrio and Photobacterium), Bacteroidales (Bacteroidetes and Macellibacteroides) and Clostridiales (Lachnoclostridium). ConclusionsOur study indicates that U. rigida macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of A. nodosum is not a suitable feed supplement in a farmed cod diet.

microbiology↗

bioRxiv2020

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter

BackgroundThe factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems Normal (N), Higher Welfare (HW) and Omega-3 Higher Welfare (O) were investigated "in a natural environment" at day 7 and day 30 with a range of extrinsic parameters assessing performance in correlation with microbial dynamics and Campylobacter presence. ResultsOur data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems, that affect feed utilisation, advance our knowledge of mechanistic underpinnings, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain. ConclusionsOverall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/084251v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@c43951org.highwire.dtl.DTLVardef@8efa5corg.highwire.dtl.DTLVardef@d6db70org.highwire.dtl.DTLVardef@1e09fb9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment or Helicobacter pylori infection

Although long thought to be a sterile and inhospitable environment, the stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of orally administered drugs such as Proton Pump Inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the commensal bacteria re-organize, due to these perturbations of the gastric environment, are in the early phase. They mainly focus on the most prevalent taxa and rely on linear techniques for multivariate analysis. Here we disclose the importance of complementing linear dimensionality reduction techniques such as Principal Component Analysis and Multidimensional Scaling with nonlinear approaches derived from the physics of complex systems. Then, we show the importance to complete multivariate pattern analysis with differential network analysis, to reveal mechanisms of re-organizations which emerge from combinatorial microbial variations induced by a medical treatment (PPIs) or an infectious state (H. pylori).

systems biology↗

bioRxiv2020

Reverse transcriptase enzyme and priming strategy affect quantification and diversity of environmental transcripts

RT-Q-PCR, and RT-PCR amplicon sequencing, provide a convenient, target-specific, high-sensitivity approach for gene expression studies and are widely used in environmental microbiology. Yet, the effectiveness and reproducibility of the reverse transcription step has not been evaluated. Therefore, we tested a combination of four commercial reverse transcriptases with two priming techniques to faithfully transcribe 16S rRNA and amoA transcripts from marine sediments. Both enzyme and priming strategy greatly affected quantification of the exact same target with differences of up to 600-fold. Furthermore, the choice of RT system significantly changed the communities recovered. For 16S rRNA, both enzyme and priming had a significant effect with enzyme having a stronger impact than priming. Inversely, for amoA only the change in priming strategy resulted in significant differences between the same sample. Specifically, more OTUs and better coverage of amoA transcripts diversity were obtained with GS priming indicating this approach was better at recovering the diversity of amoA transcripts. Moreover, sequencing of RNA mock communities revealed that, even though transcript diversities (i.e. OTU counts within a sample) can be biased by the RT, the comparison of {beta} diversities (i.e. differences in OTU counts between samples) is reliable as those biases are reproducible between environments. Originality-Significance StatementIs the complementary DNA (cDNA) produced after Reverse Transcription (RT) a faithful representation of the starting RNA? This is a fundamental and important question for transcriptomic-based studies in environmental microbiology that aim to quantify and/or examine the diversity of transcripts via RT approaches. Yet little is known about the reliability and reproducibility of this step. Here, we evaluated the effect of the two main components of the RT reaction - the retro transcriptase enzyme and priming strategy (gene specific vs random priming), on the quantification and diversity of cDNA. We found that both have a significant impact. We further provide evidence to enable informed choices as to the enzyme and priming combinations to improve the performance of RT-PCR approaches. Taken together, this work will improve the reliability and reproducibility of transcript-based studies in environmental microbiology.

molecular biology↗