Changes In Relative Abundance Research Articles

Gut microbiota plays a predominant role in affecting hypolipidemic effect of Deacetylated Konjac Glucomannan (Da-KGM)

The mechanism of Da-KGM showed poorer hypolipidemic effect, has not elucidated in previous study. Here, we performed hyperlipidemic hamsters administrated with 6% KGM (Konjac Glucomannan) and Da-KGM respectively to evaluate different underlying mechanisms. Poorer lipid-lowering effect was shown with Da-KGM treatment, and marked changes in relative abundance of Aldercreutzia and Parasutterella were not detected as KGM. Meanwhile, significant alteration of Ileibacterium was observed between KGM and Da-KGM group. Moreover, pathway of primary bile acids synthesis was enriched in cecal metabolites. KGM, not Da-KGM, remarkably increased concentration of Glycocholic acid (GCA) and Ursodeoxycholic acid (UDCA), which were negatively corrected with Ileibacterium. Marked increases in ileal Farnesoid X receptor (FXR) and hepatic Cholesterol 7α-hydroxylase (CYP7A1) were observed in KGM group, along with strong reduction of ileal Multi-drug resistance-associated protein2 (MRP2/ABCC2) and hepatic FXR expression, but not in Da-KGM group. There were no obvious changes in serum lipid level and bile acids, as well as gene expression after antibiotic treatment. Our results revealed that different hypolipidemic effects of KGM and Da-KGM might be associated with gut microbiota and bile acids metabolism.

Characterisation of faecal microbiota in horses medicated with oral doxycycline hyclate.

Antimicrobial-associated diarrhoea is a common adverse effect of antimicrobial treatment in horses and has been reported following the administration of oral doxycycline. The administration of antimicrobials has also been associated with changes in the equine intestinal microbiota diversity yet has not been explored under doxycycline treatment. To describe the dynamics of the faecal microbial diversity following a 5-day oral administration of doxycycline in healthy horses with Streptococcus zooepidemicus infected tissue chambers. Experimental prospective cohort study in a single horse group. Seven healthy adult horses with S. zooepidemicus infected tissue chambers received oral doxycycline at 10mg/kg q 12h for 5-days following the tissue chamber inoculation. Faeces were collected prior to the tissue chamber inoculation and until 28-days post inoculation. Faecal microbiota was characterised by high throughput sequencing of the V4 region of the 16S rRNA gene on the Illumina MiSeq sequencing platform. Bioinformatic analysis was performed with Mothur and statistical analysis were conducted on R Studio. A significant decrease in alpha diversity, characterised by a decrease of richness and diversity, and a decrease in beta diversity, characterised by changes in relative abundance, occurred after initiation of and during the administration of doxycycline. A decrease in Verrucomicrobia and increase in Firmicutes:Bacteroidetes ratio occurred following the initiation of treatment, with a return to initial Firmicutes:Bacteroidetes ratio during the treatment. It took 23days after discontinuing the treatment for the faecal microbiota to return close to the initial state. Lack of control population within the study. Transitory intestinal dysbiosis occurs under oral administration of doxycycline in horses.

Gut microbiome-derived glycine lipids are diet-dependent modulators of hepatic injury and atherosclerosis

Oral and gut Bacteroidetes produce unique classes of serine-glycine lipodipeptides and glycine aminolipids that signal through host Toll-like receptor 2. These glycine lipids have also been detected in human arteries, but their effects on atherosclerosis are unknown. Here, we sought to investigate the bioactivity of bacterial glycine lipids in mouse models of atherosclerosis. Lipid 654 (L654), a serine-glycine lipodipeptide species, was first tested in a high-fat diet (HFD)-fed Ldlr−/− model of atherosclerosis. Intraperitoneal administration of L654 over 7 weeks to HFD-fed Ldlr−/− mice resulted in hypocholesterolemic effects and significantly attenuated the progression of atherosclerosis. We found that L654 also reduced liver inflammatory and extracellular matrix gene expression, which may be related to inhibition of macrophage activation as demonstrated in vivo by lower major histocompatibility complex class II gene expression and confirmed in cell experiments. In addition, L654 and other bacterial glycine lipids in feces, liver, and serum were markedly reduced alongside changes in Bacteroidetes relative abundance in HFD-fed mice. Finally, we tested the bioactivities of L654 and related lipid 567 in chow-fed Apoe−/− mice, which displayed much higher fecal glycine lipids relative to HFD-fed Ldlr−/− mice. Administration of L654 or lipid 567 for 7 weeks to these mice reduced the liver injury marker alanine aminotransferase, but other effects seen in Ldlr−/− were not observed. Therefore, we conclude that conditions in which gut microbiome-derived glycine lipids are lost, such as HFD, may exacerbate the development of atherosclerosis and liver injury, whereas correction of such depletion may protect from these disorders.

Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment

ObjectivesIn hospital hygiene, it remains unclear to what extent surface contamination might represent a potential reservoir for nosocomial pathogens. This study investigates the effects of different sanitization strategies on the microbial structures and the ecological balance of the environmental microbiome in the clinical setting. MethodsThree cleaning regimes (disinfectants, detergents, and probiotics) were applied subsequently in nine independent patient rooms at a neurological ward (Charité, Berlin). Weekly sampling procedures included three different environmental sites: floor, door handle, and sink. Characterization of the environmental microbiota and detection of antibiotic resistance genes (ARGs) were performed by 16S rRNA sequencing and multiplex Taq-Man qPCR assays, respectively. ResultsOur results showed a displacement of the intrinsic environmental microbiota after probiotic sanitization, which reached statistical significance in the sink samples (median 16S-rRNA copies = 138.3; IQR: 24.38–379.5) when compared to traditional disinfection measures (median 16S rRNA copies = 1343; IQR: 330.9–9479; p < 0.05). This effect was concomitant with a significant increase in the alpha-diversity metrics in both the floor (p < 0.001) and the sink samples (p < 0.01) during the probiotic strategy. We did not observe a sanitization-dependent change in relative pathogen abundance at any tested site, but there was a significant reduction in the total ARG counts in the sink samples during probiotic cleaning (mean ARGs/sample: 0.095 ± 0.067) when compared to the disinfection strategy (mean ARGs/sample: 0.386 ± 0.116; p < 0.01). DiscussionThe data presented in this study suggest that probiotic sanitization is an interesting strategy in hospital hygiene management to be further analyzed and validated in randomized clinical studies.

PTITAN2: Permutation of treatment labels and Threshold Indicator Taxa ANalysis

Background: Taxa Indicator Threshold ANalysis (TITAN) was developed to identify thresholds along environmental gradients where rapid changes in taxa frequency and relative abundance are observed. TITAN determines separate change-points for increasing and decreasing taxa in aggregate, as well as change-points for individual taxa, with associated confidence intervals generated using bootstrapping. However, if TITAN is applied to different classes of observations, additional analyses besides using non-overlapping confidence intervals are needed to establish whether change-points differ between treatments or groups because non-overlapping confidence intervals can indicate significant differences but overlapping confidence intervals do not necessarily mean the null hypothesis cannot be rejected. Methods: To address this, we present a new R package, pTITAN2, which is an extension to the existing TITAN2 package. The pTITAN2 package was developed to enable comparisons of TITAN output between treatments by permutating the observed data between treatments and rerunning TITAN on the permuted data. Results: The pTITAN2 package includes two functions, occurrences and permute. The occurrences function selects the taxonomic codes to be used in a TITAN run while maintaining the most taxonomic details. The permute function is then used to create a list of permuted sets of taxa and environmental gradients. TITAN is then run again on the permuted data and p-value test can be calculated using the observed and permuted TITAN output to test for statistical differences between treatment effects. Conclusions: The package pTITAN2 is an extension of the existing TITAN2 package and enables users to perform the appropriate statistical tests and determine statistical differences without using overlapping confidence intervals.

Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection?

Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host’s innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.

