Cellular Microbiology

Ahn, Ji-Seon;Lkhagva, Enkhchimeg;Jung, Sunjun;Kim, Hyeon-Jin;Chung, Hea-Jong;Hong, Seong-Tshool

doi: 10.1155/2023/6868417pmid: N/A

The current gut microbiome research relies on the fecal microbiome under the assumption that the fecal microbiome represents the microbiome of the entire gastrointestinal (GI) tract. However, there have been growing concerns about using feces as a proxy to study the gut microbiome. Here, we comprehensively analyzed the composition of microbiome and metabolites in the feces and at 14 different locations of GI tracts of genetically homogenous sibling pigs to evaluate the validity of using feces as a proxy to the whole gut microbiome. The composition of intestinal microbes constituting the gut microbiome at each intestinal content and feces and their metabolic compositions were thoroughly investigated through metagenome sequencing and an ultraperformance LC-MS/MS, respectively. The fluctuation in the composition of the microbiome in the stomach and the small intestine became stabilized from the large intestine to feces and was able to be categorized into 3 groups. The taxonomic <i>&#x03B1;</i>-diversities measured by ACE (abundance-based coverage estimator) richness and Shannon diversity indicated that the microbiome in the large intestine was much more diverse than those of the small intestine and feces. The highly independent intestinal microbes in the stomach and the small intestine became flourished in the large intestine and converged into a community with tightly connected networks. <i>&#x03B2;</i>-Diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the diversities of microbiome compositions were lowest in feces while highest in the large intestine. In accordance with fluctuation of the composition of gut microbiome along with the GI tract, the metabolic composition also completely differed in a location-specific manner along with the GI tract. Comparative analysis of the fecal microbiome and metabolites with those of the whole GI tract indicated that fecal microbiome is insufficient to represent the whole gut microbiome.

Hong, Geunhye;Davies, Cadi;Omole, Zahra;Liaw, Janie;Grabowska, Anna D.;Canonico, Barbara;Corcionivoschi, Nicolae;Wren, Brendan W.;Dorrell, Nick;Elmi, Abdi;Gundogdu, Ozan

doi: 10.1155/2023/3286330pmid: N/A

<i>Campylobacter jejuni</i> is the major bacterial cause of foodborne gastroenteritis worldwide. Mechanistically, how this pathogen interacts with intrinsic defence machinery of human intestinal epithelial cells (IECs) remains elusive. To address this, we investigated how <i>C. jejuni</i> counteracts the intracellular and extracellular reactive oxygen species (ROS) in IECs. Our work shows that <i>C. jejuni</i> differentially regulates intracellular and extracellular ROS production in human T84 and Caco-2 cells. <i>C. jejuni</i> downregulates the transcription and translation of nicotinamide adenine dinucleotide phosphate (NAPDH) oxidase (NOX1), a key ROS-generating enzyme in IECs and antioxidant defence genes <i>CAT</i> and <i>SOD1</i>. Furthermore, inhibition of <i>NOX1</i> by diphenylene iodonium (DPI) and siRNA reduced <i>C. jejuni</i> ability to interact, invade, and intracellularly survive within T84 and Caco-2 cells. Collectively, these findings provide mechanistic insight into how <i>C. jejuni</i> modulates the IEC defence machinery.

Sun, Xiao Wei;Zhang, Hua;Zhang, Xiao;Xin, Peng Fei;Gao, Xue;Li, Hong Rui;Zhou, Cai Yun;Gao, Wen Min;Kou, Xuan Xuan;Zhang, Jian Gang

