Abundant Genera Research Articles

Altitude-associated trends in bacterial communities in ultrahigh-altitude residences

BackgroundIndoor bacterial communities may change with altitude because their major contributors, outdoor bacterial communities, vary with altitude. People’s health effects from bacteria inhalation exposure can also vary with altitude because human respiratory physiology changes with oxygen content in air. Accordingly, adjusting indoor bacterial communities may help to acclimate newcomers from low-altitude environments to ultrahigh-altitude environments. To lay the groundwork for further research, we aimed to first elucidate the bacterial communities in ultrahigh-altitude residences and the effects of altitude on these communities. We collected 187 environmental samples from residential communities at ultrahigh altitudes of 3811–4651 m in Ngari, China and sequenced bacterial 16S rRNA genes. ResultsOn one hand, when abundant genera in ultrahigh-altitude residences and those reported by previous studies on low-altitude residences were compared, nine genera were shared, whereas other five genera were abundant only at ultrahigh altitudes. On the other hand, when the bacterial communities of residences at different ultrahigh altitudes were further compared, the bacterial composition in indoor surface samples varied significantly with altitude. The relative abundance of five bacterial genera in indoor air samples and 10 genera and three phyla in indoor surface samples varied monotonically with altitude. ConclusionsAltitude may be a long-neglected factor that shapes residential bacterial communities and thus warrants attention.

Exploring the role of indoor microbiome and environmental characteristics in rhinitis symptoms among university students

IntroductionRhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.MethodsIn this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.ResultsThe most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).DiscussionThis study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.

Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome.

The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.

Characteristics of bacterial community in eyelashes of patients with Demodex blepharitis

BackgroundDemodex blepharitis (DB) is a common disease of the ocular surface. The characteristics of the bacterial community in eyelash roots after Demodex infestation are still unknown. Knowledge of the characteristics of the bacterial community of eyelash follicles in patients with DB can provide valuable insights for guiding the diagnosis and treatment of DB.MethodsTwenty-five patients with DB (DB group) and 21 non-DB volunteers (control group) were enrolled in the study. Eyelashes from the upper eyelid of the right eye were sampled, and 16S ribosomal DNA (rDNA) sequencing was performed to determine the V3-V4 regions of the microbial 16S rDNA gene within 1 month of infestation. The sequencing data of the two groups were analyzed and compared. The effect of the bacterium Burkholderia on the survival of Demodex mites was evaluated using Demodex obtained from 12 patients with DB other that the patients in the DB group.ResultsA total of 31 phyla and 862 genera were identified in the DB and control groups. The five most abundant phyla in the two groups were Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria. The abundance of Actinomycetes was significantly higher in the DB group than in the control group. At the genus level, the five most abundant genera in the two groups were Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, Rolstonia and Acinetobacter; Clostridium sensu stricto 1 was abundant in the control group and Corynebacterium_1 was abundant in the DB group. Compared with the control group, the abundance of Burkholderia-Caballeronia-Paraburkholderia was 2.36-fold lower in the DB group. Linear discriminant analysis Effect Size (LEfSe) analysis revealed Burkholderia-Caballeronia-Paraburkholderia, SC_I_84_unclassified, Nonmyxobacteria and Succinvibrio to be the major biomarkers in the control group and Catenibacterium and Lachnospiraceae NK4A136 group to be the major biomarkers in the DB group. To explore the performance of these optimal marker models, receiver operational characteristic curve analysis was performed, and the average area under the curve value of Burkholderia-Caballeronia-Paraburkholderia was 0.7448. Burkholderia cepacia isolated from normal human eyelashes was fermented, and the Demodex mites isolated from patient eyelashes were cultured together with its fermented supernatant. The results showed that the fermentation supernatant could significantly reduce the survival time of the Demodex mites, suggesting the potential therapeutic value of this bacterium against Demodex.ConclusionsThe composition of the bacterial community in the eyelashes of DB patients differed from that in eyelashes of healthy volunteers, revealing a decrease in bacterial diversity in infested eyelashes. This decrease may be related to the occurrence and development of DB. The supernatant of Burkholderia cepacia culture medium was found to inhibit the growth of Demodex in eyelash hair follicles, providing a new insight with potential applications for the clinical treatment of Demodex infestation.Graphical

Gut bacterial community of Cnaphalocrocis medinalis (Guenée) (Lepidoptera: Crambidae) is driven by rice varieties

