16S rRNA Gene Amplicon Sequencing Research Articles

Detection and quantitative microbial risk assessment of pathogenic Vibrio cholerae in a river used for drinking, domestic, fresh produce irrigation and recreational purposes

Cholera infection results from the ingestion of water or food contaminated with toxigenic Vibrio cholerae. This study evaluated the occurrence of toxigenic V. cholerae in Asata River, Enugu Metropolis, Nigeria, and estimated V. cholerae infection risks from use of the River water for drinking, domestic and recreational purposes. Vibrio was detected and quantified using membrane filtration technique and thiosulfate–citrate–bile salts–sucrose agar. Isolates were screened by PCR, using specific primers targeting the internal transcribed spacer (its) region between 16 and 23S rRNA and the cholera toxin (ctx) gene. Sequenced 16SrRNA gene amplicons of two selected isolates were used for phylogenetic analysis. Quantitative microbial risk assessment (QMRA) was conducted using the β-Poisson dose–response model. About 81% (58/72) of Asata River samples recorded Vibrio counts above 1.0 ×\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\ imes$$\\end{document} 103 cfu/100 mL. Of the fifty Vibrio isolates screened, its was detected in 54% (27/50), out of which 74% (20/27) had the ctx gene of toxigenic V. cholerae. Evolutionary relatedness of the sequenced isolates to V. cholerae was revealed. The estimated risks of cholera infection in persons exposed to untreated Asata River water were above 0.5 for all the exposure scenarios, for both the rainy and dry seasons. The risks were highest (~ 0.9) for exposure via drinking water and annual risk of infection was deduced to have a probability of 1.0. Therefore, dependence on the untreated Asata River water for drinking, recreational, domestic and irrigation purposes may present a potential public health risk of cholera outbreak. We recommend increased monitoring and surveillance of River water for Vibrio abundance and that Asata River be protected from further degradation.

Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.

Pollinators face many stressors, including reduced floral diversity. A low-diversity diet can impair organisms' ability to cope with additional stressors, such as pathogens, by altering the gut microbiome and/or immune function, but these effects are understudied for most pollinators. We investigated the impact of pollen diet diversity on two ecologically and economically important generalist pollinators, the social bumble bee (Bombus impatiens) and the solitary alfalfa leafcutter bee (Megachile rotundata). We experimentally tested the effect of one-, two-, or three-species pollen diets on gut bacterial communities in both species, and the melanization immune response in B. impatiens. Pollen diets included dandelion (Taraxacum officinale), staghorn sumac (Rhus typhina), and hawthorn (Crataegus sp.) alone, each pair-wise combination, or a mix of all three species. We fed bees their diet for 7 days and then dissected out guts and sequenced 16S rRNA gene amplicons to characterize gut bacterial communities. To assess melanization in B. impatiens, we inserted microfilament implants into the bee abdomen and measured melanin deposition on the implant. We found that pollen diet did not influence gut bacterial communities in M. rotundata. In B. impatiens, pollen diet composition, but not diversity, affected gut bacterial richness in older, but not newly-emerged bees. Pollen diet did not affect the melanization response in B. impatiens. Our results suggest that even a monofloral, low-quality pollen diet such as dandelion can support diverse gut bacterial communities in captive-reared adults of these bee species. These findings shed light on the effects of reduced diet diversity on bee health.

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment

Biophilic design based on indoor planting plays an important role in human physical and mental well-being. To investigate and assess the effects of indoor planting on air quality, we sequenced 16S rRNA gene amplicons to compare the airborne bacterial microbiomes of three planting rooms before and after installing natural materials (plants, soil, water, etc.) with distinct biophilic attributes. Incorporation of indoor plantings significantly increased the taxonomic diversity of the airborne microbiome in each room, and we observed different microbiome compositions in each room. The proportional contribution of each bacterial source to the airborne microbiome in the indoor planting rooms was estimated by SourceTracker2. This analysis revealed that the proportion of airborne microbial sources (e.g., plants and soil) varied depending on the natural materials installed. Our results have important implications for indoor planting with biophilic design to control the indoor airborne microbiome.

Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids

BackgroundRye intake has been associated with beneficial effects on health in human interventions, possibly due to dietary fiber in rye. In dogs, few studies have explored the effects on health of dietary fiber in general, and rye fiber in particular. The aim of this study was to investigate how inclusion of rye, compared with wheat, influenced fecal microbiota composition, short chain fatty acids (SCFA) and apparent total tract digestibility (ATTD) in dogs. Six male Beagle dogs (mean age 4.6 years, SEM 0.95 years; mean body weight 14.6 kg, SEM 0.32 kg) were fed three experimental diets, each for 21 days, including an adaptation period of six days and with 2–2.5 months between diet periods. The diets were similar regarding energy and protein, but had different carbohydrate sources (refined wheat (W), whole grain rye (R), or an equal mixture of both (RW)) comprising 50% of total weight on a dry matter (DM) basis. The diets were baked and titanium dioxide was added for ATTD determination. Fecal samples were collected before and in the end of each experimental period. Fecal microbiota was analyzed by sequencing 16S rRNA gene amplicons and fecal SCFA by high-performance liquid chromatography. Crude protein, crude fat, neutral detergent fiber, and gross energy (GE) in food and feces were analyzed and ATTD of each was determined. Univariate and multivariate statistical methods were applied in data evaluation.ResultsFaecal microbiota composition, differed depending on diet (P = 0.002), with samples collected after consumption of the R diet differing from baseline. This was primarily because of a shift in proportion of Prevotella, which increased significantly after consumption of the R diet (P < 0.001). No significant differences were found for SCFA, but there was a tendency (P < 0.06) for higher molar proportions of acetic acid following consumption of the R diet. The ATTD of crude protein, crude fat, neutral detergent fiber, and GE was lower after consumption of the R diet compared with the other diets (P < 0.05).ConclusionsConsumption of the R diet, but not RW or W diets, was associated with specific shifts in microbial community composition and function, but also with lower ATTD.

High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval

In forensic medical examinations, estimating the postmortem interval (PMI) is an important factor. Methamphetamine (MA) is a synthetic stimulant that is commonly abused, and estimation of the PMI after MA abuse has become one of the main tasks in forensic investigation. Microorganisms play a vital role in carrion decomposition. Analysing the bacterial succession patterns can be used as a forensic tool to estimate the PMI. The present study aimed to analyse bacterial succession changes during the decomposition of MA to estimate the PMI. We analysed bacterial communities in rabbits treated with three different concentrations of MA (0, 22.5, and 90 mg/kg) under the natural conditions of 20 °C and 70% humidity by sequencing 16S rRNA gene amplicons using the Illumina MiSeq system. We obtained 2 774 209 high-quality sequences and 2937 operational taxonomic units (OTUs). The relative abundances of the bacterial communities varied markedly in response to different MA concentrations. Interestingly, in response to the different concentrations of MA, Bacteroidetes became disparate in the rectum in the late PMI. Increased numbers of bacterial taxa were identified in the rectum and buccal cavity samples, except at the highest concentration of MA in the rectum samples when PMI was 0–h, than were present in live rabbits. Meanwhile, the PMI correlated significantly with bacterial succession at different taxonomic levels. Our results suggested that bacterial community succession could be used as a “microbial clock” to estimate the PMI in cases of MA-related death; however, further study is required to gain a deeper understanding of this concept. Keypoints As a forensic tool, microbiome succession patterns have great potential for PMI estimation. At different taxonomic levels, the variation in the succession of microorganisms’ under three different concentrations of MA during the processes of decomposition is significantly related to PMI for estimating MA abuse. These findings provide a new idea for the estimation of PMI of MA abused by changes in microorganisms.

Bacterial Community Structure of Panchagavya, a Fermented Liquid Bio-manure, as Revealed by High-Throughput Sequencing of 16S rRNA Gene Amplicons.

ABSTRACTPanchagavya is a fermented liquid bio-manure that is widely used in India. We aimed to determine its bacterial community structure by sequencing 16S rRNA gene amplicons. These sequences will enhance our understanding of the microbial diversity of panchagavya as well as its potential application in sectors other than agriculture.

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India.

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

Alterations of Vaginal Microbiota in Women With Infertility and Chlamydia trachomatis Infection.