Comparison of feeding value, ruminal fermentation and bacterial community of a diet comprised of various corn silages or combination with wheat straw in finishing beef cattle

Corn silage is an important feedstuff for cattle because of the joint provision of starch and physical effective fiber and its palatability. However, the whole plant corn silage is underproduced in some regions until today and could not be popularized in beef cattle raising. The objective of this study was to compare the feeding value, ruminal fermentation and bacterial community of a diet comprised of various corn silages or combination with wheat straw in finishing beef cattle. One hundred eighty Simmental crossbred steers were blocked (60 steers/block) on the basis of initial BW. The animals were randomly assigned to 1 of 12 identical research pens (4 pens/block; 15 steers/pen), where each of the 4 research diets was assigned to 1 pen within each block as follows: (1) the whole plant corn silage-based diet was used as the control diet (WPCS), (2) the mixed forages-based diet was formulated by replacing a portion of whole plant corn silage with wheat straw (WPCSW), (3) the corn stalklage-based diet (CS), and (4) the sweet corn stalklage-based diet (SCS). The four diets were formulated to be isonitrogenous and isoenergetic with same forage to concentrate ratio. Experimental diets were fed for 90 d; a diet digestibility trial was conducted at the end of this period. There were no effects (P = 0.596) of treatment on dry matter intake, but average daily gain was greater for steers offered the WPCS diet, intermediate with WPCSW and SCS and lowest with CS (P < 0.001). Dry matter digestibility was greater (P = 0.005) for WPCS and SCS diets than for WPCSW and CS diets. The nutrients digestibility of CS was less than observed for WPCS diet (P < 0.05). The concentrations of ruminal volatile fatty acids were highest for WPCS diet, intermediate with WPCSW diet and lowest with SCS and CS diets (P < 0.001). Diets treatment had no effect on the α-diversity of rumen bacteria in steers (P > 0.05), but only caused the change of relative abundance of Ruminococcaceae and Prevotellaceae (P = 0.036 and 0.037, respectively). In conclusion, the WPCS-based diet exhibited the highest feeding value. The SCS and WPCSW offered suitable alternatives to a WPCS based diet offered to beef cattle, with limited negative influence on growth, apparent digestibility of nutrients and ruminal bacterial microbiota. In contrast, the value of a CS-based diet was relatively poor. However, it may still be economical to substitute WPCS with relative low-quality corn silage in feedlot cattle diets.

Developing a Targeted Quantitative Strategy for Sulfoxide-Containing MS-Cleavable Cross-Linked Peptides to Probe Conformational Dynamics of Protein Complexes.

In recent years, cross-linking mass spectrometry (XL-MS) has made enormous strides as a technology for probing protein-protein interactions (PPIs) and elucidating architectures of multisubunit assemblies. To define conformational and interaction dynamics of protein complexes under different physiological conditions, various quantitative cross-linking mass spectrometry (QXL-MS) strategies based on stable isotope labeling have been developed. These QXL-MS approaches have effectively allowed comparative analysis of cross-links to determine their relative abundance changes at global scales. Although successful, it remains challenging to consistently obtain quantitative measurements on low-abundant cross-links. Therefore, targeted QXL-MS is needed to enable MS "Western" analysis of cross-links to enhance sensitivity and reliability in quantitation. To this end, we have established a robust parallel reaction monitoring (PRM)-based targeted QXL-MS platform using sulfoxide-containing MS-cleavable cross-linker disuccinimidyl sulfoxide (DSSO), permitting label-free comparative analysis of selected cross-links across multiple samples. In addition, we have applied this methodology to study phosphorylation-dependent conformational dynamics of the human 26S proteasome. The PRM-based targeted QXL-MS analytical platform described here is applicable for all sulfoxide-containing MS-cleavable cross-linkers and can be directly adopted for comparative studies of protein-protein interactions in various cellular contexts.

Similar zooplankton responses to low pH and calcium may impair long-term recovery from acidification.