AbstractTo understand the effect of diet on gut bacteria of Cnaphalocrocis medinalis (rice leaf folder, RLF), we compared the composition and diversity of gut bacterial community in C. medinalis larvae collected from three different rice variety fields of Minghui 82 (RLF1), Youngyong 15 (RLF2) and Minghui 2155 (RLF3), using culture‐independent PCR (V3 variable region)‐denaturing gradient gel electrophoresis (PCR‐DGGE) methods and hypervariable region (V4) of 16S rRNA sequenced by Illumina HiSeq platform. The DGGE result showed that the bacteria genera Asaia, Bacillus, Stenotrophomonas, Achromobacter and Serratia coexisted in the guts of RLF1, RLF2 and RLF3, while Cedecea, Burkholderia and Acinetobacter coexisted in the guts of RLF2 and RLF3. However, only the genus Enterococcus existed in the guts of RLF1, and Pantoea, Wolbachia and Tumebacillus in RLF3 larvae. A total of 25 bacterial phyla, 48 classes, 127 orders, 223 families, and 406 genera were identified when using 16s RNA sequencing, with 35 genera coexisted in RLF1, RLF2 and RLF3 larval guts, while 83, 36, 141 unique genera existed in RLF1, RLF2 and RLF3, respectively. The indices of ACE and Shannon were not significantly different among RLF1, RLF2 and RLF3. The dominant bacterial taxa were Proteobacteria, Bacteroidetes and Firmicutes at the phylum level, and Acinetobacter and Wolbachia at the genus level. The relative genus abundance for the genera with relative abundance (≥0.01) was significantly different among RLF1, RLF2 and RLF3. The findings indicated that different rice varieties had significant effects on the relative abundance of gut bacteria in RLF, which could provide new insights into the relationship between insect gut bacteria and their associated host plants.

Microcystin influence on soil-plant microbiota: Unraveling microbiota modulations and assembly processes in the rhizosphere of Vicia faba

Microcystins (MCs) are frequently detected in cyanobacterial bloom-impacted waterbodies and introduced into agroecosystems via irrigation water. They are widely known as phytotoxic cyanotoxins, which impair the growth and physiological functions of crop plants. However, their impact on the plant-associated microbiota is scarcely tackled and poorly understood. Therefore, we aimed to investigate the effect of MCs on microbiota-inhabiting bulk soil (BS), root adhering soil (RAS), and root tissue (RT) of Vicia faba when exposed to 100 μg L−1 MCs in a greenhouse pot experiment. Under MC exposure, the structure, co-occurrence network, and assembly processes of the bacterial microbiota were modulated with the greatest impact on RT-inhabiting bacteria, followed by BS and, to a lesser extent, RAS. The analyses revealed a significant decrease in the abundances of several Actinobacteriota-related taxa within the RT microbiota, including the most abundant and known genus of Streptomyces. Furthermore, MCs significantly increased the abundance of methylotrophic bacteria (Methylobacillus, Methylotenera) and other Proteobacteria-affiliated genera (e.g., Paucibacter), which are supposed to degrade MCs. The co-occurrence network of the bacterial community in the presence of MCs was less complex than the control network. In MC-exposed RT, the turnover in community composition was more strongly driven by deterministic processes, as proven by the beta-nearest taxon index. Whereas in MC-treated BS and RAS, both deterministic and stochastic processes can influence community assembly to some extent, with a relative dominance of deterministic processes. Altogether, these results suggest that MCs may reshape the structure of the microbiota in the soil-plant system by reducing bacterial taxa with potential phytobeneficial traits and increasing other taxa with the potential capacity to degrade MCs.

NH2-MIL-101(Fe)-mediated photo-Fenton reaction enhanced simultaneous removal of nitrogen and refractory organics in anammox process through interfacial electron transfer

In this study, H2O2 (0.1 ‰) and NH2-MIL-101(Fe)-driven (150 mg/L) photo-Fenton-coupled anammox were proposed to simultaneously improve the removal efficiency of nitrogen and humic acid. Long-term experiments showed that the total nitrogen removal efficiency was increased by the photo-Fenton reaction to 91.9 ± 1.5 % by altering the bioavailability of refractory organics. Correspondingly, the total organic carbon removal efficiency was significantly increased. Microbial community analyses indicated that Candidatus_Brocadia maintained high activity during photo-Fenton reaction and was the most abundant genus in the reactor. Dissimilatory nitrate reduction to ammonium process and denitrification process were enhanced, resulting in reduced NO3–-N production. The establishment of electron transfer between microorganisms and NH2-MIL-101 (Fe) improved the charge separation efficiency of the quantum dots and increased the intracellular adenosine triphosphate content of anammox bacteria. These results indicated that photo-Fenton-anammox process promoted the removal of nitrogen and refractory organics in one reactor which had good economic value and application prospects.

