Heme auxotrophy in abundant aquatic microbial lineages

Heme, a porphyrin ring complexed with iron, is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Several microbial groups are known to lack the de novo heme biosynthetic pathway and therefore require exogenous heme from the environment. These heme auxotroph groups are largely limited to pathogens, symbionts, or microorganisms living in nutrient-replete conditions, whereas the complete absence of heme biosynthesis is extremely rare in free-living organisms. Here, we show that the acI lineage, a predominant and ubiquitous free-living bacterial group in freshwater habitats, is auxotrophic for heme, based on the experimental or genomic evidence. We found that two recently cultivated acI isolates require exogenous heme for their growth. One of the cultured acI isolates also exhibited auxotrophy for riboflavin. According to whole-genome analyses, all (n = 20) isolated acI strains lacked essential enzymes necessary for heme biosynthesis, indicating that heme auxotrophy is a conserved trait in this lineage. Analyses of >24,000 representative genomes for species clusters of the Genome Taxonomy Database revealed that heme auxotrophy is widespread across abundant but not-yet-cultivated microbial groups, including Patescibacteria, Marinisomatota (SAR406), Actinomarinales (OM1), and Marine groups IIb and III of Euryarchaeota. Our findings indicate that heme auxotrophy is a more common phenomenon than previously thought, and may lead to use of heme as a growth factor to increase the cultured microbial diversity.

Isolation, Genomic Analysis, and Preliminary Application of a Bovine Klebsiella pneumoniae Bacteriophage vB_Kpn_B01

Klebsiella pneumoniae is an important pathogen that can infect both humans and cattle. The widespread K. pneumoniae and its high drug resistance make it difficult to treat Klebsiella infections/diseases. In this study, a lytic K. pneumoniae bacteriophage vB_Kpn_B01 was isolated from a dairy farm trough in Sichuan Province, and its biological properties were studied, and the entire genome of vB_Kpn_B01 was sequenced. The therapeutic effects of the phage on disease-causing mice were preliminarily tested. Phages found in this study are double-stranded DNA bacterial viruses belonging to the family Siphoviridae, Sugarlandvirus. The results suggest that vB_Kpn_B01 has strong specificity and low adaptability to different adverse conditions. Meanwhile, the predicted gene products of phage vB_Kpn_B01 comprised 149 coding sequences (CDS) and 25 tRNAs, of which 34 CDS had known functions. Of course, vB_Kpn_B01 did not contain any known antibiotic-resistant or virulent genes. The pathological sections of the liver and lungs of mice showed that the inflammatory scores of the treatment group were lower than in the bacterial group. Phage vB_Kpn_B01 alleviated the inflammatory response in the organs of the infected mice, and the organ tissue bacterial load of the treatment group was significantly lower than that of the bacterial group. Therefore, vB_Kpn_B01 can inhibit the proliferation of K. pneumoniae 18 in vivo and can alleviate the inflammation of target organs caused by infectious bacteria, which preliminarily indicates that vB_Kpn_B01 has a certain therapeutic effect on laboratory-infected mice.

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.

Evaluation of Microbial Loads and Physico-Chemicals of Cassava Mill Effluent Simulated Soil

Evaluation of microbial loads and physico-chemicals of cassava mill effluent simulated soil was carried out using standard microbiological and biochemical techniques. This was to determine the effect of cassava mill effluent (CME) on rhizosphere microbial loads, physicochemical properties, nitrogenous salt and heavy metals. The results showed that CME effect on the physicochemical determinants (pH, Ca, Mg, K) and heavy metal determinant (Fe, Zn, Co, Ni, Pb and Mn) was concentration dependents. The nitrogenous salts (NO3, NH4+ and NO2) levels progressively increased with no significant differences (p>0.05 ANOVA). The microbial isolates were: Saccharomyces sp, Mucorindicus, Fusarium sp and Gliocladium sp for the fungal group. The bacterial group were Chromobacterium sp, Corynebacterium sp, Bacillus sp, Acinetobacter sp and Escherichia coli while the nitrogen-fixing bacterial group were Azotobacter sp., Azospirillum sp., Frankia sp., Bradyrhizobium sp., Hebaspirillum sp., Cyanobacteria (or blue green algae), Anabaena sp, Nostoc sp., Clostridium sp. and Rhizobium sp. There was no significant differences (p>0.05) in the rhizosphere microbial load across the concentration gradient at the CME-simulated plot phyto-remediated by Centrosema pubesscens and Calopogonium mucunoides. Agricultural wastes such as cassava mill effluent should be properly treated before discharging to the environment in other to prevent the loss of nitrogen-fixing bacteria and total heterotrophic bacterial genera that could be of immense importance to man.

