Differences In Abundance Of Taxa Research Articles

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers

The goal of the study was to investigate the changes in the gut microbiota during the advancement of gastric cancer (GC) and identify pertinent taxa associated with the disease. We used a public fecal amplicon gastric cancer dataset from the Sequence Retrieval Archive (SRA), of patients with GC, gastritis, and healthy individuals. We did sequence pre-processing, including quality filtering of the sequences. Then, we performed a diversity analysis, evaluating α- and β-diversity. Next, taxonomic composition analysis was performed and the relative abundances of different taxa at the phylum and genus levels were compared between GC, gastritis, and healthy controls. The obtained results were subsequently subjected to statistical validation. To conclude, metagenomic function prediction was carried out, followed by correlation analysis between the microbiota and KEGG pathways. α analysis revealed a significant difference between male and female categories, while β analysis demonstrated significant distinctions between GC, gastritis, and healthy controls, as well as between sexes within the GC and gastritis groups. The statistically confirmed taxonomic composition analysis highlighted the presence of the microbes Bacteroides and Veillonella. Furthermore, through metagenomic prediction analysis and correlation analysis with pathways, three taxa, namely Akkermansia, Gammaproteobacteria, and Veillonella, were identified as potential biomarkers for GC. Additionally, this study reports, for the first time, the presence of two bacteria, Desulfobacteriota and Synergistota, in GC, necessitating further investigation. Overall, this research sheds light on the potential involvement of gut microbiota in GC pathophysiology; however, additional studies are warranted to explore its functional significance.

Beyond 16S sequencing for microbiome research: Nanopore sequencing resource at The University of Toledo Microbiome Consortium

Objective: The recognition that humans are holobionts has opened a new research area to examine the contributions of the microbiome to health and disease. This requires a full understanding of the identities of microbiota at the taxonomical level of the species. Introduction: The University of Toledo Microbiome Consortium currently offers the second-generation Illumina sequencing platform for 16S sequencing to determine microbiota composition. 16S sequencing of variable regions of the 16S operon, such as V3, V4, and the combination of V3 to V4, has long been the main stay for analyzing the composition of microbiota. The advantage of this approach is the ability to screen large numbers of samples at a lower cost per sample. However, the major drawback of this approach is a lower resolution whereby taxonomical identities of microbiota are limited to the genus level. To overcome this disadvantage, we introduced the third-generation sequencing technology from Nanopore into our pipeline. The known advantages of this approach are longer reads and the ability to sequence DNA in the native form without PCR-induced bias. Here we sought to conduct a comparative study of the relative effciencies of the 16S versus the nanopore technology for metagenomics. Methods: Genomic DNA was isolated from control and experimental rat fecal samples provided by an end-user. Libraries were prepared using Ligation sequencing DNA V14 (SqK-LSK114) on a Flow cell R10.4.1and Lambda DNA was used as a sequencing control. The native Libraries were run for 72hr, and high accuracy base calling was performed. The Fastq files (passed) generated by GridION were run on cloud-based CZ-ID pipeline with host and human read filtering, the results were normalized to one million bases sequenced from reads of each sample. Results and Conclusions: The 16S sequencing data highlighted the relative abundance of different taxa up to genus level such as Lactobacillus and Erysipelatoclostridium in the experimental group where as Stepcococcus and prevotellaceaeGa6A1group in the control group. However, Nanopore sequencing further identified twenty different species of Lactobacillus and , four different species of Erysipelatoclostridium. Similarly, nanopore sequencing was able to profile diverse species belonging to genera prevotellaceaeGa6A1group and Streptococcus. This species level resolution will greatly help in focusing on specific species and the pathways that a researcher intends to pursue. Therefore, the nanopore sequencing presents an opportunity to explore sequencing with a small footprint in terms of instrumentation and associated costs that greatly helps even a smaller laboratory to adopt and reap the benefits of species level resolution of metagenomic data. Summary: This study correlated well with 16S sequencing results at the genus level, while offering the added benefit of species level Identification and classification. Authors acknowledge the National Institutes of Health for funding support to Bina Joe (R01HL1430820). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Comparative analysis of fasting effects on the cecum microbiome in three guinea pig breeds: Andina, Inti, and Peru.

