The Federal Trade Commission has temporarily suspended its antitrust challenge to Whole Foods Market's (NASDAQ: WFMI) 2007 acquisition of Wild Oats to allow the company to explore settlement possibilities.

David Wales, the chief competition enforcer at the FTC, told (subscription required) The Wall Street Journal that "We're going to roll up our sleeves and take a look at what they're offering. We're hopeful that a settlement can be reached."

The FTC won't give up its battle with Whole Foods (NYSE: WFMI) over the company's long-complete merger with Wild Oats Markets, but an agreement has been reached between Whole Foods and a small, local organic and natural foods' grocery, New Seasons Market. About six weeks ago in the New Seasons blog, popular CEO Brian Rohter highlighted an invasive subpoena received from Whole Foods' attorneys, claiming that his company's secrets are party to the FTC/Whole Foods dispute. The subpoena demanded a wide variety of documents, including all documents relating to competition with Whole Foods or Wild Oats; financial information, by store; market studies and strategic plans; and all plans for future stores, expansion and renovation. Local shoppers and business owners cried foul; the subpoena, many believed, was Whole Foods playing dirty pool.

Today, thanks to pressure from both the local and national community, Whole Foods came to an agreement with New Seasons whose terms weren't released, but in which the small Pacific Northwest chain will be required to release far less sensitive information. Rohter wrote that he was "pleased" with the outcome.

It could be that Whole Foods has far bigger fish to fry than whatever advantage it could have gained from New Seasons. The FTC recently asked a judge to order Whole Foods to bring back the Wild Oats signs, and to voluntarily halt whatever integration it still hasn't completed. What's more, rumors that the company is a takeover target could be distracting management as they (depending on these reports' truth) spin the rumor mill or wheel and deal with the potential acquirers. On the days' news, the stock was down 21 cents to $12.16, about four dollars higher than its five-year low, recorded just before Thanksgiving in November 2008.

How do you de-merge two companies? The FTC thinks that the marriage of Wild Oats and Whole Foods (NASDAQ: WFMI) was anti-competitive. Too much concentration in the high-end organic food retail business.

The FTC brought charges against Whole Foods to stop the deal, but the agency did not get its bite at the apple until after the merger had closed. Now it wants to take apart what it sees as a firm created against the better interests of consumers.

According to The Wall Street Journal, the FTC wants all the stores that carried the Wild Oats name to take down their Whole Foods signs and put the old name back up. "The FTC also said it has asked Whole Foods to voluntarily halt further integration of the two companies while the FTC continues its legal challenge to the merger."

Killing a merger that is already done has to be fairly hard. If the FTC prevails, what does Whole Foods do? Does it hire a new management team and spin Wild Oats out into a new public company? Does it restate all of its recent financials to back out Wild Oats results?

From a legal standpoint, the FTC may be right, but rebuilding Wild Oats could kill the company, especially during a recession. The costs of turning it into a standalone operation could be so great that the financial burden would be more than the retailer could bear. Wild Oats might become independent again only to go bankrupt.

The government may be right, but it is not practical.

Douglas A. McIntyre is an editor at 24/7 Wall St.

With the FTC, argues Whole Foods Markets (NYSE: WFMI), it's personal. Ever since the federal agency began its review over the company's merger with Wild Oats Markets about a year and a half ago, Whole Foods says, the deck has been stacked against the organic and natural foods store chain. What's more, the FTC has continued to pursue Whole Foods to undo its deal even though the merger closed in August 2007, after the FTC lost its first challenge to the merger in federal court. Just last week, reports of an intrusive subpoena had many watchers crying foul over Whole Foods' behavior; this week, the FTC is getting its own harsh spotlight.

Whole Foods is appealing to Congress, and yesterday filed a lawsuit to stop the FTC from continuing its challenge to the long-completed merger. The FTC is running a rigged game, says CEO John Mackey, and what's more -- "we would be better off today if we hadn't done this deal" with Wild Oats. With the depressed economy (and, grocery analysts like myself would argue, Whole Foods' inability to develop a cohesive mission that resonated with sustainability-conscious shoppers), Whole Foods sales have been bottoming out, and the debt the company accrued to complete the merger is now weighing heavy on the balance sheet.

Indeed, this battle over a minority of the grocery market -- a minority the FTC inexplicably argues is called "premium and natural grocery" and is unfairly dominated by Whole Foods -- has gone on long enough.

If a new legal ruling forces Whole Foods to reverse its Wild Oats buy-out, WFMI shares could soar.