Prokaryotic Microbial Diversity Analysis and Preliminary Prediction of Metabolic Function in Salt Lakes on the Qinghai–Tibet Plateau

The Dong Taijinar (DT) and Xi Taijinar (XT) Salt Lakes have been extensively researched for their mineral richness. However, the composition and distribution of their microbial communities are still poorly known. In this study, we employed metagenomic sequencing to explore the diversity and potential functions of the microbial populations in DT and XT. Our findings indicate that the salinity levels in DT (332.18–358.30 g/L) were tenfold higher than in XT (20.09–36.83 g/L). Notably, archaea dominated the DT domain at 96.16%, while bacteria prevailed in XT at 93.09%. In DT, the bacterial community comprised 33 phyla and 1717 genera, with Marinobacter emerging as the dominant genus, showing a positive correlation with the total phosphorus content. The archaeal community in DT included four main phyla and 153 genera. The most abundant genera were Natronomonas (24.61%) and Halorubrum (23.69%), which had a strong positive correlation with the concentrations of Na+, Ca2+, and Cl−. Conversely, XT hosted 33 phyla and 1906 bacterial genera, with Loktanella as the dominant genus. The archaeal taxonomy in XT encompassed four phyla and 149 genera. In both salt lakes, Proteobacteria and Euryarchaeota were the most abundant bacterial and archaeal phyla, respectively. Our analysis of the halophilic mechanisms of these microorganisms suggests that the bacteria in XT tend to synthesize compatible solutes, whereas the archaea in DT adopt a ‘salt-in’ strategy, integrating salt into their cellular machinery to cope with the high-salinity environment.

UV-B Halotolerant Bacteria from Marakkanam Saltpan and Biology of UV-B Tolerant Pontibacillus salipaludis Based on Whole Genome Sequencing

Saltpans in South India experience intense sunlight and ultraviolet radiation (UV). Therefore, it was hypothesized that halophilic bacteria living there could tolerate UV radiation. To test this, sediment and water samples from the Marakkanam Saltpan were collected and exposed to an artificial UV-B lamp. After irradiation, an aliquot of the sample was spread on nutrient agar (prepared in sterilized source water), and two bacterial strains were obtained, named SBO and SBY. Based on 16S rRNA gene phylogeny, these strains were identified as Bacillus sp. and Pontibacillus salipaludis, respectively. Another aliquot of the UV-B-exposed sample was inoculated into the nutrient broth (in sterilized source water), and incubated for a week in the dark. Later, it was subjected to Illumina MiSeq-based sequencing for the V3-V4 region (16S rRNA gene). Results revealed the presence of 13 bacterial phyla. However, the phylum Bacillota (48.59%) and Pseudomonadota (27.36%) accounted for more than 75% of the diversity. Pontibacillus was the most abundant genus, accounting for 44% of total bacterial diversity. The whole genome of P. salipaludis was sequenced on Illumina HiSeqX to decipher possible genes and pathways involved in UV-B tolerance. The genome size was estimated to be 4.05 MB, with a mean G + C content of 40.82%. RASTtk-based genome annotation revealed 4217 coding sequences and 78 RNAs. Related to the UV-B tolerance, sixteen genes involved in carotenoid and prodigiosin biosynthetic pathways were found. antiSMASH showed the presence of terpene-type carotenoids. More than sixty genes involved in various DNA repair pathways were found.

The Maternal Diet Index and Offspring Microbiota at 1 Month of Life: Insights from the Mediterranean Birth Cohort MAMI.