Guinea pigs have historically been used as a food source and are also an important model for studying the human intestines. Fasting is the act of temporarily stopping the intake of food. This process can alter the microbiota of various animals. This study is the first to investigate the impact of fasting on the cecum microbiome of three guinea pig breeds. We investigated the impact of fasting on the microbiome population structure in the cecum of three guinea pig breeds. This was done by sequencing and analyzing the V4 hypervariable region of the 16S rRNA gene in bacterial communities found in cecum mucosa samples. To achieve this, we established two treatment groups (fasting and fed), for each of the three guinea pig breeds: Andina, Inti, and Peru. The study involved twenty-eight guinea pigs, which were divided into the following groups: Andina-fed (five), Andina-fasting (five), Inti-fed (four), Inti-fasting (five), Peru-fed (five), and Peru-fasting (four). The results indicated a significant difference in beta diversity between the treatment groups for the Peru breed (P-value = 0.049), but not for the treatment groups of the Andina and Inti breeds. The dominant phyla across all groups were Firmicutes and Bacteroidetes. We observed variations in the abundance of different taxa in the cecum microbiota when comparing the treatment groups for each breed. Additionally, there was a higher number of unique taxa observed in the fasting groups compared to the fed groups. We discovered that the genus Victivallis was the only one present in all fasting groups across all breeds. Despite the findings, the resilience of the gut microbiome was not challenged in all three breeds, which can lead to disruptive changes that may affect the overall maintenance of the cecum microbiome. Based on the observed differences in the treatment groups of the Peru breed, it can be suggested that fasting has a greater impact on this particular breed.

Effect of two insect meals on the gut commensal microbiome of healthy sea trout (Salmo trutta vr. trutta)

BackgroundThe balance of the intestinal commensal microbiome of fish and other animals plays an important role in the physiological processes of healthy animals, contributes to the defense against pathogens, stimulates the immune system and facilitates nutrient metabolism. In the last decade, the interest in the application of the insects in fish nutrition increased, although little is known regarding the effects of insect meals on the gastrointenstinal tract microbiome of the sea trout fingerlings. The aim of this study was to evaluate the effect of two diets containing mealworm (MW) and superworm (SW) on the microbiome of the digesta of sea trout fingerlings and the relative abundances of different taxa among communities under controlled conditions.ResultsThe insect meals produced a similar weight gain and survival rate to sea trout fed fishmeal. The most abundant bacterial phylum in all the treatment groups was Firmicutes followed by Proteobacteria and Actinobacteria, and significant differences in the amount of Cyanobacteria were observed in the SW group.ConclusionsThe insect meals did not produce differences in the three most abundant phyla in the sea trout digesta. However, the effect of each type of meal on the lower taxonomic levels was evident, particularly in the case of the superworm meal. These microbiome differences indicated that mealworm meal was more related to fishmeal than superworm meal. Our results highlight the potential effects of insect meals, such as mealworm and superworm meals, on the microbiota of sea trout.

Fecal microbiota of the synanthropic golden jackal (Canis aureus)

The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota. We analyzed 111 fecal samples of wild golden jackals using 16S rRNA amplicon sequencing the connection of the microbiome to animal characteristics, burden of pathogens and geographic and climate characteristics. We further compared the fecal microbiota of the golden jackal to the black-backed jackal and domestic dog. We found that the golden jackal fecal microbiota is dominated by the phyla Bacteroidota, Fusobacteriota and Firmicutes. The golden jackal fecal microbiota was associated with different variables, including geographic region, age-class, exposure to rabies oral vaccine, fecal parasites and toxoplasmosis. A remarkable variation in the relative abundance of different taxa was also found associated with different variables, such as age-class. Linear discriminant analysis effect size (LEfSe) analysis found abundance of specific taxons in each region, Megasphaera genus in group 1, Megamonas genus in group 2 and Bacteroides coprocola species in group 3. We also found a different composition between the fecal microbiota of the golden jackal, blacked-backed jackal and the domestic dog. Furthermore, LEfSe analysis found abundance of Fusobacterium and Bacteroides genera in the golden jackal, Clostridia class in blacked-backed jackal and Megamonas genus in domestic dog. The golden jackal fecal microbiota is influenced by multiple factors including host traits and pathogen burden. The characterization of the microbiota of this thriving species may aid in mapping its spread and proximity to human settlements. Moreover, understanding the jackal microbiota could inform the study of potential animal and human health risks and inform control measures.