A federal appeals court has decided that the FTC's challenge of the merger between Whole Foods (NASDAQ: WFMI) and Wild Oats should have gone forward. A lower court has said the FTC had to cease its investigation into whether the marriage was anti-competitive.

According to The Wall Street Journal, "Jeffrey Schmidt, head of the FTC's competition bureau, said the agency is hopeful the ruling will ultimately allow the FTC to undertake a full review of competitive issues raised by the combined companies."

Whole Foods ended up with 74 Wild Oats stores, which it plans to cut down to 50. The FTC could ask the new company to close other locations in areas where the new parent has two stores, and, perhaps a monopoly for that region.

The FTC could also argue that the entire merger constitutes an antitrust threat. That news could not be better for WFMI shareholders. If Wild Oat has to be spun back out, it would need to re-brand its stores, add expensive management, and undertake its own marketing. In other words, it would be a severely weakened competitor for Whole Foods, instead of a thorn in the side of WFMI shareholders.

Shares in WFMI are off well over 40% this year. Stocks in many other major food retailers are closer to flat. Part of this may be due to the concern that premium products do poorly in a recession. But it may also have to do with the fact that Wild Oats stores were considered weaker as a group than the original Whole Foods chain.

If WFMI gets to rid itself of the company it got in the buy-out, its shares might get back from $22, near their 52-week low, to the $30 to $40 range.

Douglas A. McIntyre is an editor at 247walls.com.

Here are some highlights from this past week's earnings coverage from BloggingStocks:

• AnnTaylor Stores Corp. (NYSE: ANN) sees Q1 profits beating estimates but reaffirmed the full-year outlook.
• Blockbuster Inc. (NYSE: BBI) beat Q1 earnings expectations but fell short of revenue estimates.
• Electronic Arts Inc. (NASDAQ: ERTS) posted strong Q4 and full-year results on titles such as Rock Band.
• Fossil Inc. (NASDAQ: FOSL) forecast Q1 earnings just a penny below analysts' estimates.
• IMAX Corp. (NASDAQ: IMAX) doubled its Q1 loss and missed Wall Street's expectations.
• JC Penney Co. Inc. (NYSE: JCP) profits fell 50%, and it predicted trouble would continue through the year.
• Kohl's Corp. (NYSE: KSS) posted a smaller-than-estimated Q1 profit decline and cut its full-year outlook.
• Liz Claiborne Inc. (NYSE: LIZ) swung to a Q1 loss on restructuring but beat analysts' expectations.
• Lumber Liquidators Inc. (NYSE: LL) posted strong Q1 results despite the housing slump.
• Macy's (NYSE: M) beat low Q1 expectations despite weak same-store sales.
• Nissan Motor Corp. (NASDAQ: NSANY) Q4 profit surged but it warned of lower profits this year.
• Nordstrom Inc. (NYSE: JWN) posted smaller-than-estimated Q1 profit decline and cut its full-year outlook.
• Priceline.com Inc. (NASDAQ: PCLN) beat Q1 expectations due to increased bookings.
• Sirius Satellite Radio Inc. (NASDAQ: SIRI) posted a narrower Q1 loss in line with expectations.
• Sony Corp. (NYSE: SNE) swung to a Q4 profit but fell short of Wall Street estimates.
• Sprint Nextel Corp. (NYSE: S) beat low Q1 estimates as its loss widened on charges and lost subscribers.
• Tiffany & Co. (NYSE: TIF) projected beating Q1 earnings forecasts and raised its dividend.
• Wal-Mart Stores Inc. (NYSE: WMT) posted Q1 profits up on international growth and bargain shoppers.
• Whole Foods Market Inc. (NASDAQ: WFMI) Q2 profits fell due to the Wild Oats acquistion.
• XM Satellite Radio (NASDAQ: XMSR) reported a bigger-than-expected Q1 loss and a surge in subscribers.

On Tuesday, microchip equipment maker Applied Materials Inc. (NASDAQ: AMAT) reported a drop in its fiscal second quarter earnings due in part to a glut of flash memory chips, and organic and natural food retailer Whole Foods Market Inc. (NASDAQ: WFMI) also said second quarter profits fell, due to integrating its Wild Oats acquisition.

Applied Materials posted earnings of $302.5 million, or 22 cents per share, for the quarter ended April 27, compared with a profit of $411.4 million or 29 cents per share in the same period a year ago. Its adjusted net income came to 24 cents per share, beating the average analyst forecast of 22 cents, according to Reuters estimates.

Second-quarter revenue fell to $2.15 billion from $2.53 billion in the previous year. Analysts on average had expected revenue of $2.13 billion.

Shares fell 1.3% after the news but rose 2.7% in after-hours trading to $20.40.