Throughout much of the 20th century, unprecedented industrial emissions have led to widespread acidification of regions in North America and Europe and, as lake water pH dropped, aquatic ecosystems have experienced dramatic declines in biodiversity. International emission-control agreements have led to sweeping increases in lake pH, however acid-structured zooplankton communities still persist in many lakes. Concomitantly, calcium concentrations have been declining as a legacy of acidification and are approaching or have reached concentrations that could represent a barrier to the re-establishment of zooplankton communities similar to those in non-acidified or circumneutral reference lakes. To understand how declining calcium may influence the re-establishment of zooplankton in acid-damaged lakes we manipulated calcium and pH using a factorial in-lake mesocosm experiment and assessed their individual and combined effects on a regionally diverse zooplankton assemblage. We found that the impacts of low calcium on zooplankton species were similar to those of acidification and, consequently, may prevent the recovery of acid-structured communities. Abundance of the larger bodied and acid-sensitive Daphnia pulex/pulicaria increased in high pH treatments, albeit nonsignificantly yet, by the end of our experiment, only two individuals were sampled among our 10 low calcium enclosures. In contrast, small acid-tolerant cladocerans, such as Daphnia catawba, Daphnia ambigua, and eubosminids maintained significantly higher abundances in low calcium treatments relative to all other treatment combinations. Although we did not detect an effect of calcium on mean body size, the disproportionately high abundance of small cladocerans in low calcium treatments resulted in low calcium communities with higher overall abundance and lower cladoceran evenness. Our results, along with a landscape comparison demonstrating parallel changes in zooplankton relative abundance from 34 historically acidified lakes, suggests that declining calcium will be an important, on-going factor that may limit the recovery of zooplankton, despite regional improvements in lake pH.

Nitrogen enrichment and warming shift community functional composition via distinct mechanisms: The role of intraspecific trait variability and species turnover

Abstract Global change factors may shift community functional composition by driving species turnover (species occurrence and species relative abundance) and intraspecific trait variability. However, their relative contribution in determining the functional response of community to global change, especially nitrogen enrichment and warming, remains unclear. We conducted a fully factorial field experiment in a Tibetan alpine meadow to examine the responses of plant community functional composition to nitrogen enrichment and warming by quantifying seven plant functional traits in each plot. Using the sum of squares decomposition, we further disentangled the relative contribution of intraspecific trait variability and species turnover to changes in community functional composition. We found that nitrogen enrichment caused a shift of plant community towards a more resource‐acquisitive strategy, while warming resulted in a shift towards a more resource‐conservative strategy. Plant intraspecific trait variability controls shifts in community functional composition in response to nitrogen enrichment, whereas species turnover (especially change in species relative abundance) mainly explains warming‐induced shifts. Nitrogen enrichment and warming did not show significant interactive effects on plant functional composition. These findings suggest that nitrogen enrichment and warming can alter community functional composition of alpine meadow through distinct mechanisms. Plant intraspecific trait variability confers functional resilience of Tibetan alpine meadows under nitrogen enrichment, but warming could induce significant turnover of species that pronouncedly impacts community functioning in this highland ecosystem. Read the free Plain Language Summary for this article on the Journal blog.

Biogeography and habitat preferences of red wood ants of the Formica rufa group (Hymenoptera: Formicidae) in Finland, based on citizen science data

Red wood ants (RWA) of the Formica rufa group are ecosystem engineers and important species in boreal and temperate forests. However, the permanent and temporal loss of forest habitats is a serious threat to their existence and is likely to increase with climate change. Due to the current threat of losing species, quick actions are needed. Reported here is the biogeography, relative abundance and habitat preferences of five species of RWA in Finland based on citizen science data. Species that occur in the lowlands of the Alps also occur throughout the southern parts of Finland. Only two of the five species, F. aquilonia Yarrow, 1955 and F. lugubris Zetterstedt, 1838, were common throughout the country, including northern Lapland. As their name suggests, RWAs occur mostly in forests and forest edges, but they also sometimes inhabit open or semi-open yards, mires and meadows. The most forest-specialist species is F. aquilonia and the least F. rufa Linnaeus, 1761. Surprisingly, the meadow wood ant F. pratensis Retzius, 1783 is the second most forest dwelling species, however, its preference for forest edges is clearly higher than for forest interiors. Based on current data, F. rufa may be the most tolerant of living close to buildings as its relative abundance in yards was much higher than that of the other species. The data obtained on distributions and relative abundances could be compared in the future with the results of similar surveys to detect changes in species distributions, relative abundances and habitat preferences.