Gut Microbiome Composition in Lynch Syndrome With and Without History of Colorectal Neoplasia and Non-Lynch Controls.

While Lynch syndrome (LS) is a highly penetrant colorectal cancer (CRC) syndrome, there is considerable variation in penetrance; few studies have investigated the association between microbiome and CRC risk in LS. We analyzed the microbiome composition among individuals with LS with and without personal history of colorectal neoplasia (CRN) and non-LS controls. We sequenced the V4 region of the 16S rRNA gene from the stool of 46 individuals with LS and 53 individuals without LS. We characterized within community and in between community microbiome variation, compared taxon abundance, and built machine learning models to investigate the differences in microbiome. There was no difference within or between community variations among LS groups, but there was a statistically significant difference in both within and between community variation comparing LS to non-LS. Streptococcus and Actinomyces were differentially enriched in LS-CRC compared to LS-without CRN. There were numerous differences in taxa abundance comparing LS to non-LS; notably, Veillonella was enriched and Faecalibacterium and Romboutsia were depleted in LS. Finally, machine learning models classifying LS from non-LS controls and LS-CRC from LS-without CRN performed moderately well. Differences in microbiome composition between LS and non-LS may suggest a microbiome pattern unique to LS formed by underlying differences in epithelial biology and immunology. We found specific taxa differences among LS groups, which may be due to underlying anatomy. Larger prospective studies following for CRN diagnosis and microbiome composition changes are needed to determine if microbiome composition contributes to CRN development in patients with LS.

Upper respiratory tract mycobiome alterations in different kinds of pulmonary disease.

The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient. In this study, we investigated the fungal community composition of oropharynx swab (OS) samples from patients with five kinds of pulmonary disease, including interstitial lung disease (ILD), bacterial pneumonia (BP), fungal pneumonia (FP), asthma (AS) and lung cancer (LC), and compared them with healthy controls (HCs), based on high-throughput sequencing of the amplified fungal internal transcribed spacer (ITS) region. The results showed significant differences in fungal composition and abundance between disease groups and HCs. Malassezia was the most significant genus, which was much more abundant in pulmonary diseases than in the control. In addition, many common taxa were shared among different disease groups, but differences in taxa abundance and specific species in distinct disease groups were also observed. Based on linear discriminant analysis effect size (LefSe), each group had its characteristic species. Furthermore, some species showed a significant correlation with the patient clinical characteristics. Our study deepened our understanding of the respiratory tract mycobiome in some diseases that are less studied and identified the commonalities and differences among different kinds of pulmonary disease. These results would provide the solid basis for further investigation of the association between the mycobiome and pathogenicity of pulmonary diseases.

Analysis of the bacterial communities associated with pupae and winged or wingless adults of Lipoptena fortisetosa collected from cervids in Italy.

The hippoboscid Lipoptena fortisetosa Maa, 1965 is a hematophagous ectoparasite of cervids that can bite humans. This fly is expanding its geographical range and is of concern for animal and human health since it can potentially harbour harmful microorganisms. This study was aimed at characterizing the bacterial communities of L. fortisetosa in its different life-cycle stages. Pupae and wingless adults were collected from cervids hunted in Tuscan-Emilian Apennines (central Italy) and pooled into groups of 10 by life stage (30 individual pupae; 1420 individual wingless adults). Winged flies were caught by sweep netting and separated into five pools of 10 insects. After DNA extraction, the bacterial content of each pool was analysed using 16 S metabarcoding. Results revealed that the composition and relative abundance of different taxa greatly differed in the three analysed groups. Wingless adults showed a high abundance of Bartonella (33.07%), which is almost absent in winged flies and pupae. Among the detected pathogens, four genera of concern for human health were found: Bartonella, Moraxella, Mycobacterium and Rickettsia. Interestingly reads similar to Bartonella bovis, Moraxella osloensis and Arsenophonus lipopteni Operational Taxonomic Unit (OTUs)were detected. These findings suggest the possible role of L. fortisetosa as a reservoir of pathogenic microorganisms, confirming the need for further investigation to ascertain its vectorial capacity.

