Corrigendum: Human gut microbiome across different lifestyles: from hunter-gatherers to urban populations.

[This corrects the article DOI: 10.3389/fmicb.2022.843170.].

Molecular identification and biofilm formation of aerobic and anaerobic coinfection bacterial isolated from cystic fibrosis patients in southwest Iran from 2014 to 2022.

BACKGROUND: Coinfections and resistant bacterial infections are more likely to occur in cystic fibrosis patients because their immune systems are weak. The purpose of this study was to identify by molecular means as well as the formation of biofilm of aerobic and anaerobic coinfection bacteria isolated from cystic fibrosis patients in southwest Iran from 2014 to 2022. METHODS: In this investigation, 130 clinical specimens were collected from 130 CF patients by universal primer. Biofilm formation was investigated using the microtiter plate method. Antibiotic resistance was measured using Vitec 2 device. In addition, identification of methicillin-resistant Staphylococcus aureus using genes mecA was performed. MAIN FINDINGS: In aerobic bacteria, Pseudomonas aeruginosa was detected in (32%) of samples. In anaerobic bacteria (16%) Prevotella spp. was the most frequently isolated anaerobe bacteria found in of the CF patients. In this study, 75% of the bacteria could form biofilms, while 23% were unable to biofilm formation. CONCLUSION: In conclusion, P. aeruginosa was found to be the most frequently isolated bacterium from patients with CF, and many of these bacteria could form biofilms. Additionally, the high prevalence of antibiotic resistance indicates the urgent need for increased attention to antibiotic preparation and patient screening concerning bacterial coinfections and the virulence and adhesion factors of these bacteria. Furthermore, the present study demonstrates that the coinfection of bacteria with high antibiotic resistance and a high capacity for biofilm formation can pose a life-threatening risk to CF patients, mainly due to their weakened immune systems.

Gut metabolomics and 16S rRNA sequencing analysis of the effects of arecoline on non-alcoholic fatty liver disease in rats.

Introduction: Non-alcoholic fatty liver disease (NAFLD) has gradually become the primary cause of fatty liver disease. Betel nuts have been used to treat gastrointestinal diseases. Methods: In the present study, we analyzed the pathology, serology, gut flora, and metabolites in a rat model of NAFLD, with and without betel nut alkaloid treatment, using an integrated approach involving pathology, serological testing, 16S rRNA gene sequencing, and ultra-performance liquid chromatography-mass spectrometry metabolomics. Results: Two rats were used for model validation. Thirty SD rats were included and divided into the normal group (C group), NAFLD model group (M group), low-dose group, medium-dose group (T group), and high-dose group with intraperitoneal injection of arecoline. The expression of blood lipids was significantly downregulated at all three arecoline concentrations (p < 0.05). Alpha-diversity analysis of the intestinal flora showed significant differences among the three groups, with a significant reduction in population diversity in the M group and a recovery of population diversity after arecoline treatment. At the phylum level, the relative abundance of Firmicutes was significantly higher in the T group and Proteobacteria in the M group. The KEGG metabolic pathways included polyketide sugar unit biosynthesis and hypertrophic cardiomyopathy. Thirty-three significantly different metabolites were identified among the groups. Significantly different metabolites between groups T and M included indolepyruvate, 2-deoxystreptamine, sakuranetin, glycyl-leucine, and riboflavin. The KEGG metabolic pathway suggested a potential role for arachidonic acid metabolism, serotonergic synapses, neuroactive ligand-receptor interactions, tyrosine metabolism, and regiomelanin. Vitamin digestion and absorption, as well as regulation of lipolysis in adipocytes, were the main metabolic pathways that distinguished the T vs. M groups. PGE2 is involved in several metabolic pathways. Correlation analysis showed that 29 bacterial species were significantly associated with PGE2 levels in the M and T groups. Vagococcus, Lawsonia, Christensenella, unidentified Erysipelotrichaceae, unidentified Coriobacteriaceae, and five other bacterial groups are unique in the PGE2 metabolic pathway regulated by arecoline. Discussion: Arecoline has lipid-lowering effects and may exert therapeutic effects in NAFLD through intestinal metabolites and intestinal flora, as well as through the Butyricicoccus/Christensenella/Coriobacteriaceae-COX2/PGE2 pathway. Thus, arecoline may represent a potential drug or target for NAFLD treatment.

Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations.

Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in the human microbiome. The comparison between industrialized and non-industrialized human populations in several studies has allowed to observe variation in the microbiome structure due to the population lifestyle. Nevertheless, the lifestyle of human populations is a gradient where several subcategories can be described. Yet, it is not known how these different lifestyles of human populations affect the microbiome structure on a large scale. Therefore, the main goal of this work was the collection and comparison of 16S data from the gut microbiome of populations that have different lifestyles around the world. With the data obtained from 14 studies, it was possible to compare the gut microbiome of 568 individuals that represent populations of hunter-gatherers, agricultural, agropastoral, pastoral, and urban populations. Results showed that industrialized populations present less diversity than those from non-industrialized populations, as has been described before. However, by separating traditional populations into different categories, we were able to observe patterns that cannot be appreciated by encompassing the different traditional lifestyles in a single category. In this sense, we could confirm that different lifestyles exhibit distinct alpha and beta diversity. In particular, the gut microbiome of pastoral and agropastoral populations seems to be more similar to those of urban populations according to beta diversity analysis. Beyond that, beta diversity analyses revealed that bacterial composition reflects the different lifestyles, representing a transition from hunters-gatherers to industrialized populations. Also, we found that certain groups such as Bacteoidaceae, Lanchospiraceae, and Rickenellaceae have been favored in the transition to modern societies, being differentially abundant in urban populations. Thus, we could hypothesize that due to adaptive/ecological processes; multifunctional bacterial groups (e.g., Bacteroidaceae) could be replacing some functions lost in the transition to modern lifestyle.

Association of the Cervical Microbiota With Pregnancy Outcome in a Subfertile Population Undergoing In Vitro Fertilization: A Case-Control Study.

The microorganisms of the reproductive tract have been implicated to affect in vitro fertilization (IVF) outcomes. However, studies on the reproductive tract microbiota of infertile women are limited and the correlation between cervical microbiota and IVF outcome remains elusive. This study aimed to characterize the cervical microbiota of IVF patients undergoing embryo transfer (ET) and assess associations between the cervical microbiota and pregnancy outcomes while exploring the underlying contributing factors. We launched a nested case-control study of 100 patients with two fresh or frozen-thawed cleavage embryos transferred per IVF cycle. Cervical swabs were collected on the day of ET and divided into four groups according to clinical pregnancy outcomes. Variable regions 3 and 4 (V3-V4) of the 16S rRNA gene were amplified and sequenced on the Illumina MiSeq platform. In fresh IVF-ET cycles, the clinical pregnancy group (FP, n = 25) demonstrated higher α diversity (P = 0.0078) than the non-pregnancy group (FN, n = 26). Analysis of similarity (ANOSIM) revealed a significant difference in ß diversity between the two groups (R = 0.242, P = 0.001). In frozen-thawed ET cycles, though not significant, similar higher α diversity was found in the clinical pregnancy group (TP, n = 27) compared to the non-pregnancy group (TN, n = 22) and ANOSIM analysis showed a significant difference between the two groups (R = 0.062, P = 0.045). For patients in fresh IVF-ET groups, Lactobacillus, Akkermansia, Desulfovibrio, Atopobium, and Gardnerella showed differentially abundance between pregnant and non-pregnant women and they accounted for the largest share of all taxa investigated. Among them, Lactobacillus was negatively correlated with the other genera and positively correlated with serum estradiol levels. Logistic regression analysis suggested that the composition of the cervical microbiota on the day of ET was associated with the clinical pregnancy in fresh IVF-ET cycles (P = 0.030). Our results indicate that cervical microbiota composition has an impact on the outcome of assisted reproductive therapy.

Erysipelothrix rhusiopathiae endocarditis diagnosed by broad range 16s rRNA PCR gene sequencing.

Erysipelothrix rhusiopathiae (E. rhusiopathiae) is a rare occupational opportunistic Gram-positive bacillus. Infections caused by E. rhusiopathiae are principally a sequel of occupational and recreational exposures to infected animals. Infective endocarditis is a classic, albeit it infrequent, manifestation of invasive infection with this bacterium. We present a case of E. rhusiopathiae mitral valve endocarditis in a farmer with psoriasis presented with acute intractable heart failure requiring valve replacement surgery. E. rhusiopathiae was identified by 16S rRNA-based gene sequencing from culture-negative, surgically excised mitral valve leaflets.

Rhizobacterial Community Assembly Patterns Vary Between Crop Species.

Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.

Effects of fumigation with 1,3-dichloropropene on soil enzyme activities and microbial communities in continuous-cropping soil.