An assessment of gears for sampling shovelnose sturgeon in tributaries

Despite potential importance of tributaries to Shovelnose sturgeon populations and historical declines range wide, limited population demographic and sampling efficiency information exists on shovelnose sturgeon populations in tributaries of the Upper Mississippi River. As such, we sought to evaluate the catch statistics of boat electrofishing, drifted trammel netting, and otter trawling for assessing shovelnose sturgeon populations on the Cedar River in Iowa. Trammel nets did not provide the highest estimate of CPUE or number of fish captured, however did provide the lowest CV of CPUE and thus required the least amount of effort needed to detect changes in relative abundance. Trammel netting also captured the widest size range of fish and most proportionate male:female ratio. If goals were to evaluate trends in relative abundance, male:female ratio, and spawning periodicity of females with the least amount of effort, trammel nets appear to be best suited. However, when sampling objectives require a large number of fish to be collected, the use of multiple gears may be appropriate. Our study highlights the need for an adaptive multi-gear sampling approach to properly evaluate shovelnose sturgeon in tributaries across the Upper Mississippi River.

Alterations and Prediction of Functional Profiles of Gut Microbiota After Fecal Microbiota Transplantation for Iranian Recurrent Clostridioides difficile Infection with Underlying Inflammatory Bowel Disease: A Pilot Study.

Background and PurposeFecal microbiota transplantation (FMT) has emerged for the therapeutic treatment of recurrent Clostridioides difficile infection (rCDI) with concurrent inflammatory bowel disease (IBD). As the first Iranian population cohort, we examined how gut microbiota and their functional profiles change in Iranian rCDI patients with underlying IBD before and after FMT.Patients and MethodsFMT was performed to eight IBD patients via colonoscopy. Profiles of gut microbiota from donors and recipients were investigated using 16S rRNA gene sequence analysis.ResultsPatients experienced no IBD flare-ups or other adverse effects, and all recovered to full health. Moreover, all rCDI patients lacked the Bacteroidetes present in donor samples. After FMT, the proportion of Bacteroidetes increased until a normal range was achieved. More specifically, the relative abundance of Prevotella was found to increase significantly following FMT. Prevotella was also found to correlate negatively with inflammation metrics, suggesting that Prevotella may be a key factor for resolving CDI and IBD. Gut microbiota diversity was found to increase following FMT, while dysbiosis decreased. However, the similarity of microbial communities of host and recipients did not increase, and wide variation in the extent of donor stool engraftment indicated that the gut bacterial communities of recipients do not shift towards those of donors.ConclusionFMT leads to significant alterations of the community structure of gut bacteria in rCDI patients with IBD. The change in relative abundance of Proteobacteria and bacterial diversity indicated that FMT promotes recovery from intestinal permeability and inflammation in rCDI patients. Moreover, strong negative correlation between Prevotella and inflammation index, and decreased dysbiosis index advocate that the improvement of CDI is possibly due to gut microbiome alteration. Collectively, our findings show that FMT would be a promising therapy to help reprogram the gut microbiome of Iranian rCDI patients with IBD.

Dynamic change of fungal community in the gastrointestinal tract of growing lambs