The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows

BackgroundMany dairy cows experience a state of energy deficit as they transition from late gestation to early lactation. The aims of this study were to 1) determine if the development of hyperketonemia in early lactation dairy cows is indicated by their gut microbiome, and 2) to identify microbial features which may inform health status. We conducted a prospective nested case-control study in which cows were enrolled 14 to 7 days before calving and followed through their first 14 days in milk (DIM). Hyperketonemic cows (HYK, n = 10) were classified based on a blood β-hydroxybutyrate (BHB) concentration 1.2 mmol/L within their first 14 DIM. For each HYK cow, two non-HYK (CON, n = 20) cows were matched by parity and 3 DIM, with BHB < 1.2 mmol/L. Daily blood BHB measures were used to confirm CON cows maintained their healthy status; some CON cows displayed BHB 1.2 mmol/L after matching and these cows were reclassified as control-HYK (C-HYK, n = 9). Rumen and fecal samples were collected on the day of diagnosis or matching and subjected to 16S rRNA profiling.ResultsNo differences in taxa abundance, or alpha and beta diversity, were observed among CON, C-HYK, and HYK health groups for fecal microbiomes. Similar microbiome composition based on beta diversity analysis was detected for all health statuses, however the rumen microbiome of CON and HYK cows were found to be significantly different. Interestingly, highly similar microbiome composition was observed among C-HYK cow rumen and fecal microbiomes, suggesting that these individual animals which initially appear healthy with late onset of hyperketonemia were highly similar to each other. These C-HYK cows had significantly lower abundance of Ruminococcus 2 in their rumen microbiome compared to CON and HYK groups. Multinomial regressions used to compute log-fold changes in microbial abundance relative to health status were not found to have predictive value, therefore were not useful to identify the role of certain microbial features in predicting health status.ConclusionsLower relative abundance of Ruminococcus 2 in C-HYK cow rumens was observed, suggesting these cows may be less efficient at degrading cellulose although the mechanistic role of Ruminococcus spp. in rumen metabolism is not completely understood. Substantial differences in fecal or rumen microbiomes among cows experiencing different levels of energy deficit were not observed, suggesting that hyperketonemia may not be greatly influenced by gut microbial composition, and vice versa. Further studies using higher resolution -omics approaches like meta-transcriptomics or meta-proteomics are needed to decipher the exact mechanisms at play.

Machine learning techniques to characterize functional traits of plankton from image data.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab‐based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

Extremely Acidic Eukaryotic (Micro) Organisms: Life in Acid Mine Drainage Polluted Environments—Mini-Review

Acid Mine Drainage (AMD) results from sulfide oxidation, which incorporates hydrogen ions, sulfate, and metals/metalloids into the aquatic environment, allowing fixation, bioaccumulation and biomagnification of pollutants in the aquatic food chain. Acidic leachates from waste rock dams from pyritic and (to a lesser extent) coal mining are the main foci of Acid Mine Drainage (AMD) production. When AMD is incorporated into rivers, notable changes in water hydro-geochemistry and biota are observed. There is a high interest in the biodiversity of this type of extreme environments for several reasons. Studies indicate that extreme acid environments may reflect early Earth conditions, and are thus, suitable for astrobiological experiments as acidophilic microorganisms survive on the sulfates and iron oxides in AMD-contaminated waters/sediments, an analogous environment to Mars; other reasons are related to the biotechnological potential of extremophiles. In addition, AMD is responsible for decreasing the diversity and abundance of different taxa, as well as for selecting the most well-adapted species to these toxic conditions. Acidophilic and acidotolerant eukaryotic microorganisms are mostly composed by algae (diatoms and unicellular and filamentous algae), protozoa, fungi and fungi-like protists, and unsegmented pseudocoelomata animals such as Rotifera and micro-macroinvertebrates. In this work, a literature review summarizing the most recent studies on eukaryotic organisms and micro-organisms in Acid Mine Drainage-affected environments is elaborated.

Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3 km borehole at Koyna, western India.

Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep subsurface continental crust remains under-represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 m deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing and cultivation-based analyses. Gene sequences 16S rRNA (7.37× 106 ) show considerable bacterial diversity and the existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118,064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt to elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals a major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy.

Aquatic macroinvertebrates from littoral vegetated lakes in arid Patagonia: The influence of fish introduction on community structure

Abstract Wetlands in arid regions are characterized by their great heterogeneity, often including endemic species that contribute to regional aquatic biodiversity. In the Patagonian steppe, most lakes are naturally fishless and sustain a rich aquatic biodiversity, including endemics; however, many of these lakes have been stocked with Oncorhynchus mykiss (rainbow trout) during recent decades. The introduction of predatory fish into aquatic ecosystems naturally devoid of these organisms can produce profound alterations in the structure of the original communities and in the configuration of their biotic assemblages. Aquatic invertebrates play important roles in both the structure and functioning of freshwater ecosystems, including their contribution to global biodiversity and their cascading effects across ecosystem boundaries. The aim of this study was to assess the effect of introduced non‐native fish on the pleustonic macroinvertebrate assemblage. Samples were taken from 10 shallow Patagonian lakes (five fishless and five stocked with fish) in two consecutive warm periods. Lakes with fish had higher conductivity and phosphate values. Higher inter‐annual differences were also observed in lakes with fish for phytoplanktonic chlorophyll a, nitrate, phosphate, conductivity, and water temperature. The community structure (relative abundance of different taxa, species composition, and diversity index) was affected by the presence of rainbow trout, with the differences mainly driven by the relative abundance of Ostracoda, Hyalella, Chironomidae, and Haliplus species. This approach can be used to assess the required conservation actions in shallow Patagonian steppe lakes, which have been listed as priority areas for waterbird conservation. Specifically, this study provides a baseline for monitoring future trends of the macroinvertebrate communities and for evaluating conservation and management efforts over time.

Niche Selection by Soil Bacterial Community of Disturbed Subalpine Forests in Western Sichuan

Soil bacterial microbial communities are important in the ecosystem function and succession of forests. Using high-throughput 16S rRNA gene sequencing and relative importance for linear regression, we explored how the structures of soil bacterial community were influenced by the environmental factors and restoration succession of secondary forests in the Miyaluo Mountains of western Sichuan, China. Using a space-for-time approach, field measurements and sampling were conducted in four stands at different stages of natural restoration. Results of distance-based multivariate analysis showed that soil pH, organic carbon, available phosphorus, and C/N ratio were the predominant environmental factors that collectively explained a 46.9% variation in the bacterial community structures. The community compositions were jointly controlled by the direct and indirect effects of the rehabilitation stages. The changes in soil environmental factors coincided with restoration succession could lead to the shifts in the relative abundance of different soil bacterial taxa. We screened 13 successional discriminant taxa that could quantitatively indicate the secondary succession subalpine stage. Collectively, our findings show that soil bacteria in different taxa are governed by different local soil variables and rehabilitation ages, which can lead to shifts in the relative abundance of different taxa in successional stages, ultimately changing the entire soil bacterial community with the succession of secondary forest.

The composition of the gut microbiome differs among community dwelling older people with good and poor appetite.