Background: Maternal diet during pregnancy may play a role in infant health outcomes via the maternal microbiota. We assessed the association of the maternal diet index for the Mediterranean area (MDI-med) with infant gut microbiota at 1 month of life. Methods: The MAMI study is a longitudinal birth cohort in the Mediterranean area. In this work, a cross-sectional study, including 120 mother-infant dyads with available maternal diet and infant microbiota at 1-month-old data, was undertaken. The MDI developed in the US (MDI-US) was adapted for the MAMI cohort (MDI-med). Stratification based on extreme values resulted (22 in the "lower" MDI-med group and 23 in the "upper" group from the mean). Relative microbial abundances and alpha (microbial richness and diversity indexes) and beta diversity (Bray-Curtis distance matrix) were compared between the groups. Results: Higher maternal daily vegetable intake and lower red meat intake were the characteristics of the "upper" MDI-med group. Significantly lower microbial diversity (Shannon and InvSimpson index (p = 0.01)), but no changes in richness (Chao1 index) nor in beta-diversity, using Bray-Curtis distance, were observed in the "upper" group, compared to the "lower" MDI-med group. A higher relative abundance of the Bifidobacterium genus (Actinomycetota phylum) was associated with maternal daily vegetable and yogurt intake. Conclusion: Reduced infant microbial diversity at 1 month of age was associated with "upper" MDI-med scores. Higher maternal intakes of vegetables and yogurt were associated with higher relative abundances of the Bifidobacterium genus in the infant gut. Further studies are needed to understand the link between pregnancy diet, infant microbiota, and health outcomes.

Taxonomic Variations of Bacterial and Fungal Communities depending on Fermentation Temperature in Traditional Korean Fermented Soybean Food, Doenjang.

Meju, a fermented soybean brick, is a key component in soybean foods like doenjang and ganjang, harboring a variety of microorganisms, including bacteria and fungi. These microorganisms significantly contribute to the nutritional and sensory characteristics of doenjang and ganjang. Amplicon-based next-generation sequencing was applied to investigate how the microbial communities of meju fermented at low and high temperatures differ and how this variation affects the microbial communities of doenjang, a subsequently fermented soybean food. Our metagenomic data showed distinct patterns depending on the fermentation temperature. The microbial abundance in the bacterial community was increased under both temperatures during the fermentation of meju and doenjang. Weissella was the most abundant genus before the fermentation of meju, however, it was replaced by Bacillus at high temperature-fermented meju and lactic acid bacteria such as Weissella and Latilactobacillus at low temperature-fermented meju. Leuconostoc, Logiolactobacillus, and Tetragenococcus gradually took over the dominant role during the fermentation process of doenjang, replacing the previous dominant microorganisms. Mucor was dominant in the fungal community before and after meju fermentation, whereas Debaryomyces was dominant under both temperatures during doenjang fermentation. The dominant fungal genus of doenjang was not affected regardless of the fermentation temperature of meju. Strong correlations were shown for specific bacteria and fungi linked to specific fermentation temperatures. This study helps our understanding of meju fermentation process at different fermentation temperatures and highlights different bacteria and fungi associated with specific fermentation periods which may influence the nutritional and organoleptic properties of the final fermented soybean foods doenjang.

Water quality and microecosystem of water tanks in karst mountainous area, Southwest China.

Karst mountainous areas in Southwest China, the world's largest bare karst area, are faced with growing water shortages. Rainwater harvesting plays an important role in alleviating water shortage. However, there remains a substantial gap in the research regarding the water quality of tanks. Water samples were seasonally collected from ten tanks to investigate the physicochemical properties, microbial communities, and their key influencing factors. The result showed that pH, turbidity, chroma, DOC, and CODMn exceeded drinking water guidelines. The alkaline pH value and the deterioration of sensory properties was the main feature of tank water, from which the over-standard rate of the uncleaned water tanks was higher. Moreover, principal component analyses suggested that tank water quality was influenced by human activities, catchment areas, and material cycling processes within the tanks, of which in-tank microbial activities were the most important driving factors in water quality variation. Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Verrucomicrobia were the predominant bacterial phyla in water tanks. Acinetobacter, Cyanobium-PCC-6307, CL500-29-marine-group, Candidatus-Aquiluna, and Exiguobacterium were the most abundant genera. The bacterial communities were significantly affected by the management practices. Higher relative abundance of Cyanobacteria and lower relative abundance of Proteobacteria was detected in the uncleaned tanks, which was a sign of tank water quality deterioration. The microbial community structure was closely related to the environmental factors. There was evidence that the water quality was affected by the existence of a microecosystem dominated by photosynthetic microorganisms in the water tanks. In addition, Acinetobacter, Enterobacter, Pseudomonas, and Legionella identified as the potential opportunistic pathogenic genera were frequently detected but the relative abundances except Acinetobacter were low in the tanks. Overall, our findings indicated that management style influences water quality and bacterial communities of tank water.

Structure of crude polysaccharides from Atractylodes lancea rhizome and treatment of diarrhea owing to spleen deficiency through intestinal flora.