Although fungal communities in the gastrointestinal tract have a significant role in animal health and performance, their dynamics within the tract are not well known. Thus, this study investigated fungal community dynamics in the rumen and rectum of lambs from birth to 4 mon of age by using IT1S rDNA sequencing technology together with the RandomForest approach to determine age-related changes in the fungal ecology. The results indicated that gastrointestinal fungal community composition, diversity, and abundance altered (P<0.05) with the increasing age of the lambs. Two phyla, Ascomycota and Basidiomycota, dominated the samples. Similarity within age groups of the rumen fungi increased sharply after 45 days of age, while the similarity increased (P<0.05) significantly after 60 days of age in the rectum. The age-related genera, Acremonium, Microascus, Valsonectria, Myrmecridium, Scopulariopsis, Myrothecium, Saccharomyces, and Stephanonectria, were presented in both ruminal and rectal communities, and their changes in relative abundance were consistent at both sites. The principal coordinates analysis showed significant differences (P<0.05) between the fungal communities in the rumen and rectum. Our findings demonstrate that both the age of lambs and the gastrointestinal tract region can affect the composition of these fungal communities, and this provides new insight and directions for future studies in this research area.

Changes in relative abundance of co-occurring native and alien mantids, Hierodula patellifera (Serville) and Hierodula chinensis Werner (Mantodea: Mantidae), in Hachioji City, Tokyo Metropolis

Changes in relative abundance of co-occurring native and alien mantids, Hierodula patellifera (Serville) and Hierodula chinensis Werner (Mantodea: Mantidae), in Hachioji City, Tokyo Metropolis

Power of faecal pellet count and camera trapping indices to monitor mammalian herbivore activity

Context Monitoring spatial and temporal change in relative abundance using statistically powerful designs is a critical aspect of wildlife management. Many indices of relative abundance are available, but information regarding their influence on statistical power is limited. Aims We compared the statistical power associated with occurrence-based and frequency-based indices derived from faecal pellet counts and camera trapping to detect changes in the activity of five mammalian herbivores. Methods We deployed camera traps and counted faecal pellets in native vegetation subjected to four management treatments in south-eastern Australia. We used simulation coupled with generalised linear mixed models to investigate the statistical power associated with a range of effect sizes for each combination of species, survey method and data type. Key results The index derived from camera frequency data provided the greatest statistical power to detect species’ responses and was the only index capable of detecting small effect sizes with high power. The occurrence index from camera trapping did not provide the same level of statistical power. Indices derived from faecal pellet frequency data also detected spatial and temporal changes in activity levels for some species, but large numbers of plots were required to detect medium to large effect sizes. High power to detect medium to large effects could be achieved using occurrence indices derived from pellet presence–absence data, but required larger sample sizes compared to the camera frequency index. Conclusions Both camera trapping and pellet counts can be applied to simultaneously monitor the activity of multiple mammalian herbivore species with differing activity patterns, behaviour, body size and densities, in open and closed habitat. However, using frequency indices derived from camera trapping may improve management outcomes by maximising the statistical power of monitoring programs to detect changes in abundance and habitat use. Implications Frequency indices derived from camera trapping are expected to provide the most efficient method to detect changes in abundance. Where the use of cameras is cost prohibitive, occurrence indices derived from pellet presence–absence data can be used to detect medium to large effect sizes with high power. Nonetheless, the cost-effectiveness of camera trapping will improve as equipment costs are reduced and advances in automated image recognition and processing software are made.

Diatom and Invertebrate Assemblages in High Altitude Saline Wetlands of the Argentinian Puna and their Relation to Environmental Factors

Aquatic biota in high altitude Andean wetlands is exposed to extreme environmental conditions that influence ecological parameters at population and community levels. We analyzed changes in occurrence, taxa richness and relative abundance of diatom and invertebrate assemblages in four saline wetlands located at the same altitude (approx. 3,330 masl), in the Salar de Antofalla (Catamarca, Argentina). Biological samples were taken seasonally during a 1-year period, together with water variables, which were used in ordination techniques to characterize the sites. Water ionic content and biological variables, such as microcrustacean abundance and diatom richness, were evaluated as possible factors affecting the assemblages’ distribution. The wetlands ranged from meso- to hyperhaline habitats and showed distinctive morphological, physical and chemical characteristics. Diatoms (42 taxa) and invertebrates (15 taxa) were collected from all sites, and diatom taxa richness was negatively correlated with water conductivity. According to multivariate analysis, the distribution of both communities was significantly explained by water hardness, whereas copepod abundance also influenced the diatom flora. We conclude that, at the same altitude and, consequently, UV radiation exposure, variables related to ionic content and/or biological parameters of the aquatic habitat may act as determinants of the biota distribution in these extreme environments.