BackgroundAnorexia of ageing is common and important in the development of sarcopenia in older individuals. Links have been proposed between the gut microbiota and sarcopenia. Disordered gut function is also recognized in anorexia of ageing, but how this may relate to resident gut microbiota is unexplored. Understanding this relationship may provide a basis for novel interventions for anorexia of ageing and sarcopenia. This study explores compositional differences of the gut microbiota between community dwelling healthy older adults with good or poor appetite, and associated differences in sarcopenia.MethodsWe assessed appetite by the Simplified Nutritional Appetite Questionnaire (SNAQ) in members of the TwinsUK cohort aged ≥65 years. Using a pool of 776 individuals with existing microbiome data estimated from 16S rRNA sequencing data, we identified 102 cases (SNAQ score < 14) (95% female, mean age 68 years) matched to controls (SNAQ > 14) on body mass index, gender, age, diet, calorie consumption, frailty, antibiotic use, socio‐economic status, and technical variables to minimize confounding microbiota associations. Species abundance and diversity, compositional differences, and paired differences in taxa abundance were compared between cases and controls. Additionally, we compared case and controls for sarcopenia as measured by muscle mass (appendicular lean mass/height2) and strength (chair stand time in seconds).ResultsCases with poor appetite had reduced species richness and diversity of their gut microbiome (adjusted OBSERVED: beta = −0.2, P < 0.001; adjusted SHANNON: beta = −0.17, P = 0.0135), significant compositional differences (adjusted non‐parametric multivariate analysis of variance, P = 0.0095), and significant differences in taxa abundance including reduction of genus Lachnospira (logFC = −1.015, q = 0.023). In all‐female subgroup analysis, cases with poor appetite demonstrated reduction in muscle strength (11.03 s vs. 9.26 s, P = 0.02).ConclusionsThis study is the first to observe differences in the composition of gut microbiota between healthy community dwelling older individuals with good and poor appetite. We found female individuals with reduced muscle strength had poor appetite compared with those with normal strength. These associations require further examination to understand causality and mechanisms of interaction, to inform potential strategies targeting the gut microbiota as a novel intervention for anorexia of ageing and sarcopenia.

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows.

Udder cleft dermatitis (UCD) is a skin condition affecting the fore udder attachment of dairy cows. UCD may be defined as mild (eczematous skin changes) or severe (open wounds, large skin changes). Our aims were to compare the microbiota of mild and severe UCD lesions with the microbiota of healthy skin from the fore udder attachment of control cows, and to investigate whether mastitis-causing pathogens are present in UCD lesions. Samples were obtained from cows in six dairy herds. In total, 36 UCD samples categorized as mild (n = 17) or severe (n = 19) and 13 control samples were sequenced using a shotgun metagenomic approach and the reads were taxonomically classified based on their k-mer content. The Wilcoxon rank sum test was used to compare the abundance of different taxa between different sample types, as well as to compare the bacterial diversity between samples. A high proportion of bacteria was seen in all samples. Control samples had a higher proportion of archaeal reads, whereas most samples had low proportions of fungi, protozoa and viruses. The bacterial microbiota differed between controls and mild and severe UCD samples in both composition and diversity. Subgroups of UCD samples were visible, characterized by increased proportion of one or a few bacterial genera or species, e.g. Corynebacterium, Staphylococcus, Brevibacterium luteolum, Trueperella pyogenes and Fusobacterium necrophorum. Bifidobacterium spp. were more common in controls compared to UCD samples. The bacterial diversity was higher in controls compared to UCD samples. Bacteria commonly associated with mastitis were uncommon. In conclusion, a dysbiosis of the microbiota of mild and severe UCD samples was seen, characterized by decreased diversity and an increased proportion of certain bacteria. There was no evidence of a specific pathogen causing UCD or that UCD lesions are important reservoirs for mastitis-causing bacteria.

Beaver-induced spatiotemporal patch dynamics affect landscape-level environmental heterogeneity

Beavers (Castor sp.) are ecosystem engineers that cause significant changes to their physical environment and alter the availability of resources to other species. We studied flood dynamics created by American beaver (C. canadensis K.) in a southern boreal landscape in Finland in 1970–2018. We present for the first time, to our knowledge, a temporally continuous long-term study of beaver-induced flood disturbances starting from the appearance of beaver in the area. During the 49 years, the emergence of new sites flooded by beaver and repeated floods (61% of the sites) formed a dynamic mosaic characterized by clustered patterns of beaver sites. As beaver dispersal proceeded, connectivity of beaver sites increased significantly. The mean flood duration was approximately three years, which highlights the importance of datasets with high-temporal resolution in detecting beaver-induced disturbances. An individual site was often part of the active flood mosaic over several decades, although the duration and the number of repeated floods at different sites varied considerably. Variation of flood-inundated and post-flood phases at individual sites resulted in a cumulative number of unique patches that contribute to environmental heterogeneity in space and time. A disturbance mosaic consisting of patches differing by successional age and flood history is likely to support species richness and abundance of different taxa and facilitate whole species communities. Beavers are thus a suitable means to be used in restoration of riparian habitat due to their strong and dynamic influence on abiotic environment and its biotic consequences.