doi: 10.1155/2023/7369034pmid: N/A

The tumor and tissue microbiota of human beings have recently been investigated. Gut permeability is known as a possible resource for the positive detection of tissue bacteria. Herein, we report that microbiota were detected in high abundance in the hepatocytes of healthy rats and that they were shared with the gut microbiota to an extent. We assessed male Sprague Dawley (SD) rats for the 16S ribosomal ribonucleic acid (rRNA) gene. After the rats were sacrificed by blood drainage from the portal vein, we extracted total deoxyribonucleic acid (DNA) from their ileal and colonic contents and liver tissues. The V3–V4 region of the 16S rRNA gene was amplified by polymerase chain reaction (PCR) and sequenced using an Illumina HiSeq 2500 platform. Sequences were assigned taxonomically by the SILVA database. We also detected bacterial lipopolysaccharide (LPS) and lipoteichoic acid (LTA) in situ using immunofluorescence (IF) and western blotting and the 16S rRNA gene using fluorescent in situ hybridization (FISH). In the livers of six rats, we detected <span class="inline_break"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="62.327pt" style="vertical-align:-1.57651pt" id="M1" height="9.92533pt" version="1.1" viewBox="-0.0498162 -8.34882 62.327 9.92533"><g transform="matrix(.013,0,0,-0.013,0,0)"><path id="g113-54" d="M153 550H386L412 615L406 623H120L82 318C104 327 142 338 184 338C294 338 347 275 347 187C347 112 305 39 221 39C160 39 119 71 97 89C88 97 80 96 71 90C59 80 50 67 49 57C48 45 52 36 66 23C80 9 123 -12 169 -12C221 -11 288 15 342 59C403 109 431 165 431 225C431 308 366 395 238 395C212 395 165 379 127 364L153 550Z"/></g><g transform="matrix(.013,0,0,-0.013,6.24,0)"><path id="g113-53" d="M456 178V225H360V632H320C217 496 115 347 20 206V178H280V106C280 40 276 34 189 27V0H445V27C364 34 360 39 360 106V178H456ZM280 225H82C149 335 214 431 278 520H280V225Z"/></g><g transform="matrix(.013,0,0,-0.013,12.48,0)"><path id="g113-45" d="M95 130C70 130 46 113 46 88C46 72 54 64 59 64C93 55 121 33 121 -3C121 -41 93 -68 44 -88L55 -117C117 -98 186 -56 186 22C186 91 131 130 95 130Z"/></g><g transform="matrix(.013,0,0,-0.013,17.624,0)"><path id="g113-57" d="M249 635C141 635 70 555 70 471C70 401 114 353 179 316C143 294 106 267 90 252C68 231 45 202 45 157C45 50 130 -12 237 -12C322 -12 435 52 435 169C435 256 372 304 303 343C349 374 375 398 383 407C401 429 411 458 411 487C411 569 344 635 249 635ZM238 603C285 603 337 567 337 482C337 422 310 385 276 358C205 393 145 426 145 500C145 552 179 603 238 603ZM248 20C183 20 125 70 125 163C125 218 158 268 206 300C284 261 355 217 355 143C355 66 308 20 248 20Z"/></g><g transform="matrix(.013,0,0,-0.013,23.864,0)"><path id="g113-55" d="M137 343C167 482 260 545 321 574C357 591 397 603 429 609L423 641C382 634 335 622 295 608C189 570 37 457 37 238C37 84 125 -12 242 -12C362 -12 447 89 447 209C447 311 374 393 267 393C247 393 226 386 204 376L137 343ZM227 337C318 337 361 256 361 173C361 105 336 22 258 22C176 22 126 120 126 240C126 266 127 291 132 310C155 323 189 337 227 337Z"/></g><g transform="matrix(.013,0,0,-0.013,30.104,0)"><path id="g113-56" d="M447 623H65C61 580 56 530 47 475H76C100 541 106 550 172 550H388C308 376 196 170 91 -1L98 -12L172 -2C268 204 360 408 455 611L447 623Z"/></g><g transform="matrix(.013,0,0,-0.013,36.346,0)"><path id="g113-47" d="M113 -12C146 -12 170 11 170 46C170 78 146 103 114 103S58 78 58 46C58 11 82 -12 113 -12Z"/></g><g transform="matrix(.013,0,0,-0.013,39.31,0)"><use xlink:href="#g113-54"/></g><g transform="matrix(.013,0,0,-0.013,45.55,0)"><path