The compound 1,3-D (1,3-dichloropropene) is a potential candidate soil fumigant due to the restrictions on methyl bromide (MB). To date, little is known about the soil microbial community changes induced by 1,3-D fumigation. Therefore, soil properties, related soil enzymes, genes encoding the key enzymes of ammonia oxidation in both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and bacterial diversity were investigated to assess the effects of 1,3-D fumigation on the soil microbial community. The results exhibited that fumigation with 1,3-D caused accumulation of NH4+-N, but it led to decrease in the rate of NO3--N, and the concentration of NO3--N gradually recovered. At 12 weeks after transplant (WAT) of tomato seedlings, the concentration of NH4+-N and NO3--N were not statistically significant between the 1,3-D treatment groups and the untreated control group. A similar tendency was found for organic matter, soil pH, urease and protease activities. Moreover, quantitative real-time PCR (qPCR) showed that 1,3-D decreased total bacterial abundance, AOA-amoA and AOB-amoA genes. In addition, Illumina MiSeq sequencing analysis revealed that soil bacterial community diversities were significantly reduced at earlier sampling time points, and at later sampling time points, soil bacterial diversity gradually recovered, there was no significant difference compared to the control group. The present study provides useful information to evaluate the environmental safety of 1,3-D.

Biogeography of the human ocular microbiota.

PURPOSE: The human eye is composed of numerous microhabitats. The aim of this study was to understand the communality and differences in the microbiomes of various regions of the eye. METHODS: Four ocular sites from different subject groups were assessed including the eyelid margin tissue from patients with lid abnormalities (n = 20), fornix and limbus conjunctival tissue from patients with pterygia (n = 23), ocular (conjunctival) surface swabs (n = 45) and facial skin swabs (n = 16). Microbial communities were analysed by extracting total DNA from samples and sequencing the 16S ribosomal(r)RNA gene using the Illumina MiSeq platform. Sequences were quality filtered, clustered into unique sequences (zOTUs) using the UNOISE pipeline in USEARCH and taxonomically classified using SILVA. RESULTS: A difference in bacterial richness and diversity was found between sites (P < 0.001) and for age (P < 0.035) but not for sex (P > 0.05). There was a difference in bacterial community structure and composition between sites (P < 0.001). Bacterial distribution could be broadly classified into three groups - zOTUs resident on the skin and lid margin but with low abundances at other sites (Corynebacterium, Staphylococcus), zOTUs found mainly on the ocular surface (Acinetobacter, Aeribacillus) and zOTUs mostly present in the conjunctiva and lid margin (Pseudomonas). CONCLUSION: The microhabitats of the human eye (ocular surface, conjunctiva, lid margin and skin) have a distinct bacterial biogeography with some bacteria shared between multiple regions while other bacteria occupy a more confined niche.

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling.

Chloropicrin (CP) is a potential alternative for methyl bromide as a soil fumigant given that the use of methyl bromide has become limited. However, little is known about how fumigation with CP affects the condition of the soil microbial community. In this study, 16S rRNA amplicon sequencing and quantitative PCR were combined to investigate the effect of CP on soil bacterial community. In total, 938,922 effective reads were obtained from 18 samples and clustered into 58,662 operational taxonomic units at a similarity cut-off of 97%. Both approaches showed that the primary structure of bacterial community in soil did not significantly change at the phylum level after fumigation, but CP had a significant impact on the abundance of the bacterial microbiome that was recovered and identified. Additionally, bacterial community diversity decreased significantly, and there was a shift in the predominant populations. Staphylococcus, Actinomadura, Acinetobacter and Streptomyces significantly decreased in number or disappeared, and Bacteroides, Lachnoclostridium, Pseudoalteromonas, Colwellia, Idiomarina and Cobetia became the new predominant populations. In addition, some species associated with biodegradation, such as Sphingomonas spp. and Rhodococcus spp., significantly increased in number. The abundance of ammonia-oxidizing archaea (AOA) were significantly inhibited, yet the abundance of ammonia-oxidizing bacteria (AOB) significantly increased, and denitrification was significantly promoted. These changes in bacterial flora can considerably impact soil function and health and lead to negative effects on the environment surrounding fumigated soils, indicating the need for proactive risk management. Our study provides useful information for environmental safety assessments of CP in China.

Unique hyper-thermal composting process in Kagoshima City forms distinct bacterial community structures.

A unique compost, Satsuma soil, is produced from three types of wastewater sludge using hyper-thermal processes at temperatures much higher than that of general thermophilic processes in Kagoshima City, Japan. We analyzed the bacterial community structures of this hyper-thermal compost sample and other sludges and composts by a high-throughput barcoded pyrosequencing method targeting the 16S rRNA gene. In total, 621,076 reads were derived from 17 samples and filtered. Artificial sequences were deleted and the reads were clustered based on the operational taxonomic units (OTUs) at 97% similarity. Phylum-level analysis of the hyper-thermal compost revealed drastic changes of the sludge structures (each relative abundance) from Firmicutes (average 47.8%), Proteobacteria (average 22.3%), and Bacteroidetes (average 10.1%) to two main phyla including Firmicutes (73.6%) and Actinobacteria (25.0%) with less Proteobacteria (∼0.3%) and Bacteroidetes (∼0.1%). Furthermore, we determined the predominant species (each relative abundance) of the hyper-thermal compost including Firmicutes related to Staphylococcus cohnii (13.8%), Jeotgalicoccus coquinae (8.01%), and Staphylococcus lentus (5.96%), and Actinobacteria related to Corynebacterium stationis (6.41%), and found that these species were not predominant in wastewater sludge. In contrast, we did not observe any common structures among eight other composts produced, using the hyper-thermal composts as the inoculums, under thermophilic conditions from different materials. Principle coordinate analysis of the hyper-thermal compost indicated a large difference in bacterial community structures from material sludge and other composts. These results suggested that a distinct bacterial community structure was formed by hyper-thermal composting.

Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India.

Bacterial community structure was analyzed from coastal water of Alang-Sosiya ship breaking yard (ASSBY), world's largest ship breaking yard, near Bhavnagar, using 16S rRNA gene sequencing (cultured dependent and culture independent). In clone libraries, total 2324 clones were retrieved from seven samples (coastal water of ASSBY for three seasons along with one pristine coastal water) which were grouped in 525 operational taxonomic units. Proteobacteria was found to be dominant in all samples. In pristine samples, Gammaproteobacteria was found to be dominant, whereas in polluted samples dominancy of Gammaproteobacteria has shifted to Betaproteobacteria and Epsilonproteobacteria. Richness and diversity indices also indicated that bacterial community in pristine sample was the most diverse followed by summer, monsoon and winter samples. To the best of knowledge, this is the first study describing bacterial community structure from coastal water of ASSBY, and it suggests that seasonal fluctuation and anthropogenic pollutions alters the bacterial community structure.

Antimicrobial potential of bacteriocin producing Lysinibacillus jx416856 against foodborne bacterial and fungal pathogens, isolated from fruits and vegetable waste.

In this study, antimicrobial potential, some probiotics properties and bacteriocin nature of Lysinibacillus, isolated from fruits and vegetable waste were evaluated. For this, 125 Lactobacillus isolates were tested against foodborne bacterial and fungal pathogens. Among these, an isolated Bacillus spp. showed significant aggregation-co-aggregation probiotics properties and potentially inhibits the foodborne gram positive microbial pathogens such as Staphylococcus aureus, (22 mm ZOI), Staphylococcus epedermidis and Bacillus cereus (18 mm). Phenotypically and molecularly it was identified as Lysinibacillus (NCBI accession no. JX416856) and it was found closest to Lysinibacillus fusiformis, Lysinibacillus sphaericus and Lysinibacillus xylanilyticus. Physico-biochemically, it was found to be negative for amylase, protease, gelatinase, nitrate reductase and urease while positive for catalase. The diagnostic fatty acid was 22;2 (3.51). The growth conditions and bacteriocin activity were found to be optimum with MRS media at pH 7-10, Temperature 35-40 °C and salt tolerance at 1-3%. Eventually its production was optimized with MRS broth at pH 7.6, 37 °C, for 36 h in shaking conditions at the rate of 100 rpm. Active bacteriocin was isolated at 60% ammonium sulfate precipitation. The molecular weight of given bacteriocin was found to be nearly 25-35 kDa by SDS-PAGE. Based on physico- biochemical properties, the isolated bacteriocin was to be categories in class II bacteriocin. The bacteriocin was found to be stable in the range of 4-80 °C temperature, 6-10 pH and even in the presence of surfactant (such as SDS and Tween 80). However, proteases like pepsin and trypsin were found to degrade the bacteriocin. Collectively, the broad spectrum inhibitory potential and physical stability offered the antimicrobial potential to Lysinibacillus, and its relevant bacteriocin might be used as an alternative food preservative or therapeutic agent to control spoilage of different food products.

Protease characteristics of bacteriocin producing Lysinibacilli, isolated from fruits and vegetable waste.

This study describes the physical stability and optimization of nutrient components for an extracellular protease produced by Bacillus strains isolated from fruits and vegetable waste, Lucknow, India. The isolated proteases could hydrolyze various native proteinaceous substrates such as bovine serum albumin, casein, skim milk, but not the gelatin. The strain JX416854 and isolate 10 yielded maximum protease (831; 703 U/ml) under optimized conditions: Nutrient, Casein broth; pH 7.0; shaking condition 37°C for 36 h. Crude protease exhibited activity over a wide range of pH (6.0-10.0) and found to be stable at (10-70°C), pH stable at 7- 9.0. The significant protease activity was observed with divalent cations Ca2+ and Mg2+ and EDTA. Further, significant blood destaining properties and stabilities with detergents were also observed. Thus, the significant potency and stability of these enzymes indicated their industrial importance and could be an alternative protease for various industrial applications.