The airway microbiota and exacerbations of COPD.

AimThe aim of this study was to investigate whether the compositionality of the lower airway microbiota predicts later exacerbation risk in persons with COPD in a cohort study.Materials and methodsWe collected lower airways microbiota samples by bronchoalveolar lavage and protected specimen brushes, and oral wash samples from 122 participants with COPD. Bacterial DNA was extracted from all samples, before we sequenced the V3-V4 region of the 16S RNA gene. The frequency of moderate and severe COPD exacerbations was surveyed in telephone interviews and in a follow-up visit. Compositional taxonomy and α and β diversity were compared between participants with and without later exacerbations.ResultsThe four most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria and Fusobacteria in both groups, and the four most abundant genera were Streptococcus, Veillonella, Prevotella and Gemella. The relative abundances of different taxa showed a large variation between samples and individuals, and no statistically significant difference of either compositional taxonomy, or α or β diversity could be found between participants with and without COPD exacerbations within follow-up.ConclusionThe findings from the current study indicate that individual differences in the lower airway microbiota in persons with COPD far outweigh group differences between frequent and nonfrequent COPD exacerbators, and that the compositionality of the microbiota is so complex as to present large challenges for use as a biomarker of later exacerbations.

Quorum Sensing Signals Alter in vitro Soil Virus Abundance and Bacterial Community Composition.

Cell-density dependent quorum sensing (QS) is fundamental for many coordinated behaviors among bacteria. Most recently several studies have revealed a role for bacterial QS communication in bacteriophage (phage) reproductive decisions. However, QS based phage-host interactions remain largely unknown, with the mechanistic details revealed for only a few phage-host pairs and a dearth of information available at the microbial community level. Here we report on the specific action of eight different individual QS signals (acyl-homoserine lactones; AHLs varying in acyl-chain length from four to 14 carbon atoms) on prophage induction in soil microbial communities. We show QS autoinducers, triggered prophage induction in soil bacteria and the response was significant enough to alter bacterial community composition in vitro. AHL treatment significantly decreased the bacterial diversity (Shannon Index) but did not significantly impact species richness. Exposure to short chain-length AHLs resulted in a decrease in the abundance of different taxa than exposure to higher molecular weight AHLs. Each AHL targeted a different subset of bacterial taxa. Our observations indicate that individual AHLs may trigger prophage induction in different bacterial taxa leading to changes in microbial community structure. The findings also have implications for the role of phage-host interactions in ecologically significant processes such as biogeochemical cycles, and phage mediated transfer of host genes, e.g., photosynthesis and heavy metal/antibiotic resistance.

Associations between UK tap water and gut microbiota composition suggest the gut microbiome as a potential mediator of health differences linked to water quality

Tap water composition has been widely linked to differences in human health, however the biological pathways underlying this association are less clearly defined. We provide the first investigation of the potential for the gut microbiota to mediate this association. Tap water samples and drinking habits from 85 Mono-zygotic twins with existing faecal microbiota profiles from around the UK were used to assess associations of water composition with the gut microbiome. Water composition was captured using the first 3 principle components (PCs) from multiple factor analysis of ion concentrations, additionally estimating average daily dose (ADD) of the primary three solutes contributing to its variance: chloride, sulphate and sodium. Geographic differences in water composition were assessed. We used measures of faecal microbial diversity, between-individual differences in composition and differences in taxa abundance estimated from 16S rRNA sequencing data. Differences between twin pairs were also considered. We observed significant associations of sodium ADD with microbiota diversity (Chao1), chloride, sodium and sulphate ADD with dissimilarity between samples, and significant associations for all PCs and ADD-adjusted solutes with abundances of individual microbial taxa. These results support the hypothesis that the gut microbiota could mediate the effects of tap water composition on host health, warranting further investigation into tap-water as an influencer of microbiota composition.