Chlamydia trachomatis (C. trachomatis) is the most common etiological agent of bacterial sexually transmitted infections (STIs) worldwide and causes serious health sequelae such as cervicitis, pelvic inflammatory disease, and even infertility if ascending from the lower to the upper female genital tract. Previous studies have revealed the pivotal role of vaginal microbiota in susceptibility to STIs. However, alterations in the vaginal microbiota in women who are infertile and infected with C. trachomatis remain unknown. This study used metagenomic analysis of sequenced 16S rRNA gene amplicons to examine the vaginal microbial profiles of women with tubal infertility who were C. trachomatis-negative and those who were C. trachomatis-positive pre- and post-antibiotic treatment. Women who were C. trachomatis-negative and deemed healthy were recruited as references of eubiosis and dysbiosis. Women with tubal infertility and C. trachomatis infection presented a unique Lactobacillus iners-dominated vaginal microbiota rather than one dominated by Lactobacillus crispatus and displayed a decrease in Lactobacillus, Bifidobacterium, Enterobacter, Atopobium, and Streptococcus, accompanied by decreased levels of cytokines such as interferon (IFN)-γ and interleukin (IL)-10. This altered vaginal microbiota could be restored with varying degrees after standard treatment for C. trachomatis. This shift could be a predictive vaginal microbiota signature for C. trachomatis infection among females with tubal infertility, while no significant differences in phylum, class, and operational taxonomic unit (OTU) levels were observed between women with tubal infertility who were C. trachomatis-negative and healthy controls. This is the first study to provide data on the association of vaginal microbiota with C. trachomatis infection among women with tubal infertility and highlights unprecedented potential opportunities to predict C. trachomatis infection.

Water and Sediment Bacterial Communities in a Small Mediterranean, Oxygen-Stratified, Saline Lake (Lake Alboraj, SE Spain)

Lake Alboraj, located in southeast Spain, was declared natural Microreserve and included into European Natura-2000 Network due to its contribution to environmental heritage. Unfortunately, the ecological status of the lake has changed dramatically, mainly due to the lowering of water table caused by groundwater abstractions for irrigation. It is a permanent small karstic lake whose surface has reduced in the last decades to nearly the third part of its historical water level. The water column shows a marked seasonal oxycline, that splits an aerobic upper layer (epilimnion) from an anaerobic layer below (hypolimnion). Sequencing 16S rRNA gene amplicons and applying chemical tools at epilimnion, hypolimnion and sediment, showed a clear gradient in the bacterial community structure, which support the co-existence of assimilatory and dissimilatory microbial mediated reactions. Results allows to infer that microbial stratification could provide various physical and chemical environments at different depths in the water column related to biogeochemical reactions providing N-S-C- recycling processes.

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.

The Influence of Different Physical Activity Behaviours on the Gut Microbiota of Older Irish Adults.

A 24-hour day is made up of time spent in a range of physical activity (PA) behaviours, including sleep, sedentary time, standing, light-intensity PA (LIPA) and moderate-to-vigorous PA (MVPA), all of which may have the potential to alter an individual's health through various different pathways and mechanisms. This study aimed to explore the relationship between PA behaviours and the gut microbiome in older adults. Cross-sectional study. Participants (n=100; age 69.0 [3.0] years; 44% female) from the Mitchelstown Cohort Rescreen (MCR) Study (2015-2017). Participants provided measures of gut microbiome composition (profiled by sequencing 16S rRNA gene amplicons), and objective measures of PA behaviours (by a 7-day wear protocol using an activPAL3 Micro). Standing time was positively correlated with the abundance of butyrate-producing and anti-inflammatory bacteria, including Ruminococcaceae, Lachnospiraceae and Bifidobacterium, MVPA was positively associated with the abundance of Lachnospiraceae bacteria, while sedentary time was associated with lower abundance of Ruminococcaceae and higher abundance of Streptococcus spp. Physical activity behaviours appear to influence gut microbiota composition in older adults, with different PA behaviours having diverging effects on gut microbiota composition.

Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development.

To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled Arabidopsis thaliana during 2 years at two Michigan sites and surveyed colonists by sequencing 16S rRNA gene amplicons. Mosaic and dynamic assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. Although assemblages primarily varied between roots and shoots, amplicon sequence variants (ASVs) also differentiated phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age weakened. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were not broadly shared at the family level. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established.IMPORTANCE Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed. In our study, phyllosphere tissues housed increasingly distinct microbial assemblages as plants aged, indicating that plants can be considered collections of tissue habitats in which microbial colonists-natural or synthetic-are established with differing success. Relationships between host genes and community diversity might vary depending on when samples are collected, given that assemblages grew more diverse as plants aged. Both spatial and temporal trends weakened when colonists were grouped by family, suggesting that functional rather than taxonomic profiling will be necessary to understand the basis for differences in colonization success.