Whole Foods reported that sales surged 28% in the second quarter to $1.87 billion, from $1.4 billion in the previous year. But net income fell 13% to $40 million, or 29 cents per share, in the quarter ended April 13; the acquisition of rival Wild Oats cost it 6 cents per share.

Analysts polled by Thomson Financial had predicted a profit of 30 cents per share on revenue of $1.89 billion.

Shares of Whole Foods fell $2.94, or 8.7%, to $30.70 in after-hours trading.

In a sign that you can't keep a good man down, the SEC has dropped its investigation into message board postings by Whole Foods (NASDAQ: WFMI) CEO John Mackey.

Reuters writes that the agency as "concluded a probe into its chief executive's anonymous Web chat room messages about then-rival Wild Oats Markets and recommended no action be taken."

Mackey can now go back to posting on other subjects but will have to come up with a new name to disguise his real identify. The old one, Rahodeb, has already been taken.

Douglas A. McIntyre is an editor at 247wallst.com.

Here are a few highlights from this past week's earnings coverage from BloggingStocks:

• CEC Entertainment Inc. (NYSE: CEC) reported a profit loss and flat revenue for the fourth quarter.
• Darden Restaurants Inc. (NYSE: DRI) raised its third-quarter and full-year earnings forecasts.
• Forward Air Corp. (NASDAQ: FWRD) beat earnings estimates and offered guidance.
• General Mills Inc. (NYSE: GIS) raised its 2008 and 2010 earnings forecasts on strong sales.
• Hewlett-Packard Co. (NASDAQ: HPQ) reported better-than-expected earnings and offered bullish guidance.
• Intuit Inc. (NASDAQ: INTU) second-quarter profits fell and it offered meager guidance.
• JC Penney Inc. (NYSE: JCP) reported a smaller-than-expected profit decline for the fourth quarter.
• Medtronic Inc. (NYSE: MDT) third-quarter profit and revenue beat analysts' expectations.
• OfficeMax Inc. (NYSE: OMX) easily beat fourth-quarter earnings expectations on lower costs.
• TJX Companies Inc. (NYSE: TJX) fourth-quarter profit beat estimates and helped raise the retail outlook.
• Whole Foods Market Inc. (NASDAQ: WFMI) earnings were dragged down by the Wild Oats acquistion.

Also, Douglas McIntyre examines how a slowdown in orders is likely to affect the earnings of Airbus and Boeing Co. (NYSE: BA), and Brian White looks at how HP might "do better" for the rest of this year.

Upcoming results to watch for include Lowes Companies Inc. (NYSE: LOW), Office Depot Inc. (NYSE: ODP), Home Depot Inc. (NYSE: HD), AutoZone Inc. (NYSE: AZO), Viacom Inc. (NYSE: VIA), and Freddie Mac (NYSE: FRE).

Visit AOL Money & Finance for more earnings coverage.

Although Whole Foods Market's (NASDAQ: WFMI) acquisition of Wild Oats has already been completed, the FTC is still trying to get in the way. The Commission is asking a Washington appellate court to overturn a federal district court's ruling [subscription required] that allowed the merger to proceed.

According to The Wall Street Journal, the FTC was split on whether to pursue the appeal, and it's considered a Hail Mary pass.

Regardless of whether you support or oppose the district court's ruling that allowed the deal to proceed -- and in spite of Mr. Mackey's crazy message board antics -- you have to wonder what the point of this appeal is. Are taxpayers really having their money spent wisely pursuing an appeal that has no chance?

I don't think so. Consumers would be better served if the FTC devoted some of this energy to cracking down on the numerous fraudulent multi-level marketing companies that continue to recruit distributors, uninhibited by anti-pyramid laws.

MOST NOTEWORTHY: Amazon.com (AMZN), Luminent Mortgage (LUM), Whole Foods (WFMI), Tenet Healthcare (THC) and Pediatrix Medical (PDX) were today's noteworthy upgrades:

• Bernstein upgraded Amazon.com (NASDAQ: AMZN) to Outperform from Market Perform, citing margins on 3rd party transactions that are close to eBay's (EBAY) and that the overseas merchants initiative will increase 3rd party units to 25% of sales. The move is expected to increase operating margins to 6.2% by 2011, above the previously expected improvement of 4.6% by the same time.

• JMP Securities said Luminent Mortgage's (NYSE: LUM) $64.9M emergency financing from Arco Capital may preserve some value for shareholders, and upgraded shares to Market Underperform from Sell.

• JP Morgan added Whole Foods (NASDAQ: WFMI) to its Focus List, and expects the Wild Oats (NASDAQ: OATS) acquisition to be a catalyst for shares.