Bacterial Succession during Vermicomposting of Silver Wattle (Acacia dealbata Link).

Vermicomposting is the process of organic waste degradation through interactions between earthworms and microbes. A variety of organic wastes can be vermicomposted, producing a nutrient-rich final product that can be used as a soil biofertilizer. Giving the prolific invasive nature of the Australian silver wattle Acacia dealbata Link in Europe, it is important to find alternatives for its sustainable use. However, optimization of vermicomposting needs further comprehension of the fundamental microbial processes. Here, we characterized bacterial succession during the vermicomposting of silver wattle during 56 days using the earthworm species Eisenia andrei. We observed significant differences in α- and β-diversity between fresh silver wattle (day 0) and days 14 and 28, while the bacterial community seemed more stable between days 28 and 56. Accordingly, during the first 28 days, a higher number of taxa experienced significant changes in relative abundance. A microbiome core composed of 10 amplicon sequence variants was identified during the vermicomposting of silver wattle (days 14 to 56). Finally, predicted functional profiles of genes involved in cellulose metabolism, nitrification, and salicylic acid also changed significantly during vermicomposting. This study, hence, provides detailed insights of the bacterial succession occurring during vermicomposting of the silver wattle and the characteristics of its final product as a sustainable plant biofertilizer.

A population-level strain genotyping method to study pathogen strain dynamics in human infections.

A hallmark of chronic bacterial infections is the long-term persistence of 1 or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually present. However, infection with multiple strains of a given species, strain acquisition and loss, and changes in strain relative abundance can occur. Detecting strain-level changes and their effects on disease is challenging because most methods require labor-intensive isolate-by-isolate analyses, and thus, only a few cells from large infecting populations can be examined. Here, we present a population-level method for enumerating and measuring the relative abundance of strains called population multi-locus sequence typing (PopMLST). The method exploits PCR amplification of strain-identifying polymorphic loci, next-generation sequencing to measure allelic variants, and informatic methods to determine whether variants arise from sequencing errors or low-abundance strains. These features enable PopMLST to simultaneously interrogate hundreds of bacterial cells that are cultured en masse from patient samples or are present in DNA directly extracted from clinical specimens without ex vivo culture. This method could be used to detect epidemic or super-infecting strains, facilitate understanding of strain dynamics during chronic infections, and enable studies that link strain changes to clinical outcomes.

Dynamics of microbiotic patterns reveal surface water groundwater interactions in intermittent and perennial streams

Exchange between groundwater (GW), hyporheic zone waters (HZ) and surface waters (SW) is critical for water quality, quantity, and the ecological health and functioning of all three ecosystems. Hydrological exchange is particularly important in intermittent creeks, such as in the Murray Darling Basin, Australia, where stream reaches shift from losing to gaining depending on the volume of surface flows. In this study we used hydrochemistry to identify SW-GW exchange and combined this with eDNA data to analyse the response of eukaryote and prokaryote communities to differing flow conditions within intermittent and perennial stream reaches. Our study suggested that SW and GW microbial communities were only around 30% similar. Differences in microbiota between SW, HZ and GW habitats were driven by changes in relative abundances of surface water dominant organisms (such as those capable of photosynthesis) as well as anaerobic taxa typical of GW environments (e.g., methanogens), with GW and HZ microbial communities becoming increasingly different to those in SW as flow ceased in intermittent creeks. Fine-scale hydrologic changes were identified through microbial communities in the perennial Maules Creek, indicating the importance of GW-SW exchange to biotic communities. This study highlights the importance of flow in shaping microbial communities and biogeochemical cycling within intermittent creeks and their connected alluvial aquifers. Our results suggest that microbiota may prove a useful indicator of SW-GW exchange, and in some circumstances, may be more sensitive in demonstrating fine-scale changes in SW-GW interactions than water chemistry. This knowledge furthers our understanding of GW-SW exchange and its impacts on ecological health.