Gut microbiota changes in inflammatory bowel diseases and ankylosing spondilytis

Background and Aims: Both inflammatory bowel diseases (IBD) and ankylosing spondylitis (AS) can be considered chronic immune disorders sharing common etiopathogenetic mechanisms. Changes in the composition of the intestinal microbiota, which can lead to an abnormal mucosal response, could be the missing link between these two diseases. Our study evaluate the composition of intestinal microbiota and to characterize gut dysbiosis in patients with IBD and AS. Methods: We conducted a prospective case-control study that enrolled 124 patients [20 Crohn’s disease (CD), 27 ulcerative colitis (UC), 28 AS, 17 IBD + AS and 32 controls). Intestinal microbiota analysis was performed by real-time polymerase chain reaction in stool samples. Results: The total quantity of bacteria was decreased in all investigated groups compared to the control group. In studied groups, we noticed an increased percentage of Bacteroides and Escherichia coli (E.coli) and a decreased percentage of Clostridium coccoides, Clostridium leptum, and Faecalibacterium prausnitzii compared to the control group. The percentages of Bifidobacterium (p=0.010) as well as Lactobacillus group (p=0.023) were higher in the L3 form of CD patients. In the E2 form of UC, the quantity of Bacteroides was much higher compared to the E3 form (p=0.004). In AS patients, significant correlations were observed only for the Bifidobacterium species, significantly increased in the axial form compared to peripheral disease (p=0.035). Statistically significant correlations were demonstrated between the Crohn Disease Activity Index score and the total bacterial group (p=0.023, r=-0.507), respectively Bacteroides (p=0.021, r=-0.511) and between the Mayo score and Lactobacillus (p=0.001), respectively E. coli (p=0.001). In IBD + AS group, the Crohn Disease Activity Index score was inversely correlated with the total bacterial group (p=0.010) and directly correlated with Lactobacillus (p=0.047). Conclusions: Intestinal dysbiosis is associated with both IBD and AS. In the association of IBD with AS, dysbiosis is intermediate, but it is associated with the more severe articular disease. Bifidobacterium and Lactobacillus (commonly used as probiotics!) were found to be increased in the association between active IBD and active AS. Further studies are needed to understand how dysbiosis regulates the gut immune system and contributes to intestinal and articular inflammation.

Effects of Probiotic Fermented Kitchen Waste on the Growth and Propagation of Rotifer Brachionus calyciflorus

Kitchen waste containing a large number of nutrients such as carbohydrates, proteins, lipids, and minerals can be used as fermentation substrates for producing probiotics, and then can be taken as microbial feed to cultivate rotifer. This approach not only emphasizes resource utilization of kitchen waste but also improves the growth and propagation of rotifer. In this study, kitchen wastewater and solid waste were used as fermentation substrates, respectively, while yeast, lactic acid bacteria, compound bacteria (yeast + lactic acid bacteria), and effective microorganisms (EM) bacteria were inoculated to harvest the microbial feed for the cultivation of rotifer. The population density, eggholding rate, body length, and the egg volume of rotifer were determined. These results indicate that the growth and propagation of rotifer were effectively improved by using kitchen wastewater or solid waste as fermentation substrates. When compared with the direct usage of kitchen waste for rotifer cultivation, the effect of kitchen waste fermented by probiotics on rotifer was more obvious, such as in the population density, egg-holding rate, body length, and egg volume, in the following sequence EM bacterial group > yeast group > compound bacterial group > lactic acid bacterial group ^ control group. Hence, EM bacteria can be considered as the best one for kitchen waste fermentation to prepare microbial feed for rotifer. It is thus feasible to use probiotic fermented kitchen waste to cultivate rotifer.

Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN archaea

DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 569 newly reconstructed genomes. Protein family content clearly separates DPANN from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.