Spatial and Temporal Dynamics in Attached and Suspended Bacterial Communities in Three Drinking Water Distribution Systems with Variable Biological Stability.

Microbial presence and regrowth in drinking water distribution systems (DWDSs) is routinely monitored to assess the biological stability of drinking water without a residual disinfectant, but the conventional microbiological culture methods currently used target only a very small fraction of the complete DWDS microbiome. Here, we sequenced 16S rRNA gene amplicons to elucidate the attached and suspended prokaryotic community dynamics within three nonchlorinated DWDSs with variable regrowth conditions distributing similarly treated surface water from the same source. One rural location, with less regrowth related issues, differed most strikingly from the other two urban locations by the exclusive presence of Pseudonocardia (Actinobacteria) in the biofilm and the absence of Limnobacter (Betaproteobacteriales) in the water and loose deposits during summer. There was a dominant seasonal effect on the drinking water microbiomes at all three locations. For one urban location, it was established that the most significant changes in the microbial community composition on a spatial scale occurred shortly after freshly treated water entered the DWDS. However, summerly regrowth of Limnobacter, one of the dominant genera in the distributed drinking water, already occurred in the clean water reservoir at the treatment plant before further distribution. The highlighted bacterial lineages within these highly diverse DWDS communities might be important new indicators for undesirable regrowth conditions affecting the final drinking water quality.

Soil structure, nutrient status and water holding capacity shape Uruguayan grassland prokaryotic communities.

Soil microbial communities play critical roles in maintaining natural ecosystems such as the Campos biome grasslands of southern South America. These grasslands are characterized by a high diversity of soils, low available phosphorus (P) and limited water holding capacity. This work aimed to describe prokaryotic communities associated with different soil types and to examine the relationship among these soil communities, the parent material and the soil nutrient status. Five Uruguayan soils with different parent material and nutrient status, under natural grasslands, were compared. The structure and diversity of prokaryotic communities were characterized by sequencing 16S rRNA gene amplicons. Proteobacteria, Actinobacteria, Firmicutes,Verrucomicrobia, Acidobacteria, Planctomycetes and Chloroflexi were the predominant phyla. Ordination based on several distance measures was able to discriminate clearly between communities associated with different soil types. Edge-PCA phylogeny-sensitive ordination and differential relative abundance analyses identified Archaea and the bacterial phyla Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia as those with significant differences among soil types. Canonical analysis of principal coordinates identified porosity, clay content, available P, soil organic carbon and water holding capacity as the main variables contributing to determine the characteristic prokaryotic communities of each soil type.

Gut Microbiota Associations with Metabolic Health and Obesity Status in Older Adults.

Emerging evidence links the gut microbiota with several chronic diseases. However, the relationships between metabolic syndrome (MetS), obesity and the gut microbiome are inconsistent. This study aimed to investigate associations between gut microbiota composition and diversity and metabolic health status in older adults (n = 382; median age = 69.91 [± 5 years], male = 50.79%) with and without obesity. Gut microbiome composition was determined by sequencing 16S rRNA gene amplicons. Results showed that alpha diversity and richness, as indicated by the Chao1 index (p = 0.038), phylogenetic diversity (p = 0.003) and observed species (p = 0.038) were higher among the metabolically healthy non-obese (MHNO) individuals compared to their metabolically unhealthy non-obese (MUNO) counterparts. Beta diversity analysis revealed distinct differences between the MHNO and MUNO individuals on the phylogenetic distance scale (R2 = 0.007, p = 0.004). The main genera contributing to the gut composition among the non-obese individuals were Prevotella, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. Prevotella, Blautia, Bacteroides, and unclassified Ruminococcaceae mainly contributed to the variation among the obese individuals. Co-occurrence network analysis displayed different modules pattern among different metabolic groups and revealed groups of microbes significantly correlated with individual metabolic health markers. These findings confirm relationships between metabolic health status and gut microbiota composition particularly, among non-obese older adults.

16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary.

Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 16,165 unique amplicon sequence variants were recovered, and Proteobacteria was the dominant phylum.