id="g113-49" d="M241 635C89 635 35 457 35 312C35 153 89 -12 240 -12C390 -12 443 166 443 312C443 466 390 635 241 635ZM238 602C329 602 354 454 354 312C354 172 330 22 240 22C152 22 124 173 124 313S148 602 238 602Z"/></g><g transform="matrix(.013,0,0,-0.013,54.696,0)"><path id="g117-37" d="M535 290V340H323V533H265V340H52V290H265V84H323V290H535ZM535 -22V28H52V-22H535Z"/></g></svg><span class="ibiop"/><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="40.867pt" style="vertical-align:-1.57651pt" height="9.92533pt" version="1.1" viewBox="65.1821838 -8.34882 40.867 9.92533"><g transform="matrix(.013,0,0,-0.013,65.232,0)"><use xlink:href="#g113-55"/></g><g transform="matrix(.013,0,0,-0.013,71.472,0)"><use xlink:href="#g113-53"/></g><g transform="matrix(.013,0,0,-0.013,77.713,0)"><use xlink:href="#g113-54"/></g><g transform="matrix(.013,0,0,-0.013,83.953,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,90.193,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,93.157,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,99.397,0)"><path id="g113-52" d="M285 378C315 398 338 416 353 432C373 451 384 474 384 503C384 579 325 635 236 635H235C182 635 136 610 108 579L65 516L85 496C110 533 150 575 205 575C258 575 300 543 300 481C300 407 232 369 141 339L147 310C163 315 188 321 211 321C268 321 338 284 338 192C338 94 288 40 217 40C160 40 119 68 93 91C85 98 77 97 69 91C60 84 47 71 46 58C44 46 48 35 62 22C75 10 116 -12 162 -12C234 -12 424 62 424 224C424 297 373 359 285 376V378Z"/></g></svg></span> effective tags of the 16S rRNA gene and clustered them into 1003 kinds of operational taxonomic units (OTUs; <span class="inline_break"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="44.703pt" style="vertical-align:-0.3499298pt" id="M2" height="8.69875pt" version="1.1" viewBox="-0.0498162 -8.34882 44.703 8.69875"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-57"/></g><g transform="matrix(.013,0,0,-0.013,6.24,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,12.48,0)"><use xlink:href="#g113-54"/></g><g transform="matrix(.013,0,0,-0.013,18.72,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,21.684,0)"><use xlink:href="#g113-55"/></g><g transform="matrix(.013,0,0,-0.013,27.924,0)"><use xlink:href="#g113-56"/></g><g transform="matrix(.013,0,0,-0.013,37.072,0)"><use xlink:href="#g117-37"/></g></svg><span class="ibiop"/><span class="nowrap"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="28.282pt" style="vertical-align:-0.3499298pt" height="8.69875pt" version="1.1" viewBox="47.5591838 -8.34882 28.282 8.69875"><g transform="matrix(.013,0,0,-0.013,47.609,0)"><use xlink:href="#g113-56"/></g><g transform="matrix(.013,0,0,-0.013,53.851,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,60.091,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,63.055,0)"><path id="g113-50" d="M384 0V27C293 34 287 42 287 114V635C232 613 172 594 109 583V559L157 557C201 555 205 550 205 499V114C205 42 199 34 109 27V0H384Z"/></g><g transform="matrix(.013,0,0,-0.013,69.295,0)"><use xlink:href="#g113-53"/></g></svg>,</span></span> 729–893). Rats showed conservation of bacterial richness, abundance, and evenness. LPS and the 16S rRNA gene were detected in the nuclei of hepatocytes. The main function composition of the genomes of annotated bacteria was correlated with metabolism (<span class="inline_break"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="38.465pt" style="vertical-align:-0.4673595pt" id="M3" height="8.85534pt" version="1.1" viewBox="-0.0498162 -8.38798 38.465 8.85534"><g transform="matrix(.013,0,0,-0.013,0,0)"><use