To optimize the extraction process of crude polysaccharides from Atractylodes and elaborate the mechanism of Atractylodes polysaccharides in treating diarrhea owing to spleen deficiency, so as to lay a foundation for further development and utilization of Atractylodes lancea, we used an orthogonal test to optimize the extraction process and established a model of spleen deficiency. It was further combined with histopathology and intestinal flora to elaborate the mechanism of Atractylodes polysaccharides in the treatment of spleen-deficiency diarrhea. The optimized extraction conditions were as follows: the ratio of material to liquid was 1:25; the rotational speed was 150rpm; the extraction temperature was 60°C; the extraction time was 2h; and the extraction rate was about 23%. The therapeutic effect of Atractylodes polysaccharides on a spleen-deficiency diarrhea model in mice showed that the water content of stools and diarrhea grade in the treatment group were alleviated, and the levels of gastrin, motilin and d-xylose were improved. The analysis results based on gut microbiota showed that the model group had a higher diversity of gut microbiota than the normal group and treatment group, and the treatment group could correct the diversity of gut microbiota in model mice. Analysis based on the level of phylum and genus showed that the treatment group could inhibit the abundance of Helicobacter pylori genus and increase beneficial bacteria genera. The conclusion was that the optimized extraction process of Atractylodes polysaccharides was reasonable and feasible, and had a good therapeutic effect on spleen deficiency diarrhea.

Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis.

The insect larvae Protaetia brevitarsis seulensis have recently been researched as a nutritious food source and concentrated on their environmental impacts. Therefore, their gut microbiota has been studied to elucidate their effects and roles on the environment. Of the abundance of bacterial genus identified based on the 16S rRNA genes from isolates of the gut of insect larva Protaetia brevitarsis seulensis, six of the prominent genus were identified as Bacillus (40.2%), Cellulosimicrobium (33.5%), Microbacterium (2.8%), Streptomyces (3%), Krasilnikoviella (17.5%), and Isoptericola (3%) and their similarity of 16S rRNA blast changed from 99 to 100%. Cellulosimicrobium protaetiae BI34T showed strong denitrification and cellulose degradation activity. The newly complete genome sequence of BI34T and the genomes of five species was published in the genus Cellulosimicrobium with emphasis on the denitrification and secondary metabolite genes. In order to elucidate the relationship between the strain BI34T and the host insect larva, the whole-genome sequence was analyzed and compared with the genomes of five strains in the same genus, Cellulosimicrobium, loaded from GenBank. Our results revealed the composition of the gut microbiota of the insect larvae and analyzed the genomic data for the new strain to predict its characteristics and to understand the nitrogen metabolism pathway.

Effects of carbon source addition in rearing water on sediment characteristics, growth and health of cultured marron (Cherax cainii)

Carbon sources are considered as critical input for the health and immunity of aquatic animals. The present study investigated the impact of different carbon sources on water quality parameters, carbon to nitrogen (C/N) ratio and microbial community in sediments, and health responses of marron (Cherax cainii) under laboratory conditions. Following one week of acclimation, 120 marron were randomly assigned to 12 experimental tanks. There were four treatments including one untreated control and three groups with carbon addition to maintain a C/N ratio of 12 maintained in culture water. Carbon supplementation groups included corn flour (CBC12), molasses (MBC12) and wheat flour (WBC12). At the end of the 60-day trial, MBC12 resulted in the highest sediment C/N ratio, followed by CBC12. Weight gain and specific growth rate were higher in MBC12, compared to control. The protease activity in marron hepatopancreas, total haemocyte count and lysozyme activity in haemolymph were highest in MBC12. Analysis of 16S rRNA sequence data of tank sediments revealed increased bacterial alpha diversity in MBC12 and WBC12. Proteobacteria was the most abundant phylum in MBC12 (88.6%), followed by control (82.4%) and CBC12 (72.8%). Sphingobium and Novosphingobium were the most abundant genera in control and MBC12 groups, respectively. Higher Aeromonas abundance in CBC12 and Flavobacterium in WBC12 were observed. Overall results indicated that MBC12 led to improved water quality, retaining high C/N ratio and enriched the bacterial populations in sediments resulting in improved growth and immune performance of marron.