Abstract B33: Racial differences in tumor-associated microbes in early colorectal carcinogenesis

Abstract African Americans (AA) have a higher incidence of colorectal cancer (CRC) than Caucasian Americans (CA). Emerging evidence indicates that pathogenic tumor-associated microbes (TAMs) within preinvasive lesions may promote carcinogenesis. Since AAs are more prone than CAs to robust inflammatory responses to bacteria and fungi, especially at younger ages, infiltrates in early neoplasms may differ by race and age. To study this issue, we selected a convenience sample of 35 preinvasive cases diagnosed between October 2013 and October 2016 at the Medical University of South Carolina for microbial analysis. The study pathologist diagnosed the degree of dysplasia and predominant histology for each lesion. We extracted DNA from 10-micron-thick FFPE sections and sequenced 16S rRNA gene amplicons to determine the microbial communities. We normalized the data using central log ratio transformation with pseudo-counts and selected 20 microbes previously associated with CRC for analysis. Linear regression was used to assess associations between TAMs and race while adjusting for age and sex. We also examined these associations by colorectal location (distal, proximal), degree of dysplasia (high, not high), and age (&amp;lt; 55, 55+) using product interaction terms in our statistical models. 49% of cases were AAs, 57% were female, and 51% were less than 55 years of age. We analyzed 4 serrated polyps, 6 tubular adenoma, 16 tubulovillous adenomas, and 9 villous adenomas. 40% of the cases had high-grade dysplasia (including focal) and 51% of all lesions were from the distal colon (and rectum). We observed that AAs compared to CAs had a significantly higher microbial abundance of genus Escherichia (coef. 1.42 p=0.005), species Escherichia coli (coef. 1.38, p=0.007), and genus Shigella (coef. 1.15, p=0.02). Moreover, AAs had relatively higher TAM infiltration with these microbes in distal colorectal lesions than CAs, but there were no differences by race in the proximal colon. Finally, we observed that in comparison to older CAs, older AAs had relatively higher abundance of Escherichia (coef. 2.50; p &amp;lt; 0.001; p for interaction=0.056), E. coli (coef. 2.45, p=0.001; p for interaction=0.04), and Shigella (coef. 2.24, p=0.001; p for interaction=0.04), but there were no significant differences in younger patients by race. Two additional microbes, Porphyromonas (p=0.01) and Ruminococcus gnavus (p=0.02), were found in lower relative abundance in AAs vs. CAs. We identified racial differences in TAMs associated with the Enterobacteriaceae family. The stronger racial differences in TAMs observed in the older but not younger patients may reflect age-related differences in bacterial clearance. In future studies, it will be important to compare the TAMs, immune reactions with markers of tumor progression. Citation Format: Kristin Wallace, David N. Lewin, Christine Bookhout, Shaoli Sun, Brianna Bronsky, Chentha Vasu, Brenda J. Hoffman, John A. Baron, Alexander V. Alekseyenko. Racial differences in tumor-associated microbes in early colorectal carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B33.

Liming does not counteract the influence of long-term fertilization on soil bacterial community structure and its co-occurrence pattern

Chemical fertilizer application is a common agronomic practice to improve crop productivity and liming is often used to counteract the soil acidification caused by long-term fertilization; however, it is unclear whether liming will counteract the effect of long-term fertilization on soil bacterial community structure and its co-occurrence pattern. Here, we examined the influence of long-term fertilization (NPKS) and liming (L) on soil bacterial community structure and its co-occurrence networks by sequencing 16S rRNA gene amplicons. Our results showed that liming counteracted the influence of long-term fertilization on soil pH, but not on soluble organic carbon (SOC) and electrical conductivity (EC). Long-term fertilization affected the abundance of Acidobacteriia, Deltaproteobacteria and Gammaproteobacteria in the 0–10 cm soil, and that of Deltaproteobacteria, Gammaproteobacteria and Gemmatimonadetes in the 10–20 cm soil; whereas liming affected the abundance of Acidobacteriia, Gammaproteobacteria, and Chloracidobacteria in the 0–10 cm soil and that of Deltaproteobacteria in the 10–20 cm soil. The bacterial community structure in soils with the NPKS-L treatment was different from that with other treatments, and was mainly affected by SOC, EC, and NO3− concentration. The link numbers in bacterial co-occurrence networks were decreased by long-term fertilization or liming alone, but were increased by the NPKS-L treatment. Notwithstanding the fact that liming alleviates fertilization-induced soil acidification, this study indicates that liming did not counteract the effect of long-term fertilization on soil bacterial community structure and its co-occurrence pattern, hence cannot recuperate the soil microbial functionality that is changed by long-term fertilization.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake.

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.