xlink:href="#g113-56"/></g><g transform="matrix(.013,0,0,-0.013,6.242,0)"><path id="g113-58" d="M244 635C114 635 38 519 38 422C38 317 111 240 217 240C236 240 255 244 277 256L345 292C311 140 203 39 59 15L64 -15C89 -15 150 -5 204 17C339 72 440 202 440 386C440 521 368 635 244 635ZM228 602C326 602 352 479 352 390C352 370 351 347 348 324C327 308 293 296 258 296C174 296 124 369 124 458C124 517 152 602 228 602Z"/></g><g transform="matrix(.013,0,0,-0.013,12.483,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,15.447,0)"><use xlink:href="#g113-58"/></g><g transform="matrix(.013,0,0,-0.013,21.689,0)"><path id="g113-51" d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z"/></g><g transform="matrix(.013,0,0,-0.013,30.834,0)"><use xlink:href="#g117-37"/></g></svg><span class="ibiop"/><span class="nowrap"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="31.858pt" style="vertical-align:-0.4673595pt" height="8.85534pt" version="1.1" viewBox="41.3211838 -8.38798 31.858 8.85534"><g transform="matrix(.013,0,0,-0.013,41.371,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,47.611,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,50.575,0)"><use xlink:href="#g113-51"/></g><g transform="matrix(.013,0,0,-0.013,56.815,0)"><use xlink:href="#g113-53"/></g><g transform="matrix(.013,0,0,-0.013,63.055,0)"><path id="g121-35" d="M594 629L561 652L159 -9L190 -32L594 629ZM194 635C92 635 49 534 49 453C49 374 92 272 193 272C295 272 338 374 338 454S295 635 194 635ZM193 605C257 605 265 504 265 453C265 405 257 302 194 302C133 302 122 403 122 454S133 605 193 605ZM567 351C465 351 421 250 421 169C421 90 465 -12 566 -12S710 90 710 170S667 351 567 351ZM566 322C628 322 637 221 637 169C637 121 628 18 567 18S494 119 494 170C494 223 506 322 566 322Z"/></g></svg>).</span></span> Gram negativity was about 1.6 times higher than gram positivity. The liver microbiome was shared with both the small and large intestines but showed significantly higher richness and evenness than the gut microbiome, and the <i>β</i>-diversity results showed that the liver microbiome exhibited significantly higher similarity than the small and large intestines (<span class="inline_break"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="19.289pt" style="vertical-align:-0.6370001pt" id="M4" height="9.2729pt" version="1.1" viewBox="-0.0498162 -8.6359 19.289 9.2729"><g transform="matrix(.013,0,0,-0.013,0,0)"><path id="g113-81" d="M600 480C600 590 528 650 384 650H143L137 622C222 614 225 607 210 531L130 127C113 41 106 36 23 28L17 0H294L300 28C204 36 195 42 212 127L243 284L314 263C327 263 339 263 352 264C465 271 600 337 600 480ZM508 481C508 351 402 304 329 304C289 304 265 311 250 317L295 559C302 594 310 606 323 611C335 616 350 619 367 619C455 619 508 573 508 481Z"/></g><g transform="matrix(.013,0,0,-0.013,11.658,0)"><path id="g117-91" d="M512 -3V55L134 254V256L512 456V514L75 281V230L512 -3Z"/></g></svg><span class="irelop"/><span class="nowrap"><svg xmlns:xlink="http://www.w3.org/1999/xlink" xmlns="http://www.w3.org/2000/svg" width="21.918pt" style="vertical-align:-0.6370001pt" height="9.2729pt" version="1.1" viewBox="22.8711838 -8.6359 21.918 9.2729"><g transform="matrix(.013,0,0,-0.013,22.921,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,29.161,0)"><use xlink:href="#g113-47"/></g><g transform="matrix(.013,0,0,-0.013,32.125,0)"><use xlink:href="#g113-49"/></g><g transform="matrix(.013,0,0,-0.013,38.365,0)"><use xlink:href="#g113-54"/></g></svg>).</span></span> Our results suggest that the bacteria in the liver microbiome are hidden intracellular inhabitants in healthy rat livers.