• Deutsche Bank upgraded Tenet Healthcare (NYSE: THC) to Hold from Sell.

• Matrix USA raised Pediatrix Medical (NYSE: PDX) to Buy from Hold, citing valuation...

OTHER UPGRADES:

• AGL Resources (NYSE: ATG) and Atmos Energy (NYSE: ATO) were upgraded to Buy from Neutral at Calyon.

• Rowan Co (NYSE: RDC) was upgraded to Outperform from Peer Perform at Bear Stearns.

• Goldman raised O'Reilly Automotive (NASDAQ: ORLY) to Buy from Neutral.

• BMO Capital upgraded General Mills (NYSE: GIS) to Outperform from Market Perform.

Analyst summaries provided by TheFlyOnTheWall.com (subscription required).

Things looked pretty rough for the Whole Foods Market (NASDAQ: WFMI) bid to merge with smaller rival Wild Oats (NASDAQ: OATS). In late July, the Whole Foods CEO got himself in trouble over online message board comments and that pushed the stock to a 52-week low of $36. Then the FTC tried to block the merger on the grounds that putting the two companies together would create an operation that would raise prices on organic food.

Since late July, however, Whole Food shares are up 25% while Wild Oats trades just below its 52-week high, at $18.46. In August, short sellers cut their position in Whole Foods by 9.3 million shares to 15.1 million. It was the largest single drop in shares sold short for any company traded on the Nasdaq.

The FTC went so far as to take the fate of the merger to federal court, but both a District and Appeals Court failed to halt the merger. The first case was filed in June and, according to MarketWatch, asked the judge "for a preliminary injunction blocking the deal, pending a full review."

A successful merger is likely to have quick benefits for Whole Foods. Last quarter the smaller Wild Oats made only $1.9 million on almost $312 million of revenue. The organic food retailers costs need to come down.

Cutting those costs is likely to be the first thing that Whole Foods does.

Douglas A. McIntyre is a partner at 24/7 Wall St.

Wal-Mart (NYSE: WMT) has been buying retail chains and entering joint ventures all over the world to improve its international exposure. Now, with same-store sale in the U.S. in trouble, it is setting up a unit to look at acquisitions in the U.S. as well.

According to the Financial Times [subscription], with UK retailer Tesco moving into the U.S. with its "Fresh & Easy" small format neighborhood groceries, Wal-Mart may think that it cannot afford to ignore the success of niche stores.

Wal-Mart could certainly use something to jump start sales in its home market, and groceries may be a good place to start.

There are several retailer operators that could end up on Wal-Mart's radar. One is likely to be Whole Foods (NASDAQ: WFMI), which is about to merge with competing organic food chain Wild Oats (NASDAQ: OATS). At the larger end of the market are operators like Kroger (NYSE: KR), which has a market cap of over $19 billion but has about 3,500 stores and annual sales of over $66 billion. Wal-Mart's market cap is $179 billion.

Wal-Mart needs a lot of help in the U.S. -- it may just buy itself a turnaround.

Douglas A. McIntyre is a partner at 24/7 Wall St.

The FTC's bid to block Whole Foods' (NASDAQ: WFMI) acquisition of Wild Oats (NASDAQ: OATS) has ended in failure. A three-judge panel of D.C.'s U.S. Court of Appeals rejected the government's appeal to have the merger blocked. The judges ruled that the FTC had failed to show that Judge Paul Friedman, who denied the government's motion a week ago today, had acted improperly. Last Thursday, the

Whole Foods says it will close the deal as soon as possible. CEO John Mackey likely remains on the hot-seat, and his anonymous message board ramblings are still the subject of an SEC investigation.

Now that the merger is done, investors can begin to discuss how the merger will impact Whole Foods as a stock. The FTC's effort to block it indicates that it should be very good indeed.

"Whole Foods Market (NASDAQ: WFMI) has rallied recently due to two main factors: a better-than-expected earnings report released in early August coupled with a breakthrough on WFMI's deal to acquire rival Wild Oats Markets," notes Paul Tracy.

The editor of StreetAuthority Market Advisor, plains, ""Whole Foods reported same-store sales growth of 7% in the second quarter. That's not quite as strong as the 9% reported a year ago, but it still represents solid growth and was above what analysts had expected."

He adds that wWhile earnings fell on a year-over-year basis, that was due mainly to costs associated with WFMI's new store openings. These costs, he suggests, represent an investment in future growth; analysts had already been expecting these higher start-up costs, and Whole Foods' earnings actually beat consensus estimates by two cents.