Exopolysaccharide secreted by Lactiplantibacillus plantarum Y12 showed inhibitory effect on the pathogenicity of Shigella flexneri in vitro and in vivo

Shigella flexneri is a prevalent foodborne and waterborne pathogen that threatens human health. Our previous research indicated that the Lactiplantibacillus plantarum Y12 exopolysaccharide (L-EPS) potentially inhibited the pathogenicity of S. flexneri. The in vitro results of this study demonstrated that L-EPS effectively mitigated the symptoms induced by S. flexneri in HT-29 cells, including inhibited gene expression levels of IL-1β, IL-6, IL-8, TNF-α, TLR 2/4, and NOD1/2; decreased apoptosis ratio; and alleviated damage degree of intestinal barrier function (Zona occludens 1, Occludin, and Claudin-1). The in vivo results demonstrated that S. flexneri treated with L-EPS elicited mild adverse physiological manifestations, an inflammatory response, and tissue damage. The infection of S. flexneri caused significant alterations in the abundance of phylum (Firmicutes, Bacteroidota, Actinobacteriota, and Proteobacteria), family (Lachnospiraceae, Muribaculaceae, Rikenellaceae, Prevotellaceaea, Ruminococcaceae, and Lactobaillaceae), and genus (Escherichia Shigella and Lachnospirillaceae NK4A136 group) within the cecal microbiota. These changes were accompanied by perturbations in taurine and hypotaurine metabolism, tricarboxylic acid (TCA) cycle activity, arginine biosynthesis, and histidine metabolic pathways. However, intervention with L-EPS attenuated the dysbiosis of cecal microbiota and metabolic disturbances. In summary, our research suggested a potential application of L-EPS as a functional food additive for mitigating S. flexneri infection.

Dynamic changes in the migratory microbial components of colon tissue during different periods of sepsis in an LPS-induced rat model.

Previous studies have shown that bacterial translocation may play an important role in worsening gastrointestinal injury during sepsis. However, the dynamics of specific microbiota components in intestinal tissues at different sepsis stages remain unclear. Rats receiving intraperitoneal lipopolysaccharide (LPS) were sacrificed at 12 h and 48 h post-injection. Routine blood, serum cytokines, and microbiota in colon tissue, colonic contents, and lung tissue at different time points were assessed. Migratory microbial components in colonic tissue at 12 h and 48 h post-LPS were identified using source tracking, characteristic component identification, and abundance difference analyses. Colonic tissue microbiota changed dynamically over time after LPS injection, involving translocation of microbial components from colon contents and lung tissue at different time points. Bacteria migrating to colon tissue at 12 h sepsis were mainly from colonic contents, while those at 48 h were predominantly from the lung tissue. The migratory microbial components in colon tissue were widely associated with blood indicators and colonizing genus abundance and microbiota functionality in colon tissue. In this study, the temporal dynamics of bacterial translocation from various sources into colon tissues at different sepsis progression stages were characterized for the first time, and the species composition of these migrating microbes was delineated. These bacterial migrants may contribute to the pathophysiological processes in sepsis through direct interactions or indirectly by modulating colonic microbiota community structure and function.

Assessment of genetic diversity of latent bacteria in coconut leaves associated with lethal yellowing disease symptoms in Kenya

AbstractCoconut (Cocos nucifera) is an economically important palm tree with diverse applications. However, limited scientific research exists on coconut diseases in the Kenyan coastal region. This cross‐sectional study aimed to investigate the genetic diversity of latent bacteria associated with yellowing symptoms in coconut plants along the Kenyan coast. Sixty‐two samples with symptoms were collected and their bacterial diversity assessed using culture‐independent methods. DNA was extracted from controls and symptomatic samples using the cetyl trimethyl ammonium bromide (CTAB) method. Next‐generation sequencing with Illumina MiSeq was used to profile the bacterial communities using amplicons of 16S ribosomal RNA sequences (V4 region). Sequence data were analysed using the Quantitative Insights Into Microbial Ecology 2 (QIIME 2) pipeline. A total of 113,330 reads were obtained, which clustered into 285 Operational Taxonomic Units. Bacterial diversity was highest in Kilifi, followed by Kwale and Lamu, while control samples exhibited low bacterial diversity. Actinobacteria was the predominant phylum across all counties, and Streptomyces was the most abundant genus. Kilifi and Kwale counties were more affected than Lamu. This is a pioneer study that provides insight into the bacterial diversity associated with yellowing disease symptoms in coconut plants in Kenya and will help with future elucidation of the agents causing or exacerbating coconut disease symptoms.

Phytoplankton ecology in the early years of a boreal oil sands end pit lake

BackgroundBase Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.ResultsThe phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016–2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019–2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.ConclusionsBML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.

Description of the vaginal microbiota in nulliparous ewes during natural mating and pregnancy: preliminary signs of the male preputial microbiota modulation.

The vaginal microbiota plays a key role in animals' health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams' prepuce were the same as in the ewes' vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram's preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes' vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe's reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.